diff --git a/.github/dependabot.yml b/.github/dependabot.yml deleted file mode 100644 index fc595922..00000000 --- a/.github/dependabot.yml +++ /dev/null @@ -1,15 +0,0 @@ -# To get started with Dependabot version updates, you'll need to specify which -# package ecosystems to update and where the package manifests are located. -# Please see the documentation for all configuration options: -# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates - -version: 2 -updates: - - package-ecosystem: "maven" # See documentation for possible values - directory: "/" # Location of package manifests - schedule: - interval: "daily" - - package-ecosystem: "github-actions" - directory: "/" - schedule: - interval: "daily" diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index 72258cf5..00000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,41 +0,0 @@ -# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time -# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-maven - -name: Java CI with Maven - -on: - push: - branches: [ cwl-1.2.0 ] - pull_request: - branches: [ cwl-1.2.0 ] - -# The maven-dependency-submission-action -# uses an API that requires write permission on the repository to submit dependencies -permissions: - contents: write - -jobs: - build: - - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v6 - - name: Set up JDK 11 - uses: actions/setup-java@v5 - with: - java-version: '11' - distribution: 'temurin' - cache: maven - - name: Build with Maven - run: mvn --batch-mode --update-snapshots test - - name: Coverage report - run: | - mvn prepare-package -DskipTests=true - mvn --errors test org.jacoco:jacoco-maven-plugin:report org.eluder.coveralls:coveralls-maven-plugin:report --no-transfer-progress -DrepoToken=$COVERALLS_SECRET -DpullRequest=${{ github.event.number }} - env: - CI_NAME: github - COVERALLS_SECRET: ${{ secrets.GITHUB_TOKEN }} - # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive - - name: Update dependency graph - uses: advanced-security/maven-dependency-submission-action@v5.0.0 diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml deleted file mode 100644 index 69218034..00000000 --- a/.github/workflows/codeql-analysis.yml +++ /dev/null @@ -1,71 +0,0 @@ -# For most projects, this workflow file will not need changing; you simply need -# to commit it to your repository. -# -# You may wish to alter this file to override the set of languages analyzed, -# or to provide custom queries or build logic. -# -# ******** NOTE ******** -# We have attempted to detect the languages in your repository. Please check -# the `language` matrix defined below to confirm you have the correct set of -# supported CodeQL languages. -# -name: "CodeQL" - -on: - push: - branches: [ cwl-1.2.0 ] - pull_request: - # The branches below must be a subset of the branches above - branches: [ cwl-1.2.0 ] - schedule: - - cron: '37 13 * * 5' - -jobs: - analyze: - name: Analyze - runs-on: ubuntu-latest - permissions: - actions: read - contents: read - security-events: write - - strategy: - fail-fast: false - matrix: - language: [ 'java'] - # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ] - # Learn more: - # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed - - steps: - - name: Checkout repository - uses: actions/checkout@v6 - - # Initializes the CodeQL tools for scanning. - - name: Initialize CodeQL - uses: github/codeql-action/init@v4 - with: - languages: ${{ matrix.language }} - # If you wish to specify custom queries, you can do so here or in a config file. - # By default, queries listed here will override any specified in a config file. - # Prefix the list here with "+" to use these queries and those in the config file. - # queries: ./path/to/local/query, your-org/your-repo/queries@main - - # Autobuild attempts to build any compiled languages (C/C++, C#, or Java). - # If this step fails, then you should remove it and run the build manually (see below) - - name: Autobuild - uses: github/codeql-action/autobuild@v4 - - # ℹ️ Command-line programs to run using the OS shell. - # 📚 https://git.io/JvXDl - - # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines - # and modify them (or add more) to build your code if your project - # uses a compiled language - - #- run: | - # make bootstrap - # make release - - - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v4 diff --git a/.gitignore b/.gitignore index 179df44e..fa6a9a8a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,22 @@ -target/ -.classpath -.project -.settings -/bin/ +# Created by .ignore support plugin (hsz.mobi) +*.iml +.idea +*.class +*.swp + +# Mobile Tools for Java (J2ME) +.mtj.tmp/ + +# Package Files # +*.war +*.ear + +# Mac +.DS_Store + +# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml +/target/ +dependency-reduced-pom.xml +core/target/ +tools/target/ + diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 00000000..cfde1364 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,23 @@ +language: java +jdk: + - oraclejdk8 + +install: + # install a specific version of the cwl dependencies to test with + - pip2.7 install --user cwl-runner cwltool==1.0.20160108200940 schema-salad==1.4.20160108200836 + - git clone https://github.com/common-workflow-language/common-workflow-language + # convert CWL schema salad CWL to standard Avro json + - python -mschema_salad --print-avro common-workflow-language/draft-3/CommonWorkflowLanguage.yml > cwl.avsc + # get rid of invalid avro symbols + - sed '/draft-3/d' cwl.avsc > cwl.edited.avsc + - wget https://repo1.maven.org/maven2/org/apache/avro/avro-tools/1.7.7/avro-tools-1.7.7.jar + # generate Java model classes + - java -jar avro-tools-1.7.7.jar compile schema cwl.edited.avsc cwl-temp + # create packages for the classes + - sed -i '1i package io.cwl.avro;' cwl-temp/* + - rm -Rf core/src/main/java/io/cwl/avro + - cp -R cwl-temp core/src/main/java/io/cwl/avro + - echo "the output below should show that the generated API more-or-less matches the checked-in API for convenience" + - git diff + +script: mvn -B clean install diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/testdir/a b/AUTHORS.TXT similarity index 100% rename from src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/testdir/a rename to AUTHORS.TXT diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 00000000..d6456956 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md index 75928d4a..828236c9 100644 --- a/README.md +++ b/README.md @@ -1,38 +1,41 @@ -[![Coverage Status](https://coveralls.io/repos/github/common-workflow-language/cwljava/badge.svg?branch=cwl-1.2.0)](https://coveralls.io/github/common-workflow-language/cwljava?branch=cwl-1.2.0) +CWL Java SDK +============ -# org.commonwl.cwlsdk +This is a work-in-progress implementation for creating a Java SDK for CWL. +Please read the "CWL Java SDK Manual.PDF" in the doc directory for how to generate the SDK. -This project contains Java objects and utilities auto-generated by Schema Salad for parsing documents corresponding to the https://w3id.org/cwl/cwl# schema. +The SDK is available as a JAR file in the lib directory as "cwl.jar". The CWL specifications are defined as classes in "org.commonwl.lang" and JSONReader, CWLReader and SystemCommandExecution classes have been written under "org.commonwl.util" -## License +Example Using The SDK +===================== -This project is licensed under the [Apache License, Version 2.0](https://www.apache.org/licenses/LICENSE-2.0.txt). +To run an example just proceed to tot he examples directory and run the following two commands: -## Contributing +./compile-demo.sh -This project is auto-generated by [Schema Salad](https://github.com/common-workflow-language/schema_salad) -and likely should not be modified directly. Instead consider filing an issue or opening -a pull request against the Schema Salad repository. +./run-demo.sh wc-tool.cwl wc-job.json -## Requirements +You should see the following result: -This Java library requires Java 8+. Building and testing this project requires -[Apache Maven](https://maven.apache.org/) (``mvn``). + 16 198 1111 whale.txt -## Usage +Generating The SDK +================== -Compile the project, test it, and build a jar +To generate the SDK just proceed to the "sdk-and-javadoc-generation" folder and run the following commands: - $ mvn install - $ ls target/ # jar file in here +./step0-download-draft-3-yaml-files.sh +./step1-generate_sdk.sh +./step2-compile-sdk-files-for-jar.sh +./step3-compile-util-files-for-jar.sh +./step4-generate-jar-files.sh -Building a standalone jar with all dependencies included and use it to validate a document +./step5-generate-javadoc.sh - $ mvn install - $ mvn assembly:single - $ java -jar target/-0.0.1-SNAPSHOT-jar-with-dependencies.jar ../path/to/document.yml +The first one ("step0-download-draft-3-yaml-files.sh") is optional as the CWL specification YAML files are already provided in the "cwl-yaml-specs" directory. -Building and viewing JavaDocs +All comments and recommendations are welcome. - $ mvn javadoc:javadoc - $ open target/site/apidocs/index.html +Thank you, + +Paul diff --git a/UML_Class_Diagram/UML_Diagram_of_CWLJava_Version_1_0.png b/UML_Class_Diagram/UML_Diagram_of_CWLJava_Version_1_0.png new file mode 100644 index 00000000..31b42a45 Binary files /dev/null and b/UML_Class_Diagram/UML_Diagram_of_CWLJava_Version_1_0.png differ diff --git a/WIP/Dynamic Graph Workflows/Dynamic Graph Workflows.pdf b/WIP/Dynamic Graph Workflows/Dynamic Graph Workflows.pdf new file mode 100644 index 00000000..4a99c730 Binary files /dev/null and b/WIP/Dynamic Graph Workflows/Dynamic Graph Workflows.pdf differ diff --git a/WIP/Dynamic Graph Workflows/README.md b/WIP/Dynamic Graph Workflows/README.md new file mode 100644 index 00000000..0004bd82 --- /dev/null +++ b/WIP/Dynamic Graph Workflows/README.md @@ -0,0 +1,38 @@ +Dynamic Graph Workflows +======================= + +The program was generated using Node.js to demonstrate how one can have a dynamic collection of interactive nodes – created ad hoc – in order to interact and run processes. The program has a broker (`cwl_node.js`) and a node program (`cwl_node.js`). One first launches the broker and then an interactive node program on two separate terminal windows, as follows: + +``` +node cwl_broker.js + +node cwl_node.js 127.0.0.1 4000 interactive +``` + +The node program is launched with the local IP address and port of the broker, including name of this node (`interactive`). It is recommended that the node name is kept as ‘interactive’ since it is used by the broker to broadcast information. + +Sending Commands on the Interactive node +======================================== + +Please read the **Dynamic Graph Workflows.pdf** manual for a full description of commands, but below is a example of commands one can run - as this program is still alpha, please wait a second between sending commands: + +``` +make_node 1 +make_node 2 +on 1 command="wc" +on 2 input="whale.txt" +from 1 command +from 2 input +run 1 with 2 using input store_as wc_result +from 1 wc_result +on 1 command="ls -l" +on 2 input="*.js" +run 1 with 2 using input store_as ls_result +from 1 ls_result +``` + +All comments and recommendations are welcome, and please feel free to contribute. + +Thank you, + +Paul \ No newline at end of file diff --git a/WIP/Dynamic Graph Workflows/cwl_broker.js b/WIP/Dynamic Graph Workflows/cwl_broker.js new file mode 100644 index 00000000..c2a786d2 --- /dev/null +++ b/WIP/Dynamic Graph Workflows/cwl_broker.js @@ -0,0 +1,239 @@ + +/************************************************************************* +* +* Authors: +* +* * Paul Grosu , Northeastern University +* +* Purpose: +* +* To demonstrate a dynamic graph of running nodes for connecting them to run processes +* +* Requirements: +* +* * Node.js + +* Below is the command-line on how to run the collection of +* programs: +* +* To run: +* +* 1) First launch the broker: +* +* node cwl_broker.js +* +* 2) Then launch the interactive node: +* +* node cwl_node.js 127.0.0.1 4000 interactive +* +* +* Use the interactive node send commands and check the broker's console for information.: +* +* +* +*************************************************************************/ + + +var dgram = require('dgram'); + +var server = dgram.createSocket('udp4'); + +var node_port_by_id = {}; +var node_id_by_port = {}; + +var client_port = 4000; + +var port = 4000; + +var this_stdout = []; + + +process.stdin.resume(); + +server.on('message', function(message, rinfo) { + + if ( message.length > 0 ) { + + cmd = message.toString().trim(); + cmdArray = cmd.split( " " ); + + originating_port = cmdArray[0].toString().trim(); + cmdArray.splice(0, 1); //remove the originating port + + verb = cmdArray[0].toString().trim(); + cmdArray.splice(0, 1); //remove the verb + } + + // Create a node + if ( verb === "make_node" ) { + + var exec = require('child_process').exec; + + exec('node cwl_node.js 127.0.0.1 ' + client_port + " " + cmdArray.join( " " ), function(err, stdout, stderr) { + + // The node creation exited or the launching failed + if (err) { + + // In case we had an error launching the process + console.log('child process exited with error code', err.code); + return; + } + + }); + + } + + // Adding the new node's port information to the dictionary + if ( verb === "add_node" ) { + + node_port = cmdArray[0]; + cmdArray.splice(0, 1); //remove the port + + node_id = cmdArray[0]; + cmdArray.splice(0, 1); //remove the node id + if ( !(node_port === undefined) ) { + console.log( "Adding node at port " + node_port + " for node id: " + node_id ); + + node_port_by_id[ node_id ] = node_port; + node_id_by_port[ node_port ] = node_id; + } + + } + + + // Adding variables to nodes + if ( verb === "on" ) { + + node_id = cmdArray[0]; + node_port = node_port_by_id[node_id]; + cmdArray.splice(0, 1); //remove the node + + // set the value on a node + set_on_node( node_port, cmdArray.join( " " ) ); + + } + + + // Inspecting the value of a variable on a node + if ( verb === "from" ) { + + node_id = cmdArray[0]; + data_node_port = node_port_by_id[node_id]; + + node_id = cmdArray[0]; + destination_node_port = originating_port; + + node_id = cmdArray[0]; // this will not be needed and just removed + cmdArray.splice(0, 1); //remove the node + + // get the value of a variable from a noe + get_from_node_to_print( data_node_port, destination_node_port, cmdArray.join( " " ) ); + + } + + // Printing some information a node + if ( verb === "print_from" ) { + + node_id = cmdArray[0]; + cmdArray.splice(0, 1); //remove the node + + node_port = node_port_by_id[ node_id ]; + + print_from( node_port, cmdArray.join( " " ) ); + + } + + // Printing some information to the broker's console + if ( verb === "print_broker" ) { + + node_id = cmdArray[0]; + cmdArray.splice(0, 1); //remove the node + + console.log( "Getting the value from node id: " + node_id ); + console.log( cmdArray.join( " " ) ); + + // Broadcast information to interactive node + interactive_node_port = node_port_by_id[ 'interactive' ]; + + print_to_interactive( interactive_node_port, cmdArray.join( " " ) ); + + } + + // Run a command on a node using another node's input value + if ( verb === "run" ) { + + command_node = cmdArray[0]; + cmdArray.splice(0, 1); //remove the command_node + + cmdArray.splice(0, 1); //remove the "with" + + input_node = cmdArray[0]; + cmdArray.splice(0, 1); //remove the input_node + + cmdArray.splice(0, 1); //remove the "using" + using_variable = cmdArray[0]; + cmdArray.splice(0, 1); //remove the input variable + + cmdArray.splice(0, 1); //remove the "store_stdout_in" + store_stdout_in = cmdArray[0]; + + run_a_node( command_node, input_node, using_variable, store_stdout_in ); + + } + + if ( verb === "hello" ) { + // Broadcast hello to all + for(var key in node_id_by_port) { + message = new Buffer("hello from broker"); + server.send( message, 0, message.length, key, '127.0.0.1' ); + } + } + +}); + + +server.on('listening', function() { + var address = server.address(); + console.log("The broker is running..."); + console.log(''); +}); + +server.bind(port); + + +// Functions of commands + +// Get variable from to node to print it +get_from_node_to_print = function( data_node_port, destination_node_port, information ) { + message = new Buffer( "get_to_print " + data_node_port + " " + destination_node_port + " " + information ); + server.send( message, 0, message.length, data_node_port, '127.0.0.1' ); +} + +// Set a value on a node +set_on_node = function( node_port, instruction ) { + message = new Buffer( "set " + instruction ); + server.send( message, 0, message.length, node_port, '127.0.0.1' ); +} + +// Print a value from a node +print_from_node = function( node_port, instruction ) { + message = new Buffer( "print " + instruction ); + server.send( message, 0, message.length, node_port, '127.0.0.1' ); +} + +// Print a value from a node +print_to_interactive = function( interactive_node_port, instruction ) { + message = new Buffer( "print_to_interactive " + instruction ); + server.send( message, 0, message.length, interactive_node_port, '127.0.0.1' ); +} + +// The function that will launch an execution job on a node +run_a_node = function( command_node, input_node, using_variable, store_stdout_in ) { + + command_node_port = node_port_by_id[ command_node ]; + input_node_port = node_port_by_id[ input_node ]; + + message = new Buffer( "run_command_from " + command_node_port + " with_input_from " + input_node_port + " using " + using_variable + " store_stdout_in " + store_stdout_in ); + server.send( message, 0, message.length, command_node_port, '127.0.0.1' ); + +} \ No newline at end of file diff --git a/WIP/Dynamic Graph Workflows/cwl_node.js b/WIP/Dynamic Graph Workflows/cwl_node.js new file mode 100644 index 00000000..c8a98fa3 --- /dev/null +++ b/WIP/Dynamic Graph Workflows/cwl_node.js @@ -0,0 +1,308 @@ + +/************************************************************************* +* +* Authors: +* +* * Paul Grosu , Northeastern University +* +* Purpose: +* +* To demonstrate a dynamic graph of running nodes for connecting them to run processes +* +* Requirements: +* +* * Node.js + +* Below is the command-line on how to run the collection of +* programs: +* +* To run: +* +* 1) First launch the broker: +* +* node cwl_broker.js +* +* 2) Then launch the interactive node: +* +* node cwl_node.js 127.0.0.1 4000 interactive +* +* +* Use the interactive node send commands and check the broker's console for information.: +* +* +* +*************************************************************************/ + +var dgram = require('dgram'); + +var host = process.argv[2]; +var port = parseInt(process.argv[3], 10); +var client = dgram.createSocket('udp4'); +var id = process.argv[4]; +var this_port = ""; + +var this_stdout = []; +var custom_stdout_placeholder = ""; + +// Timer for the queue +var tick = 1000; +var inReadyState = true; +var processQueue = new Queue(); +var currentProcess = ""; + +// The queue of instructions to process that depended on other information to populate +runNextInQueue = function() { + + if ( inReadyState && !(processQueue.isEmpty()) ) { + + if ( currentProcess.length === 0 ) { + currentProcess = processQueue.dequeue(); + } + + eval( currentProcess ); + + } +} + +// Launch the ticker to periodically check the queue +setInterval( runNextInQueue , tick ); + +process.stdin.resume(); + +process.stdin.on('data', function(data) { + + //All messages to the broker add the originating port as a prefix in the message + var originating_port_with_data = new Buffer( this_port + " " + data); + client.send(originating_port_with_data, 0, originating_port_with_data.length, port, '127.0.0.1'); + +}); + +// Process commands +client.on('message', function(message) { + + cmd = message.toString().trim(); + cmdArray = cmd.split( " " ); + + verb = cmdArray[0].toString().trim(); + cmdArray.splice(0, 1); //remove the verb + + + // Message back to all the nodes from a broadcast + if ( verb === "hello from broker" ) { + console.log(verb); + } + + // Adding variables with values to current node + if ( verb === "set" ) { + eval( cmdArray.join(" ") ); + } + + // Store a result in this_stdout + if ( verb === "stdout_store" ) { + + this_stdout = cmdArray.join(" "); + inReadyState = true; // allow the queue to proceed + + } + + // Inspecting a node's variable to print + if ( verb === "get_to_print" ) { + + data_node_port = cmdArray[0]; + cmdArray.splice(0, 1); // remove the data port + + destination_node_port = cmdArray[0]; + cmdArray.splice(0, 1); // remove the dest port + + data = new Buffer( "print " + eval(cmdArray.join(" ")) ); + client.send(data, 0, data.length, this_port, '127.0.0.1'); + } + + // Store a value at a destination node + if ( verb === "get_to_store" ) { + + data_node_port = cmdArray[0]; + cmdArray.splice(0, 1); // remove the data port + + destination_node_port = cmdArray[0]; + cmdArray.splice(0, 1); //remove the dest port + + //data = new Buffer( "print_from " + id + " " + eval(cmdArray.join(" ")) ); + data = new Buffer( "stdout_store " + eval(cmdArray.join(" ")) ); + client.send(data, 0, data.length, destination_node_port, '127.0.0.1'); + + } + + + // Print information on the interactive node + if ( verb === "print_to_interactive" ) { + + result = cmdArray.join(" "); + console.log( result ); + + } + + // Print information to the broker + if ( verb === "print" ) { + + result = cmdArray.join(" "); + + // Prepare the information to print to the broker + full_message = new Buffer(this_port + " print_broker " + id + " " + result ); + + // Send to broker console + client.send(full_message, 0, full_message.length, port, '127.0.0.1'); + + + } + + // Run a command from this node using the input from another node and + // store it in specific variable on this node + if ( verb === "run_command_from" ) { + + cmdArray.splice(0, 1); //remove command_node_port + cmdArray.splice(0, 1); //remove with_input_from + + input_port = cmdArray[0]; + cmdArray.splice(0, 1); //remove the input_port + + cmdArray.splice(0, 1); //remove the "using" + using_variable = cmdArray[0]; + cmdArray.splice(0, 1); //remove the input variable + + cmdArray.splice(0, 1); //remove the "store_stdout_in" + custom_stdout_placeholder = cmdArray[0]; + + data_node_port = input_port; + destination_node_port = this_port; + information = using_variable; + message = new Buffer( "get_to_store " + data_node_port + " " + destination_node_port + " " + information ); + + // Set the node's state to false and queue the command to execute until all the information has + // propagated properly + inReadyState = false; + processQueue.enqueue( "execute_command( command + ' ' + this_stdout, custom_stdout_placeholder )" ); + + // Ask the port that contains the input for the input data + client.send(message, 0, message.length, input_port, '127.0.0.1'); + + } + +}); + +client.on('listening', function () { + + var address = client.address(); + + this_port = address.port.toString(); + + // Request the node's port to be added to the broker's dictionary + data = new Buffer(this_port + " add_node " + address.port.toString() + " " + id); + client.send(data, 0, data.length, port, '127.0.0.1'); + +}); + + +// Ensure that the client.on('listening',...) function executes so that the "add_node" +// portion is processed when the node is first launched +function start() { + var data = new Buffer(""); + client.send(data, 0, data.length, port, '127.0.0.1'); +} +start(); + +console.log(''); +console.log('Start sending commands to the broker...'); +console.log(''); + +// The function to execute a command +execute_command = function( command_to_execute, store_stdout_in ) { + var exec = require('child_process').exec; + + exec(command_to_execute, function(err, stdout, stderr) { + + // The command exited or the launching failed + if (err) { + // This is in case we get an error launching the process + console.log('child process exited with error code', err.code); + return; + } + // Store the results in the new variable created after the ("store_as") in the command-line + eval(store_stdout_in + "=[]"); + eval(store_stdout_in + ".push(stdout.toString())"); + + }); +} + +// Functions + +// Request to get a variable's value from a node +get_from_node = function( node_port, information ) { + message = new Buffer( "get " + information ); + server.send( message, 0, message.length, node_port, '127.0.0.1' ); +} + +// I did not want implement a Queue, so I copied the following from the web: + +/* + * The Queue portion was created by Stephen Morley - http://code.stephenmorley.org/ - and released under + * the terms of the CC0 1.0 Universal legal code: + * http://creativecommons.org/publicdomain/zero/1.0/legalcode + * Creates a new queue. A queue is a first-in-first-out (FIFO) data structure - + * items are added to the end of the queue and removed from the front. + * + */ +function Queue(){ + + // initialise the queue and offset + var queue = []; + var offset = 0; + + // Returns the length of the queue. + this.getLength = function(){ + return (queue.length - offset); + } + + // Returns true if the queue is empty, and false otherwise. + this.isEmpty = function(){ + return (queue.length == 0); + } + + /* Enqueues the specified item. The parameter is: + * + * item - the item to enqueue + */ + this.enqueue = function(item){ + queue.push(item); + } + + /* Dequeues an item and returns it. If the queue is empty, the value + * 'undefined' is returned. + */ + this.dequeue = function(){ + + // if the queue is empty, return immediately + if (queue.length == 0) return undefined; + + // store the item at the front of the queue + var item = queue[offset]; + + // increment the offset and remove the free space if necessary + if (++ offset * 2 >= queue.length){ + queue = queue.slice(offset); + offset = 0; + } + + // return the dequeued item + return item; + + } + + /* Returns the item at the front of the queue (without dequeuing it). If the + * queue is empty then undefined is returned. + */ + this.peek = function(){ + return (queue.length > 0 ? queue[offset] : undefined); + } + +} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/whale.txt b/WIP/Dynamic Graph Workflows/whale.txt similarity index 100% rename from src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/whale.txt rename to WIP/Dynamic Graph Workflows/whale.txt diff --git a/adding_new_cwl_versions.txt b/adding_new_cwl_versions.txt deleted file mode 100644 index ca4b8c3b..00000000 --- a/adding_new_cwl_versions.txt +++ /dev/null @@ -1,12 +0,0 @@ -# discover the valid CWL files from the conformance tests: - -cd ~/cwl-v1.1 # my local checkout of https://github.com/common-workflow-language/cwl-v1.1/ -git ls-files -- tests | grep cwl$ | xargs -I{} bash -c 'cwltool --relax-path-checks --validate {} >/dev/null 2>/dev/null && echo {}' > valid_examples.txt -#git ls-files -- tests | grep cwl$ | xargs -I{} bash -c 'cwltool --relax-path-checks --validate {} >/dev/null 2>/dev/null || echo {}' > invalid_examples.txt -mkdir valid-examples; for file in $(cat valid_examples.txt); do cp ${file} valid-examples/valid_$(basename ${file}) ; done - -# build the Java parser -schema-salad-tool --codegen java --codegen-package org.commonwl.cwlsdk.cwl1_1 --codegen-examples ~/cwl-v1.1/valid-examples ~/cwl-v1.1/CommonWorkflowLanguage.yml - -mvn test -# copy missing files into ./src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils diff --git a/doc/ Java SDK for CWL Manual.pdf b/doc/ Java SDK for CWL Manual.pdf new file mode 100644 index 00000000..bdb71b6d Binary files /dev/null and b/doc/ Java SDK for CWL Manual.pdf differ diff --git a/doc/Java SDK for CWL.pptx b/doc/Java SDK for CWL.pptx new file mode 100755 index 00000000..ff3f426d Binary files /dev/null and b/doc/Java SDK for CWL.pptx differ diff --git a/examples/CWLJavaCodeGeneratorDemo.java b/examples/CWLJavaCodeGeneratorDemo.java new file mode 100644 index 00000000..c84438b5 --- /dev/null +++ b/examples/CWLJavaCodeGeneratorDemo.java @@ -0,0 +1,48 @@ + +// Compile: ./compile-demo.sh wc-tool.cwl wc-job.json +// +// Run: ./run-demo.sh wc-tool.cwl wc-job.json + +import java.util.*; +import org.commonwl.lang.*; +import org.commonwl.util.*; + +public class CWLJavaCodeGeneratorDemo { + + public static void main( String [] args ) throws Exception { + + CWLJavaCodeGenerator cwlJCG = new CWLJavaCodeGenerator( args[0] ); + cwlJCG.processFile(); + /* + //CWLReader tool = new CWLReader("wc-tool.cwl"); + CWLReader tool = new CWLReader( args[0] ); + tool.processFile(); + CommandLineTool CommandLineTool_Instance = tool.getCommandLineToolInstance(); + + //JSONReader job = new JSONReader("wc-job.json"); + JSONReader job = new JSONReader( args[1] ); + job.processFile(); + + // Execute the job + SystemCommandExecution engine = new SystemCommandExecution(); + + // Initialize a new command to execute + engine.newExecutionCommand(); + + // Prepare the command to execute + engine.extendExecutionCommand( CommandLineTool_Instance.getbaseCommand() ); + String stdinPath = (String) CommandLineTool_Instance.getstdin(); + stdinPath = stdinPath.replace( "inputs.", "" ); + engine.extendExecutionCommand( job.getValue( stdinPath ) ); + + // Execute the command + engine.executeCommand(); + + // Return the result + System.out.println( engine.getStandardOutput() ); + + */ + + } + +} diff --git a/examples/CommandLineToolDemo.java b/examples/CommandLineToolDemo.java new file mode 100644 index 00000000..3ae77132 --- /dev/null +++ b/examples/CommandLineToolDemo.java @@ -0,0 +1,43 @@ + +// Compile: ./compile-demo.sh wc-tool.cwl wc-job.json +// +// Run: ./run-demo.sh wc-tool.cwl wc-job.json + +import java.util.*; +import org.commonwl.lang.*; +import org.commonwl.util.*; + +public class CommandLineToolDemo { + + public static void main( String [] args ) throws Exception { + + //CWLReader tool = new CWLReader("wc-tool.cwl"); + CWLReader tool = new CWLReader( args[0] ); + tool.processFile(); + CommandLineTool CommandLineTool_Instance = tool.getCommandLineToolInstance(); + + //JSONReader job = new JSONReader("wc-job.json"); + JSONReader job = new JSONReader( args[1] ); + job.processFile(); + + // Execute the job + SystemCommandExecution engine = new SystemCommandExecution(); + + // Initialize a new command to execute + engine.newExecutionCommand(); + + // Prepare the command to execute + engine.extendExecutionCommand( CommandLineTool_Instance.getbaseCommand() ); + String stdinPath = (String) CommandLineTool_Instance.getstdin(); + stdinPath = stdinPath.replace( "inputs.", "" ); + engine.extendExecutionCommand( job.getValue( stdinPath ) ); + + // Execute the command + engine.executeCommand(); + + // Return the result + System.out.println( engine.getStandardOutput() ); + + } + +} diff --git a/examples/compile-demo.sh b/examples/compile-demo.sh new file mode 100755 index 00000000..c1fc7c52 --- /dev/null +++ b/examples/compile-demo.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +javac -cp ../lib/cwl.jar:../lib/json-simple-1.1.1.jar:../lib/snakeyaml-1.16.jar:. CommandLineToolDemo.java + +rm CWLReader.class JSONReader.class SystemCommandExecution.class diff --git a/examples/compile_and_run-CWLJavaCodeGeneratorDemo.sh b/examples/compile_and_run-CWLJavaCodeGeneratorDemo.sh new file mode 100755 index 00000000..4dba679d --- /dev/null +++ b/examples/compile_and_run-CWLJavaCodeGeneratorDemo.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +javac -cp ../lib/cwl.jar:../lib/json-simple-1.1.1.jar:../lib/snakeyaml-1.16.jar:. CWLJavaCodeGeneratorDemo.java +java -cp ../lib/cwl.jar:../lib/json-simple-1.1.1.jar:../lib/snakeyaml-1.16.jar:. CWLJavaCodeGeneratorDemo $1 diff --git a/examples/run-demo.sh b/examples/run-demo.sh new file mode 100755 index 00000000..3eccb7ff --- /dev/null +++ b/examples/run-demo.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +java -cp ../lib/cwl.jar:../lib/json-simple-1.1.1.jar:../lib/snakeyaml-1.16.jar:. CommandLineToolDemo $1 $2 \ No newline at end of file diff --git a/examples/sdk-example-for-presentation.txt b/examples/sdk-example-for-presentation.txt new file mode 100644 index 00000000..743703e7 --- /dev/null +++ b/examples/sdk-example-for-presentation.txt @@ -0,0 +1,67 @@ + +import java.util.*; + +public class sdktest { + + public static void main( String [] args ) throws Exception { + + CWLReader cwlr = new CWLReader("wc-tool.cwl"); + cwlr.processFile(); + CommandLineTool CommandLineTool_Instance = cwlr.getCommandLineToolInstance(); + // CommandLineTool clt = new CommandLineTool(); + + // CommandInputParameter [] cip = new CommandInputParameter[1]; + // cip[0] = new CommandInputParameter(); + // cip[0].setid("file1"); + // cip[0].settype("File"); + + // CommandOutputParameter [] cop = new CommandOutputParameter[1]; + // cop[0] = new CommandOutputParameter(); + // cop[0].setid("output"); + // cop[0].settype("File"); + + // CommandOutputBinding cob = new CommandOutputBinding(); + // cob.setglob( new String( "output" ) ); + + // cop[0].setoutputBinding( cob ); + + + // clt.setinputs( cip ); + // clt.setoutputs( cop ); + + // clt.setbaseCommand( "wc" ); + + // clt.setstdin( "inputs.file1.path" ); + // clt.setstdout( "output" ); + + // Ref: wc-job.json + // Map json = new HashMap(); + // json.put("file1.class", "File"); + // json.put("file1.path" , "whale.txt"); + + JSONReader jr = new JSONReader("wc-job.json"); + jr.processFile(); + + //write engine file + + // Expected: wc file1.class.path > output + //process( clt, json ); + + // org.commonwl.lang.*; + + //Process p = Runtime.getRuntime().exec("ps -ef"); + //SystemCommandExecution sce = new SystemCommandExecution("ls -l"); + SystemCommandExecution sce = new SystemCommandExecution(); + sce.newExecutionCommand(); + //sce.extendExecutionCommand( clt.getbaseCommand() ); + sce.extendExecutionCommand( CommandLineTool_Instance.\ ); + String stdinPath = (String) CommandLineTool_Instance.getstdin(); + stdinPath = stdinPath.replace( "inputs.", "" ); + sce.extendExecutionCommand( jr.getValue( stdinPath ) ); + //sce.extendExecutionCommand( json.get( "file1.path" ) ); + sce.executeCommand(); + System.out.println( sce.getStandardOutput() ); + + } + +} diff --git a/examples/wc-job.json b/examples/wc-job.json new file mode 100644 index 00000000..32ffc842 --- /dev/null +++ b/examples/wc-job.json @@ -0,0 +1,6 @@ +{ + "file1": { + "class": "File", + "path": "whale.txt" + } +} diff --git a/examples/wc-tool.cwl b/examples/wc-tool.cwl new file mode 100644 index 00000000..6e26b988 --- /dev/null +++ b/examples/wc-tool.cwl @@ -0,0 +1,15 @@ +#!/usr/bin/env cwl-runner + +class: CommandLineTool +cwlVersion: cwl:draft-3 + +inputs: + - { id: file1, type: File } + +"outputs": + - { id: output, type: File, outputBinding: { glob: output } } + +baseCommand: [wc] + +stdin: $(inputs.file1.path) +stdout: output diff --git a/examples/whale.txt b/examples/whale.txt new file mode 100644 index 00000000..425d1ed0 --- /dev/null +++ b/examples/whale.txt @@ -0,0 +1,16 @@ +Call me Ishmael. Some years ago--never mind how long precisely--having +little or no money in my purse, and nothing particular to interest me on +shore, I thought I would sail about a little and see the watery part of +the world. It is a way I have of driving off the spleen and regulating +the circulation. Whenever I find myself growing grim about the mouth; +whenever it is a damp, drizzly November in my soul; whenever I find +myself involuntarily pausing before coffin warehouses, and bringing up +the rear of every funeral I meet; and especially whenever my hypos get +such an upper hand of me, that it requires a strong moral principle to +prevent me from deliberately stepping into the street, and methodically +knocking people's hats off--then, I account it high time to get to sea +as soon as I can. This is my substitute for pistol and ball. With a +philosophical flourish Cato throws himself upon his sword; I quietly +take to the ship. There is nothing surprising in this. If they but knew +it, almost all men in their degree, some time or other, cherish very +nearly the same feelings towards the ocean with me. diff --git a/javadoc/allclasses-frame.html b/javadoc/allclasses-frame.html new file mode 100644 index 00000000..b5d22f3f --- /dev/null +++ b/javadoc/allclasses-frame.html @@ -0,0 +1,100 @@ + + + + + +All Classes + + + + + +

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    • +
  • +

    Index

    +

    The Index contains an alphabetic list of all classes, interfaces, constructors, methods, and fields.

    +
    • +
  • +

    Prev/Next

    +

    These links take you to the next or previous class, interface, package, or related page.

    +
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    Frames/No Frames

    +

    These links show and hide the HTML frames. All pages are available with or without frames.

    +
    • +
  • +

    All Classes

    +

    The All Classes link shows all classes and interfaces except non-static nested types.

    +
    • +
  • +

    Serialized Form

    +

    Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.

    +
    • +
  • +

    Constant Field Values

    +

    The Constant Field Values page lists the static final fields and their values.

    +
    • +
+This help file applies to API documentation generated using the standard doclet.
+ +
+ + +
Skip navigation links
+ + + + +
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    • +
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+ + + diff --git a/javadoc/index-all.html b/javadoc/index-all.html new file mode 100644 index 00000000..a52272c5 --- /dev/null +++ b/javadoc/index-all.html @@ -0,0 +1,5242 @@ + + + + + +Index + + + + + + + + +
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A B C D E F G H I J L M N O P R S T V W _  + + +

A

+
+
abstract_value - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
If true, this record is abstract and may be used as a base for other records, but is not valid on its own.
+
+
addIndentedNewline(String) - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
This method adds a newline character to a string of text.
+
+
addNewline(String) - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
This method adds a newline character to a string of text.
+
+
Any - Class in org.commonwl.lang
+
+
The Any type validates for any non-null value.
+
+
Any(Object) - Constructor for class org.commonwl.lang.Any
+
 
+
arguments - Variable in class org.commonwl.lang.CommandLineTool
+
+
Command line bindings which are not directly associated with input parameters.
+
+
ArraySchema - Class in org.commonwl.lang
+
 
+
ArraySchema() - Constructor for class org.commonwl.lang.ArraySchema
+
 
+
+ + + +

B

+
+
baseCommand - Variable in class org.commonwl.lang.CommandLineTool
+
+
Specifies the program to execute.
+
+
basename - Variable in class org.commonwl.lang.Directory
+
+
The base name of the directory, that is, the name of the file without any leading directory path.
+
+
basename - Variable in class org.commonwl.lang.File
+
+
The base name of the file, that is, the name of the file without any leading directory path.
+
+
+ + + +

C

+
+
checksum - Variable in class org.commonwl.lang.File
+
+
Optional hash code for validating file integrity.
+
+
class_value - Variable in class org.commonwl.lang.CommandLineTool
+
 
+
class_value - Variable in class org.commonwl.lang.Directory
+
+
Must be `Directory` to indicate this object describes a Directory.
+
+
class_value - Variable in class org.commonwl.lang.DockerRequirement
+
+
Always 'DockerRequirement'
+
+
class_value - Variable in class org.commonwl.lang.EnvVarRequirement
+
+
Always 'EnvVarRequirement'
+
+
class_value - Variable in class org.commonwl.lang.ExpressionTool
+
 
+
class_value - Variable in class org.commonwl.lang.File
+
+
Must be `File` to indicate this object describes a file.
+
+
class_value - Variable in class org.commonwl.lang.InitialWorkDirRequirement
+
+
InitialWorkDirRequirement
+
+
class_value - Variable in class org.commonwl.lang.InlineJavascriptRequirement
+
+
Always 'InlineJavascriptRequirement'
+
+
class_value - Variable in class org.commonwl.lang.MultipleInputFeatureRequirement
+
+
Always 'MultipleInputFeatureRequirement'
+
+
class_value - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Always 'ResourceRequirement'
+
+
class_value - Variable in class org.commonwl.lang.ScatterFeatureRequirement
+
+
Always 'ScatterFeatureRequirement'
+
+
class_value - Variable in class org.commonwl.lang.SchemaDefRequirement
+
+
Always 'SchemaDefRequirement'
+
+
class_value - Variable in class org.commonwl.lang.ShellCommandRequirement
+
+
Always 'ShellCommandRequirement'
+
+
class_value - Variable in class org.commonwl.lang.SoftwareRequirement
+
+
Always 'SoftwareRequirement'
+
+
class_value - Variable in class org.commonwl.lang.StepInputExpressionRequirement
+
+
Always 'StepInputExpressionRequirement'
+
+
class_value - Variable in class org.commonwl.lang.SubworkflowFeatureRequirement
+
+
Always 'SubworkflowFeatureRequirement'
+
+
class_value - Variable in class org.commonwl.lang.Workflow
+
 
+
cleanStandardInput(String) - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
Purpose: To remove the paranthesis "()" and dollar sign ($) + standard input.
+
+
cleanStandardInput(String) - Method in class org.commonwl.util.CWLReader
+
+
Purpose: To remove the paranthesis "()" and dollar sign ($) + standard input.
+
+
cleanupClassName(String) - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method removes the "class" string from the class name, produced by the getClass() method.
+
+
COMMAND_LINE_TOOL - Variable in class org.commonwl.util.CWLReader
+
+
The CommandLineTool used for storing class in the CWL file.
+
+
CommandInputArraySchema - Class in org.commonwl.lang
+
 
+
CommandInputArraySchema() - Constructor for class org.commonwl.lang.CommandInputArraySchema
+
 
+
CommandInputEnumSchema - Class in org.commonwl.lang
+
 
+
CommandInputEnumSchema() - Constructor for class org.commonwl.lang.CommandInputEnumSchema
+
 
+
CommandInputParameter - Class in org.commonwl.lang
+
+
An input parameter for a CommandLineTool.
+
+
CommandInputParameter() - Constructor for class org.commonwl.lang.CommandInputParameter
+
 
+
CommandInputRecordField - Class in org.commonwl.lang
+
 
+
CommandInputRecordField() - Constructor for class org.commonwl.lang.CommandInputRecordField
+
 
+
CommandInputRecordSchema - Class in org.commonwl.lang
+
 
+
CommandInputRecordSchema() - Constructor for class org.commonwl.lang.CommandInputRecordSchema
+
 
+
CommandLineBinding - Class in org.commonwl.lang
+
 
+
CommandLineBinding() - Constructor for class org.commonwl.lang.CommandLineBinding
+
 
+
CommandLineTool - Class in org.commonwl.lang
+
+
This defines the schema of the CWL Command Line Tool Description document.
+
+
CommandLineTool() - Constructor for class org.commonwl.lang.CommandLineTool
+
 
+
CommandOutputArraySchema - Class in org.commonwl.lang
+
 
+
CommandOutputArraySchema() - Constructor for class org.commonwl.lang.CommandOutputArraySchema
+
 
+
CommandOutputBinding - Class in org.commonwl.lang
+
+
Describes how to generate an output parameter based on the files produced by a CommandLineTool.
+
+
CommandOutputBinding() - Constructor for class org.commonwl.lang.CommandOutputBinding
+
 
+
CommandOutputEnumSchema - Class in org.commonwl.lang
+
 
+
CommandOutputEnumSchema() - Constructor for class org.commonwl.lang.CommandOutputEnumSchema
+
 
+
CommandOutputParameter - Class in org.commonwl.lang
+
+
An output parameter for a CommandLineTool.
+
+
CommandOutputParameter() - Constructor for class org.commonwl.lang.CommandOutputParameter
+
 
+
CommandOutputRecordField - Class in org.commonwl.lang
+
 
+
CommandOutputRecordField() - Constructor for class org.commonwl.lang.CommandOutputRecordField
+
 
+
CommandOutputRecordSchema - Class in org.commonwl.lang
+
 
+
CommandOutputRecordSchema() - Constructor for class org.commonwl.lang.CommandOutputRecordSchema
+
 
+
contents - Variable in class org.commonwl.lang.File
+
+
File contents literal.
+
+
coresMax - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Maximum reserved number of CPU cores
+
+
coresMin - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Minimum reserved number of CPU cores
+
+
CWL_FILE - Variable in class org.commonwl.util.CWLJavaCodeGenerator
+
+
The String used for storing CWL filename.
+
+
CWL_FILE - Variable in class org.commonwl.util.CWLReader
+
+
The String used for storing CWL filename.
+
+
CWL_JAVA_CLASS_NAME - Variable in class org.commonwl.util.CWLJavaCodeGenerator
+
+
The String used for storing CWL Java code-generated class name.
+
+
CWL_JAVA_FILE - Variable in class org.commonwl.util.CWLJavaCodeGenerator
+
+
The String used for storing CWL Java code-generated filename.
+
+
CWL_OBJECT - Variable in class org.commonwl.util.CWLJavaCodeGenerator
+
+
The String used for storing CWL Java code-generated filename.
+
+
CWLJavaCodeGenerator - Class in org.commonwl.util
+
 
+
CWLJavaCodeGenerator(String) - Constructor for class org.commonwl.util.CWLJavaCodeGenerator
+
+
The CommandOutputParameter used for storing outputs in the CWL file.
+
+
CWLReader - Class in org.commonwl.util
+
 
+
CWLReader(String) - Constructor for class org.commonwl.util.CWLReader
+
 
+
CWLType - Enum in org.commonwl.lang
+
+
- Extends primitive types with the concept of a file and directory as a builtin type.
+
+
CWLType() - Constructor for enum org.commonwl.lang.CWLType
+
 
+
cwlVersion - Variable in class org.commonwl.lang.CommandLineTool
+
+
CWL document version.
+
+
CWLVersion - Enum in org.commonwl.lang
+
+
Version symbols for published CWL document versions.
+
+
CWLVersion() - Constructor for enum org.commonwl.lang.CWLVersion
+
 
+
cwlVersion - Variable in class org.commonwl.lang.ExpressionTool
+
+
CWL document version.
+
+
cwlVersion - Static variable in interface org.commonwl.lang.Process
+
+
CWL document version.
+
+
cwlVersion - Variable in class org.commonwl.lang.Workflow
+
+
CWL document version.
+
+
+ + + +

D

+
+
default_value - Variable in class org.commonwl.lang.CommandInputParameter
+
+
The default value for this parameter if not provided in the input object.
+
+
default_value - Variable in class org.commonwl.lang.InputParameter
+
+
The default value for this parameter if not provided in the input object.
+
+
default_value - Variable in class org.commonwl.lang.WorkflowStepInput
+
+
The default value for this parameter if there is no `source` field.
+
+
Directory - Class in org.commonwl.lang
+
+
Represents a directory to present to a command line tool.
+
+
Directory() - Constructor for class org.commonwl.lang.Directory
+
 
+
Dirent - Class in org.commonwl.lang
+
+
Define a file or subdirectory that must be placed in the designated output directory prior to executing the command line tool.
+
+
Dirent() - Constructor for class org.commonwl.lang.Dirent
+
 
+
dirname - Variable in class org.commonwl.lang.File
+
+
The name of the directory containing file, that is, the path leading up to the final slash in the path such that `dirname + '/' + basename == path`.
+
+
doc - Variable in class org.commonwl.lang.CommandInputParameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.CommandInputRecordField
+
+
A documentation string for this field
+
+
doc - Variable in class org.commonwl.lang.CommandLineTool
+
+
A long, human-readable description of this process object.
+
+
doc - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.CommandOutputRecordField
+
+
A documentation string for this field
+
+
doc - Static variable in interface org.commonwl.lang.DocType
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.Documentation
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.ExpressionTool
+
+
A long, human-readable description of this process object.
+
+
doc - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.InputParameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.InputRecordField
+
+
A documentation string for this field
+
+
doc - Variable in class org.commonwl.lang.OutputParameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.OutputRecordField
+
+
A documentation string for this field
+
+
doc - Static variable in interface org.commonwl.lang.Parameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Static variable in interface org.commonwl.lang.Process
+
+
A long, human-readable description of this process object.
+
+
doc - Variable in class org.commonwl.lang.RecordField
+
+
A documentation string for this field
+
+
doc - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.SaladRecordField
+
+
A documentation string for this field
+
+
doc - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Static variable in interface org.commonwl.lang.SchemaDefinedType
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.Workflow
+
+
A long, human-readable description of this process object.
+
+
doc - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.WorkflowStep
+
+
A long, human-readable description of this process object.
+
+
docAfter - Static variable in interface org.commonwl.lang.DocType
+
+
Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
+
+
docAfter - Variable in class org.commonwl.lang.Documentation
+
+
Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
+
+
docAfter - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
+
+
docAfter - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
+
+
docAfter - Static variable in interface org.commonwl.lang.SchemaDefinedType
+
+
Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
+
+
docChild - Static variable in interface org.commonwl.lang.DocType
+
+
Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
+
+
docChild - Variable in class org.commonwl.lang.Documentation
+
+
Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
+
+
docChild - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
+
+
docChild - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
+
+
docChild - Static variable in interface org.commonwl.lang.SchemaDefinedType
+
+
Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
+
+
dockerFile - Variable in class org.commonwl.lang.DockerRequirement
+
+
Supply the contents of a Dockerfile which will be built using `docker build`.
+
+
dockerImageId - Variable in class org.commonwl.lang.DockerRequirement
+
+
The image id that will be used for `docker run`.
+
+
dockerImport - Variable in class org.commonwl.lang.DockerRequirement
+
+
Provide HTTP URL to download and gunzip a Docker images using `docker import.
+
+
dockerLoad - Variable in class org.commonwl.lang.DockerRequirement
+
+
Specify a HTTP URL from which to download a Docker image using `docker load`.
+
+
dockerOutputDirectory - Variable in class org.commonwl.lang.DockerRequirement
+
+
Set the designated output directory to a specific location inside the Docker container.
+
+
dockerPull - Variable in class org.commonwl.lang.DockerRequirement
+
+
Specify a Docker image to retrieve using `docker pull`.
+
+
DockerRequirement - Class in org.commonwl.lang
+
+
Indicates that a workflow component should be run in a [Docker](http://docker.com) container, and specifies how to fetch or build the image.
+
+
DockerRequirement() - Constructor for class org.commonwl.lang.DockerRequirement
+
 
+
docParent - Static variable in interface org.commonwl.lang.DocType
+
+
Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
+
+
docParent - Variable in class org.commonwl.lang.Documentation
+
+
Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
+
+
docParent - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
+
+
docParent - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
+
+
docParent - Static variable in interface org.commonwl.lang.SchemaDefinedType
+
+
Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
+
+
DocType - Interface in org.commonwl.lang
+
 
+
Documentation - Class in org.commonwl.lang
+
+
A documentation section.
+
+
Documentation() - Constructor for class org.commonwl.lang.Documentation
+
 
+
documentRoot - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
If true, indicates that the type is a valid at the document root.
+
+
documentRoot - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
If true, indicates that the type is a valid at the document root.
+
+
documentRoot - Static variable in interface org.commonwl.lang.SchemaDefinedType
+
+
If true, indicates that the type is a valid at the document root.
+
+
+ + + +

E

+
+
entry - Variable in class org.commonwl.lang.Dirent
+
+
If the value is a string literal or an expression which evaluates to a string, a new file must be created with the string as the file contents.
+
+
entryname - Variable in class org.commonwl.lang.Dirent
+
+
The name of the file or subdirectory to create in the output directory.
+
+
EnumSchema - Class in org.commonwl.lang
+
+
Define an enumerated type.
+
+
EnumSchema() - Constructor for class org.commonwl.lang.EnumSchema
+
 
+
envDef - Variable in class org.commonwl.lang.EnvVarRequirement
+
+
The list of environment variables.
+
+
EnvironmentDef - Class in org.commonwl.lang
+
+
Define an environment variable that will be set in the runtime environment by the workflow platform when executing the command line tool.
+
+
EnvironmentDef() - Constructor for class org.commonwl.lang.EnvironmentDef
+
 
+
envName - Variable in class org.commonwl.lang.EnvironmentDef
+
+
The environment variable name
+
+
envValue - Variable in class org.commonwl.lang.EnvironmentDef
+
+
The environment variable value
+
+
EnvVarRequirement - Class in org.commonwl.lang
+
+
Define a list of environment variables which will be set in the execution environment of the tool.
+
+
EnvVarRequirement() - Constructor for class org.commonwl.lang.EnvVarRequirement
+
 
+
executeCommand() - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method executes the command and returns a String array of the standard input, + standard output, and standard error.
+
+
Expression - Enum in org.commonwl.lang
+
+
'Expression' is not a real type.
+
+
Expression() - Constructor for enum org.commonwl.lang.Expression
+
 
+
expression - Variable in class org.commonwl.lang.ExpressionTool
+
+
The expression to execute.
+
+
expressionLib - Variable in class org.commonwl.lang.InlineJavascriptRequirement
+
+
Additional code fragments that will also be inserted before executing the expression code.
+
+
ExpressionTool - Class in org.commonwl.lang
+
+
Execute an expression as a Workflow step.
+
+
ExpressionTool() - Constructor for class org.commonwl.lang.ExpressionTool
+
 
+
ExpressionToolOutputParameter - Class in org.commonwl.lang
+
 
+
ExpressionToolOutputParameter() - Constructor for class org.commonwl.lang.ExpressionToolOutputParameter
+
 
+
extendExecutionCommand(Object) - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method is a helper method to process any object being requested to be run, such as + the ones returned by getbaseCommand() which are actually a String type.
+
+
extendExecutionCommand(String) - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method is a method to process a String command being requested to be run.
+
+
extends_value - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
Indicates that this enum inherits symbols from a base enum.
+
+
extends_value - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
Indicates that this record inherits fields from one or more base records.
+
+
+ + + +

F

+
+
File - Class in org.commonwl.lang
+
+
Represents a file (or group of files if `secondaryFiles` is specified) that must be accessible by tools using standard POSIX file system call API such as open(2) and read(2).
+
+
File() - Constructor for class org.commonwl.lang.File
+
 
+
format - Variable in class org.commonwl.lang.CommandInputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
format - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
format - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
format - Variable in class org.commonwl.lang.File
+
+
The format of the file: this must be an IRI of a concept node that represents the file format, preferrably defined within an ontology.
+
+
format - Variable in class org.commonwl.lang.InputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
format - Variable in class org.commonwl.lang.OutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
format - Static variable in interface org.commonwl.lang.Parameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
format - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
+ + + +

G

+
+
get() - Method in class org.commonwl.lang.Any
+
+
This method returns the value of Any.
+
+
get() - Method in class org.commonwl.lang.PrimitiveType
+
+
This method returns the value of PrimitiveType.
+
+
get_container() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of _container.
+
+
get_id() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of _id.
+
+
get_type() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of _type.
+
+
getabstract() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of abstract_value.
+
+
getarguments() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of arguments.
+
+
getbaseCommand() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of baseCommand.
+
+
getbasename() - Method in class org.commonwl.lang.Directory
+
+
This method returns the value of basename.
+
+
getbasename() - Method in class org.commonwl.lang.File
+
+
This method returns the value of basename.
+
+
getchecksum() - Method in class org.commonwl.lang.File
+
+
This method returns the value of checksum.
+
+
getclass() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.Directory
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.EnvVarRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.File
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.InlineJavascriptRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.MultipleInputFeatureRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.ScatterFeatureRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.SchemaDefRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.ShellCommandRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.SoftwareRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.StepInputExpressionRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.SubworkflowFeatureRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of class_value.
+
+
getCommandLineToolInstance() - Method in class org.commonwl.util.CWLReader
+
+
Purpose: Returns the populated CommandLineTool instance.
+
+
getcontents() - Method in class org.commonwl.lang.File
+
+
This method returns the value of contents.
+
+
getcoresMax() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of coresMax.
+
+
getcoresMin() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of coresMin.
+
+
getcwlVersion() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of cwlVersion.
+
+
getcwlVersion() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of cwlVersion.
+
+
getcwlVersion() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of cwlVersion.
+
+
getcwlVersion() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of cwlVersion.
+
+
getdefault() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of default_value.
+
+
getdefault() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of default_value.
+
+
getdefault() - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method returns the value of default_value.
+
+
getdirname() - Method in class org.commonwl.lang.File
+
+
This method returns the value of dirname.
+
+
getdoc() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method returns the value of doc.
+
+
getdoc() - Method in interface org.commonwl.lang.DocType
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.Documentation
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.InputRecordField
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.OutputRecordField
+
+
This method returns the value of doc.
+
+
getdoc() - Method in interface org.commonwl.lang.Parameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.RecordField
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.SaladRecordField
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of doc.
+
+
getdoc() - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of doc.
+
+
getdocAfter() - Method in interface org.commonwl.lang.DocType
+
+
This method returns the value of docAfter.
+
+
getdocAfter() - Method in class org.commonwl.lang.Documentation
+
+
This method returns the value of docAfter.
+
+
getdocAfter() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of docAfter.
+
+
getdocAfter() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of docAfter.
+
+
getdocAfter() - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method returns the value of docAfter.
+
+
getdocChild() - Method in interface org.commonwl.lang.DocType
+
+
This method returns the value of docChild.
+
+
getdocChild() - Method in class org.commonwl.lang.Documentation
+
+
This method returns the value of docChild.
+
+
getdocChild() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of docChild.
+
+
getdocChild() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of docChild.
+
+
getdocChild() - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method returns the value of docChild.
+
+
getdockerFile() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of dockerFile.
+
+
getdockerImageId() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of dockerImageId.
+
+
getdockerImport() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of dockerImport.
+
+
getdockerLoad() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of dockerLoad.
+
+
getdockerOutputDirectory() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of dockerOutputDirectory.
+
+
getdockerPull() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of dockerPull.
+
+
getdocParent() - Method in interface org.commonwl.lang.DocType
+
+
This method returns the value of docParent.
+
+
getdocParent() - Method in class org.commonwl.lang.Documentation
+
+
This method returns the value of docParent.
+
+
getdocParent() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of docParent.
+
+
getdocParent() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of docParent.
+
+
getdocParent() - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method returns the value of docParent.
+
+
getdocumentRoot() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of documentRoot.
+
+
getdocumentRoot() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of documentRoot.
+
+
getdocumentRoot() - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method returns the value of documentRoot.
+
+
getentry() - Method in class org.commonwl.lang.Dirent
+
+
This method returns the value of entry.
+
+
getentryname() - Method in class org.commonwl.lang.Dirent
+
+
This method returns the value of entryname.
+
+
getenvDef() - Method in class org.commonwl.lang.EnvVarRequirement
+
+
This method returns the value of envDef.
+
+
getenvName() - Method in class org.commonwl.lang.EnvironmentDef
+
+
This method returns the value of envName.
+
+
getenvValue() - Method in class org.commonwl.lang.EnvironmentDef
+
+
This method returns the value of envValue.
+
+
getexpression() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of expression.
+
+
getexpressionLib() - Method in class org.commonwl.lang.InlineJavascriptRequirement
+
+
This method returns the value of expressionLib.
+
+
getextends() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of extends_value.
+
+
getextends() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of extends_value.
+
+
getFirstElementOfArrayList(ArrayList) - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
Purpose: Returns the first element of an ArrayList as a String.
+
+
getFirstElementOfArrayList(ArrayList) - Method in class org.commonwl.util.CWLReader
+
+
Purpose: Returns the first element of an ArrayList as a String.
+
+
getformat() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of format.
+
+
getformat() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of format.
+
+
getformat() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of format.
+
+
getformat() - Method in class org.commonwl.lang.File
+
+
This method returns the value of format.
+
+
getformat() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of format.
+
+
getformat() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of format.
+
+
getformat() - Method in interface org.commonwl.lang.Parameter
+
+
This method returns the value of format.
+
+
getformat() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of format.
+
+
getglob() - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method returns the value of glob.
+
+
gethints() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of hints.
+
+
gethints() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of hints.
+
+
gethints() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of hints.
+
+
gethints() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of hints.
+
+
gethints() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of hints.
+
+
getid() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of id.
+
+
getid() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.WorkflowStepOutput
+
+
This method returns the value of id.
+
+
getidentity() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of identity.
+
+
getin() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of in.
+
+
getinputBinding() - Method in class org.commonwl.lang.CommandInputArraySchema
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.CommandInputEnumSchema
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.InputArraySchema
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.InputEnumSchema
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.InputRecordField
+
+
This method returns the value of inputBinding.
+
+
getinputs() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of inputs.
+
+
getinputs() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of inputs.
+
+
getinputs() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of inputs.
+
+
getinputs() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of inputs.
+
+
getitemSeparator() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of itemSeparator.
+
+
getjsonldPredicate() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of jsonldPredicate.
+
+
getjsonldPredicate() - Method in class org.commonwl.lang.SaladRecordField
+
+
This method returns the value of jsonldPredicate.
+
+
getjsonldPredicate() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of jsonldPredicate.
+
+
getjsonldPredicate() - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method returns the value of jsonldPredicate.
+
+
getlabel() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.InputArraySchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.InputEnumSchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.InputRecordField
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.InputRecordSchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in interface org.commonwl.lang.InputSchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.OutputArraySchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.OutputEnumSchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.OutputRecordSchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in interface org.commonwl.lang.OutputSchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in interface org.commonwl.lang.Parameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of label.
+
+
getlabel() - Method in interface org.commonwl.lang.SchemaBase
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of label.
+
+
getlinkMerge() - Method in interface org.commonwl.lang.Sink
+
+
This method returns the value of linkMerge.
+
+
getlinkMerge() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of linkMerge.
+
+
getlinkMerge() - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method returns the value of linkMerge.
+
+
getlisting() - Method in class org.commonwl.lang.Directory
+
+
This method returns the value of listing.
+
+
getlisting() - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method returns the value of listing.
+
+
getloadContents() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of loadContents.
+
+
getloadContents() - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method returns the value of loadContents.
+
+
getloadContents() - Method in interface org.commonwl.lang.InputBinding
+
+
This method returns the value of loadContents.
+
+
getlocation() - Method in class org.commonwl.lang.Directory
+
+
This method returns the value of location.
+
+
getlocation() - Method in class org.commonwl.lang.File
+
+
This method returns the value of location.
+
+
getmapPredicate() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of mapPredicate.
+
+
getmapSubject() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of mapSubject.
+
+
getname() - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.Documentation
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.InputRecordField
+
+
This method returns the value of name.
+
+
getname() - Method in interface org.commonwl.lang.NamedType
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.OutputRecordField
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.RecordField
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.SaladRecordField
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of name.
+
+
getnameext() - Method in class org.commonwl.lang.File
+
+
This method returns the value of nameext.
+
+
getnameroot() - Method in class org.commonwl.lang.File
+
+
This method returns the value of nameroot.
+
+
getnoLinkCheck() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of noLinkCheck.
+
+
getout() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of out.
+
+
getoutdirMax() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of outdirMax.
+
+
getoutdirMin() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of outdirMin.
+
+
getoutputBinding() - Method in class org.commonwl.lang.CommandOutputArraySchema
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.CommandOutputEnumSchema
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.OutputArraySchema
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.OutputEnumSchema
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.OutputRecordField
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of outputBinding.
+
+
getoutputEval() - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method returns the value of outputEval.
+
+
getoutputs() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of outputs.
+
+
getoutputs() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of outputs.
+
+
getoutputs() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of outputs.
+
+
getoutputs() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of outputs.
+
+
getoutputSource() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of outputSource.
+
+
getpackage() - Method in class org.commonwl.lang.SoftwarePackage
+
+
This method returns the value of package_value.
+
+
getpackages() - Method in class org.commonwl.lang.SoftwareRequirement
+
+
This method returns the value of packages.
+
+
getpath() - Method in class org.commonwl.lang.Directory
+
+
This method returns the value of path.
+
+
getpath() - Method in class org.commonwl.lang.File
+
+
This method returns the value of path.
+
+
getpermanentFailCodes() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of permanentFailCodes.
+
+
getposition() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of position.
+
+
getprefix() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of prefix.
+
+
getramMax() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of ramMax.
+
+
getramMin() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of ramMin.
+
+
getrefScope() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of refScope.
+
+
getrequirements() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of requirements.
+
+
getrequirements() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of requirements.
+
+
getrequirements() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of requirements.
+
+
getrequirements() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of requirements.
+
+
getrequirements() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of requirements.
+
+
getrun() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of run.
+
+
getscatter() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of scatter.
+
+
getscatterMethod() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of scatterMethod.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.File
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in interface org.commonwl.lang.Parameter
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of secondaryFiles.
+
+
getseparate() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of separate.
+
+
getshellQuote() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of shellQuote.
+
+
getsize() - Method in class org.commonwl.lang.File
+
+
This method returns the value of size.
+
+
getsource() - Method in interface org.commonwl.lang.Sink
+
+
This method returns the value of source.
+
+
getsource() - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method returns the value of source.
+
+
getspecialize() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of specialize.
+
+
getspecializeFrom() - Method in class org.commonwl.lang.SpecializeDef
+
+
This method returns the value of specializeFrom.
+
+
getspecializeTo() - Method in class org.commonwl.lang.SpecializeDef
+
+
This method returns the value of specializeTo.
+
+
getspecs() - Method in class org.commonwl.lang.SoftwarePackage
+
+
This method returns the value of specs.
+
+
getStandardError() - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method returns the last value of the standard error.
+
+
getStandardInput() - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method returns the last value of the standard input.
+
+
getStandardOutput() - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method returns the last value of the standard output.
+
+
getStatusCode() - Method in class org.commonwl.util.SystemCommandExecution
+
 
+
getstderr() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of stderr.
+
+
getstdin() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of stdin.
+
+
getstdout() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of stdout.
+
+
getsteps() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of steps.
+
+
getstreamable() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of streamable.
+
+
getstreamable() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of streamable.
+
+
getstreamable() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of streamable.
+
+
getstreamable() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of streamable.
+
+
getstreamable() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of streamable.
+
+
getstreamable() - Method in interface org.commonwl.lang.Parameter
+
+
This method returns the value of streamable.
+
+
getstreamable() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of streamable.
+
+
getsuccessCodes() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of successCodes.
+
+
gettemporaryFailCodes() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of temporaryFailCodes.
+
+
gettmpdirMax() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of tmpdirMax.
+
+
gettmpdirMin() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of tmpdirMin.
+
+
gettype() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.Documentation
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.InputRecordField
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.OutputRecordField
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.RecordField
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.SaladRecordField
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of type.
+
+
gettypeDSL() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of typeDSL.
+
+
gettypes() - Method in class org.commonwl.lang.SchemaDefRequirement
+
+
This method returns the value of types.
+
+
getValue(String) - Method in class org.commonwl.util.JSONReader
+
+
This method is used to request the value using a key in the processed JSON file.
+
+
getvalueFrom() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of valueFrom.
+
+
getvalueFrom() - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method returns the value of valueFrom.
+
+
getversion() - Method in class org.commonwl.lang.SoftwarePackage
+
+
This method returns the value of version.
+
+
getwritable() - Method in class org.commonwl.lang.Dirent
+
+
This method returns the value of writable.
+
+
glob - Variable in class org.commonwl.lang.CommandOutputBinding
+
+
Find files relative to the output directory, using POSIX glob(3) pathname matching.
+
+
+ + + +

H

+
+
hints - Variable in class org.commonwl.lang.CommandLineTool
+
+
Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process.
+
+
hints - Variable in class org.commonwl.lang.ExpressionTool
+
+
Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process.
+
+
hints - Static variable in interface org.commonwl.lang.Process
+
+
Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process.
+
+
hints - Variable in class org.commonwl.lang.Workflow
+
+
Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process.
+
+
hints - Variable in class org.commonwl.lang.WorkflowStep
+
+
Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this workflow step.
+
+
+ + + +

I

+
+
id - Variable in class org.commonwl.lang.CommandInputParameter
+
+
The unique identifier for this parameter object.
+
+
id - Variable in class org.commonwl.lang.CommandLineTool
+
+
The unique identifier for this process object.
+
+
id - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
The unique identifier for this parameter object.
+
+
id - Variable in class org.commonwl.lang.ExpressionTool
+
+
The unique identifier for this process object.
+
+
id - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
The unique identifier for this parameter object.
+
+
id - Variable in class org.commonwl.lang.InputParameter
+
+
The unique identifier for this parameter object.
+
+
id - Variable in class org.commonwl.lang.OutputParameter
+
+
The unique identifier for this parameter object.
+
+
id - Static variable in interface org.commonwl.lang.Process
+
+
The unique identifier for this process object.
+
+
id - Variable in class org.commonwl.lang.Workflow
+
+
The unique identifier for this process object.
+
+
id - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
The unique identifier for this parameter object.
+
+
id - Variable in class org.commonwl.lang.WorkflowStep
+
+
The unique identifier for this workflow step.
+
+
id - Variable in class org.commonwl.lang.WorkflowStepInput
+
+
A unique identifier for this workflow input parameter.
+
+
id - Variable in class org.commonwl.lang.WorkflowStepOutput
+
+
A unique identifier for this workflow output parameter.
+
+
identity - Variable in class org.commonwl.lang.JsonldPredicate
+
+
If true and `_type` is `@id` this indicates that the parent field must be resolved according to identity resolution rules instead of link resolution rules.
+
+
in - Variable in class org.commonwl.lang.WorkflowStep
+
+
Defines the input parameters of the workflow step.
+
+
InitialWorkDirRequirement - Class in org.commonwl.lang
+
+
Define a list of files and subdirectories that must be created by the workflow platform in the designated output directory prior to executing the command line tool.
+
+
InitialWorkDirRequirement() - Constructor for class org.commonwl.lang.InitialWorkDirRequirement
+
 
+
InlineJavascriptRequirement - Class in org.commonwl.lang
+
+
Indicates that the workflow platform must support inline Javascript expressions.
+
+
InlineJavascriptRequirement() - Constructor for class org.commonwl.lang.InlineJavascriptRequirement
+
 
+
InputArraySchema - Class in org.commonwl.lang
+
 
+
InputArraySchema() - Constructor for class org.commonwl.lang.InputArraySchema
+
 
+
inputBinding - Variable in class org.commonwl.lang.CommandInputArraySchema
+
 
+
inputBinding - Variable in class org.commonwl.lang.CommandInputEnumSchema
+
 
+
inputBinding - Variable in class org.commonwl.lang.CommandInputParameter
+
+
Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
+
+
inputBinding - Variable in class org.commonwl.lang.CommandInputRecordField
+
 
+
inputBinding - Variable in class org.commonwl.lang.InputArraySchema
+
 
+
InputBinding - Interface in org.commonwl.lang
+
 
+
inputBinding - Variable in class org.commonwl.lang.InputEnumSchema
+
 
+
inputBinding - Variable in class org.commonwl.lang.InputParameter
+
+
Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
+
+
inputBinding - Variable in class org.commonwl.lang.InputRecordField
+
 
+
InputEnumSchema - Class in org.commonwl.lang
+
 
+
InputEnumSchema() - Constructor for class org.commonwl.lang.InputEnumSchema
+
 
+
InputParameter - Class in org.commonwl.lang
+
 
+
InputParameter() - Constructor for class org.commonwl.lang.InputParameter
+
 
+
InputRecordField - Class in org.commonwl.lang
+
 
+
InputRecordField() - Constructor for class org.commonwl.lang.InputRecordField
+
 
+
InputRecordSchema - Class in org.commonwl.lang
+
 
+
InputRecordSchema() - Constructor for class org.commonwl.lang.InputRecordSchema
+
 
+
inputs - Variable in class org.commonwl.lang.CommandLineTool
+
+
Defines the input parameters of the process.
+
+
inputs - Variable in class org.commonwl.lang.ExpressionTool
+
+
Defines the input parameters of the process.
+
+
inputs - Static variable in interface org.commonwl.lang.Process
+
+
Defines the input parameters of the process.
+
+
inputs - Variable in class org.commonwl.lang.Workflow
+
+
Defines the input parameters of the process.
+
+
INPUTS - Variable in class org.commonwl.util.CWLReader
+
+
The CommandInputParameter used for storing inputs in the CWL file.
+
+
InputSchema - Interface in org.commonwl.lang
+
 
+
itemSeparator - Variable in class org.commonwl.lang.CommandLineBinding
+
+
Join the array elements into a single string with the elements separated by by `itemSeparator`.
+
+
+ + + +

J

+
+
JSON_FILE - Variable in class org.commonwl.util.JSONReader
+
+
The String used for storing the JSON filename.
+
+
JsonldPredicate - Class in org.commonwl.lang
+
+
Attached to a record field to define how the parent record field is handled for URI resolution and JSON-LD context generation.
+
+
JsonldPredicate() - Constructor for class org.commonwl.lang.JsonldPredicate
+
 
+
jsonldPredicate - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
Annotate this type with linked data context.
+
+
jsonldPredicate - Variable in class org.commonwl.lang.SaladRecordField
+
+
Annotate this type with linked data context.
+
+
jsonldPredicate - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
Annotate this type with linked data context.
+
+
jsonldPredicate - Static variable in interface org.commonwl.lang.SchemaDefinedType
+
+
Annotate this type with linked data context.
+
+
jsonMap - Variable in class org.commonwl.util.JSONReader
+
+
The key-value pairs in a JSON file that sit underneath the root key in a JSON file.
+
+
JSONReader - Class in org.commonwl.util
+
+
This is used reading and processing a JSON file.
+
+
JSONReader(String) - Constructor for class org.commonwl.util.JSONReader
+
 
+
+ + + +

L

+
+
label - Variable in class org.commonwl.lang.CommandInputParameter
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.CommandInputRecordField
+
+
A short, human-readable label of this process object.
+
+
label - Variable in class org.commonwl.lang.CommandLineTool
+
+
A short, human-readable label of this process object.
+
+
label - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.ExpressionTool
+
+
A short, human-readable label of this process object.
+
+
label - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.InputArraySchema
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.InputEnumSchema
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.InputParameter
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.InputRecordField
+
+
A short, human-readable label of this process object.
+
+
label - Variable in class org.commonwl.lang.InputRecordSchema
+
+
A short, human-readable label of this object.
+
+
label - Static variable in interface org.commonwl.lang.InputSchema
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.OutputArraySchema
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.OutputEnumSchema
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.OutputParameter
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.OutputRecordSchema
+
+
A short, human-readable label of this object.
+
+
label - Static variable in interface org.commonwl.lang.OutputSchema
+
+
A short, human-readable label of this object.
+
+
label - Static variable in interface org.commonwl.lang.Parameter
+
+
A short, human-readable label of this object.
+
+
label - Static variable in interface org.commonwl.lang.Process
+
+
A short, human-readable label of this process object.
+
+
label - Static variable in interface org.commonwl.lang.SchemaBase
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.Workflow
+
+
A short, human-readable label of this process object.
+
+
label - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.WorkflowStep
+
+
A short, human-readable label of this process object.
+
+
linkMerge - Static variable in interface org.commonwl.lang.Sink
+
+
The method to use to merge multiple inbound links into a single array.
+
+
linkMerge - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
The method to use to merge multiple sources into a single array.
+
+
linkMerge - Variable in class org.commonwl.lang.WorkflowStepInput
+
+
The method to use to merge multiple inbound links into a single array.
+
+
LinkMergeMethod - Enum in org.commonwl.lang
+
+
The input link merge method, described in [WorkflowStepInput](#WorkflowStepInput).
+
+
LinkMergeMethod() - Constructor for enum org.commonwl.lang.LinkMergeMethod
+
 
+
listing - Variable in class org.commonwl.lang.Directory
+
+
List of files or subdirectories contained in this directory.
+
+
listing - Variable in class org.commonwl.lang.InitialWorkDirRequirement
+
+
The list of files or subdirectories that must be placed in the designated output directory prior to executing the command line tool.
+
+
loadContents - Variable in class org.commonwl.lang.CommandLineBinding
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
loadContents - Variable in class org.commonwl.lang.CommandOutputBinding
+
+
For each file matched in `glob`, read up to the first 64 KiB of text from the file and place it in the `contents` field of the file object for manipulation by `outputEval`.
+
+
loadContents - Static variable in interface org.commonwl.lang.InputBinding
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
location - Variable in class org.commonwl.lang.Directory
+
+
An IRI that identifies the directory resource.
+
+
location - Variable in class org.commonwl.lang.File
+
+
An IRI that identifies the file resource.
+
+
+ + + +

M

+
+
mapPredicate - Variable in class org.commonwl.lang.JsonldPredicate
+
+
Only applies if `mapSubject` is also provided.
+
+
mapSubject - Variable in class org.commonwl.lang.JsonldPredicate
+
+
If the value of the field is a JSON object, it must be transformed into an array of JSON objects, where each key-value pair from the source JSON object is a list item, the list items must be JSON objects, and the key is assigned to the field specified by `mapSubject`.
+
+
MultipleInputFeatureRequirement - Class in org.commonwl.lang
+
+
Indicates that the workflow platform must support multiple inbound data links listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).
+
+
MultipleInputFeatureRequirement() - Constructor for class org.commonwl.lang.MultipleInputFeatureRequirement
+
 
+
+ + + +

N

+
+
name - Variable in class org.commonwl.lang.CommandInputRecordField
+
+
The name of the field
+
+
name - Variable in class org.commonwl.lang.CommandOutputRecordField
+
+
The name of the field
+
+
name - Variable in class org.commonwl.lang.Documentation
+
+
The identifier for this type
+
+
name - Variable in class org.commonwl.lang.InputRecordField
+
+
The name of the field
+
+
name - Static variable in interface org.commonwl.lang.NamedType
+
+
The identifier for this type
+
+
name - Variable in class org.commonwl.lang.OutputRecordField
+
+
The name of the field
+
+
name - Variable in class org.commonwl.lang.RecordField
+
+
The name of the field
+
+
name - Variable in class org.commonwl.lang.SaladRecordField
+
+
The name of the field
+
+
name - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
The identifier for this type
+
+
NamedType - Interface in org.commonwl.lang
+
 
+
nameext - Variable in class org.commonwl.lang.File
+
+
The basename extension such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period.
+
+
nameroot - Variable in class org.commonwl.lang.File
+
+
The basename root such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period.
+
+
newExecutionCommand() - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method resets the standard input String.
+
+
noLinkCheck - Variable in class org.commonwl.lang.JsonldPredicate
+
+
If true, this indicates that link validation traversal must stop at this field.
+
+
+ + + +

O

+
+
org.commonwl.lang - package org.commonwl.lang
+
 
+
org.commonwl.util - package org.commonwl.util
+
 
+
out - Variable in class org.commonwl.lang.WorkflowStep
+
+
Defines the parameters representing the output of the process.
+
+
outdirMax - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
+
+
outdirMin - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
+
+
OutputArraySchema - Class in org.commonwl.lang
+
 
+
OutputArraySchema() - Constructor for class org.commonwl.lang.OutputArraySchema
+
 
+
outputBinding - Variable in class org.commonwl.lang.CommandOutputArraySchema
+
 
+
outputBinding - Variable in class org.commonwl.lang.CommandOutputEnumSchema
+
 
+
outputBinding - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
Describes how to handle the outputs of a process.
+
+
outputBinding - Variable in class org.commonwl.lang.CommandOutputRecordField
+
 
+
outputBinding - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
Describes how to handle the outputs of a process.
+
+
outputBinding - Variable in class org.commonwl.lang.OutputArraySchema
+
 
+
OutputBinding - Interface in org.commonwl.lang
+
 
+
outputBinding - Variable in class org.commonwl.lang.OutputEnumSchema
+
 
+
outputBinding - Variable in class org.commonwl.lang.OutputParameter
+
+
Describes how to handle the outputs of a process.
+
+
outputBinding - Variable in class org.commonwl.lang.OutputRecordField
+
 
+
outputBinding - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
Describes how to handle the outputs of a process.
+
+
OutputEnumSchema - Class in org.commonwl.lang
+
 
+
OutputEnumSchema() - Constructor for class org.commonwl.lang.OutputEnumSchema
+
 
+
outputEval - Variable in class org.commonwl.lang.CommandOutputBinding
+
+
Evaluate an expression to generate the output value.
+
+
OutputParameter - Class in org.commonwl.lang
+
 
+
OutputParameter() - Constructor for class org.commonwl.lang.OutputParameter
+
 
+
OutputRecordField - Class in org.commonwl.lang
+
 
+
OutputRecordField() - Constructor for class org.commonwl.lang.OutputRecordField
+
 
+
OutputRecordSchema - Class in org.commonwl.lang
+
 
+
OutputRecordSchema() - Constructor for class org.commonwl.lang.OutputRecordSchema
+
 
+
outputs - Variable in class org.commonwl.lang.CommandLineTool
+
+
Defines the parameters representing the output of the process.
+
+
outputs - Variable in class org.commonwl.lang.ExpressionTool
+
+
Defines the parameters representing the output of the process.
+
+
outputs - Static variable in interface org.commonwl.lang.Process
+
+
Defines the parameters representing the output of the process.
+
+
outputs - Variable in class org.commonwl.lang.Workflow
+
+
Defines the parameters representing the output of the process.
+
+
OUTPUTS - Variable in class org.commonwl.util.CWLReader
+
+
The CommandOutputParameter used for storing outputs in the CWL file.
+
+
OutputSchema - Interface in org.commonwl.lang
+
 
+
outputSource - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
Specifies one or more workflow parameters that supply the value of to the output parameter.
+
+
+ + + +

P

+
+
package_value - Variable in class org.commonwl.lang.SoftwarePackage
+
+
The common name of the software to be configured.
+
+
packages - Variable in class org.commonwl.lang.SoftwareRequirement
+
+
The list of software to be configured.
+
+
Parameter - Interface in org.commonwl.lang
+
+
Define an input or output parameter to a process.
+
+
path - Variable in class org.commonwl.lang.Directory
+
+
The local path where the Directory is made available prior to executing a CommandLineTool.
+
+
path - Variable in class org.commonwl.lang.File
+
+
The local host path where the File is available when a CommandLineTool is executed.
+
+
permanentFailCodes - Variable in class org.commonwl.lang.CommandLineTool
+
+
Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail.
+
+
position - Variable in class org.commonwl.lang.CommandLineBinding
+
+
The sorting key.
+
+
prefix - Variable in class org.commonwl.lang.CommandLineBinding
+
+
Command line prefix to add before the value.
+
+
PrimitiveType - Class in org.commonwl.lang
+
+
Salad data types are based on Avro schema declarations.
+
+
PrimitiveType(Object) - Constructor for class org.commonwl.lang.PrimitiveType
+
 
+
Process - Interface in org.commonwl.lang
+
 
+
processClass(String) - Method in class org.commonwl.util.CWLReader
+
+
This method processes the class in a CWL file, and updates the CommandLineTool contents.
+
+
processContents(Map) - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
This method processing of the contents of a CWL file for populating a CommandLineTool instance.
+
+
processContents(String, Object) - Method in class org.commonwl.util.CWLReader
+
+
This method processing of the contents of a CWL file for populating a CommandLineTool instance.
+
+
processFile() - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
This method starts the processing of the CWL file for populating the contents in a CommandLineTool.
+
+
processFile() - Method in class org.commonwl.util.CWLReader
+
+
This method starts the processing of the CWL file for populating the contents in a CommandLineTool.
+
+
processFile() - Method in class org.commonwl.util.JSONReader
+
+
This method will process a JSON file an store it's contents.
+
+
processInputs(Map) - Method in class org.commonwl.util.CWLReader
+
+
This method processes the intputs in a CWL file, and updates the CommandLineTool contents.
+
+
processOutputs(Map) - Method in class org.commonwl.util.CWLReader
+
+
This method processes the outputs in a CWL file, and updates the CommandLineTool contents.
+
+
ProcessRequirement - Interface in org.commonwl.lang
+
+
A process requirement declares a prerequisite that may or must be fulfilled before executing a process.
+
+
+ + + +

R

+
+
ramMax - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Maximum reserved RAM in mebibytes (2**20)
+
+
ramMin - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Minimum reserved RAM in mebibytes (2**20)
+
+
RecordField - Class in org.commonwl.lang
+
+
A field of a record.
+
+
RecordField() - Constructor for class org.commonwl.lang.RecordField
+
 
+
RecordSchema - Class in org.commonwl.lang
+
 
+
RecordSchema() - Constructor for class org.commonwl.lang.RecordSchema
+
 
+
refScope - Variable in class org.commonwl.lang.JsonldPredicate
+
+
If the field contains a relative reference, it must be resolved by searching for valid document references in each successive parent scope in the document fragment.
+
+
removeBrackets(String) - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
Purpose: To remove the brackets ([]) in a baseCommand.
+
+
removeBrackets(String) - Method in class org.commonwl.util.CWLReader
+
+
Purpose: To remove the brackets ([]) in a baseCommand.
+
+
requirements - Variable in class org.commonwl.lang.CommandLineTool
+
+
Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process.
+
+
requirements - Variable in class org.commonwl.lang.ExpressionTool
+
+
Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process.
+
+
requirements - Static variable in interface org.commonwl.lang.Process
+
+
Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process.
+
+
requirements - Variable in class org.commonwl.lang.Workflow
+
+
Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process.
+
+
requirements - Variable in class org.commonwl.lang.WorkflowStep
+
+
Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this workflow step.
+
+
ResourceRequirement - Class in org.commonwl.lang
+
+
Specify basic hardware resource requirements.
+
+
ResourceRequirement() - Constructor for class org.commonwl.lang.ResourceRequirement
+
 
+
ROOT_KEY - Variable in class org.commonwl.util.JSONReader
+
+
The String used for storing the key of the root of a JSON file's contents.
+
+
run - Variable in class org.commonwl.lang.WorkflowStep
+
+
Specifies the process to run.
+
+
+ + + +

S

+
+
SaladEnumSchema - Class in org.commonwl.lang
+
+
Define an enumerated type.
+
+
SaladEnumSchema() - Constructor for class org.commonwl.lang.SaladEnumSchema
+
 
+
SaladRecordField - Class in org.commonwl.lang
+
+
A field of a record.
+
+
SaladRecordField() - Constructor for class org.commonwl.lang.SaladRecordField
+
 
+
SaladRecordSchema - Class in org.commonwl.lang
+
 
+
SaladRecordSchema() - Constructor for class org.commonwl.lang.SaladRecordSchema
+
 
+
scatter - Variable in class org.commonwl.lang.WorkflowStep
+
 
+
ScatterFeatureRequirement - Class in org.commonwl.lang
+
+
Indicates that the workflow platform must support the `scatter` and `scatterMethod` fields of [WorkflowStep](#WorkflowStep).
+
+
ScatterFeatureRequirement() - Constructor for class org.commonwl.lang.ScatterFeatureRequirement
+
 
+
ScatterMethod - Enum in org.commonwl.lang
+
+
The scatter method, as described in [workflow step scatter](#WorkflowStep).
+
+
ScatterMethod() - Constructor for enum org.commonwl.lang.ScatterMethod
+
 
+
scatterMethod - Variable in class org.commonwl.lang.WorkflowStep
+
+
Required if `scatter` is an array of more than one element.
+
+
SchemaBase - Interface in org.commonwl.lang
+
 
+
SchemaDefinedType - Interface in org.commonwl.lang
+
+
Abstract base for schema-defined types.
+
+
SchemaDefRequirement - Class in org.commonwl.lang
+
+
This field consists of an array of type definitions which must be used when interpreting the `inputs` and `outputs` fields.
+
+
SchemaDefRequirement() - Constructor for class org.commonwl.lang.SchemaDefRequirement
+
 
+
secondaryFiles - Variable in class org.commonwl.lang.CommandInputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
secondaryFiles - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
secondaryFiles - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
secondaryFiles - Variable in class org.commonwl.lang.File
+
+
A list of additional files that are associated with the primary file and must be transferred alongside the primary file.
+
+
secondaryFiles - Variable in class org.commonwl.lang.InputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
secondaryFiles - Variable in class org.commonwl.lang.OutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
secondaryFiles - Static variable in interface org.commonwl.lang.Parameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
secondaryFiles - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
separate - Variable in class org.commonwl.lang.CommandLineBinding
+
+
If true (default), then the prefix and value must be added as separate command line arguments; if false, prefix and value must be concatenated into a single command line argument.
+
+
set(Object) - Method in class org.commonwl.lang.Any
+
+
This method sets the value of Any.
+
+
set(Boolean) - Method in class org.commonwl.lang.PrimitiveType
+
+
This method sets the value of PrimitiveType.
+
+
set(Integer) - Method in class org.commonwl.lang.PrimitiveType
+
+
This method sets the value of PrimitiveType.
+
+
set(Long) - Method in class org.commonwl.lang.PrimitiveType
+
+
This method sets the value of PrimitiveType.
+
+
set(Float) - Method in class org.commonwl.lang.PrimitiveType
+
+
This method sets the value of PrimitiveType.
+
+
set(Double) - Method in class org.commonwl.lang.PrimitiveType
+
+
This method sets the value of PrimitiveType.
+
+
set(String) - Method in class org.commonwl.lang.PrimitiveType
+
+
This method sets the value of PrimitiveType.
+
+
set_container(String) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of _container.
+
+
set_id(String) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of _id.
+
+
set_type(String) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of _type.
+
+
setabstract(Boolean) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of abstract_value.
+
+
setarguments(Expression[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of arguments.
+
+
setarguments(CommandLineBinding[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of arguments.
+
+
setarguments(String[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of arguments.
+
+
setbaseCommand(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of baseCommand.
+
+
setbaseCommand(String[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of baseCommand.
+
+
setbasename(String) - Method in class org.commonwl.lang.Directory
+
+
This method sets the value of basename.
+
+
setbasename(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of basename.
+
+
setchecksum(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of checksum.
+
+
setclass(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of class_value.
+
+
setclass(Directory) - Method in class org.commonwl.lang.Directory
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.EnvVarRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of class_value.
+
+
setclass(File) - Method in class org.commonwl.lang.File
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.InlineJavascriptRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.MultipleInputFeatureRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.ScatterFeatureRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.SchemaDefRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.ShellCommandRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.SoftwareRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.StepInputExpressionRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.SubworkflowFeatureRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of class_value.
+
+
setcontents(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of contents.
+
+
setcoresMax(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of coresMax.
+
+
setcoresMax(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of coresMax.
+
+
setcoresMax(Integer) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of coresMax.
+
+
setcoresMin(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of coresMin.
+
+
setcoresMin(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of coresMin.
+
+
setcoresMin(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of coresMin.
+
+
setcwlVersion(CWLVersion) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of cwlVersion.
+
+
setcwlVersion(CWLVersion) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of cwlVersion.
+
+
setcwlVersion(CWLVersion) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of cwlVersion.
+
+
setcwlVersion(CWLVersion) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of cwlVersion.
+
+
setdefault(Any) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of default_value.
+
+
setdefault(Any) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of default_value.
+
+
setdefault(Any) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of default_value.
+
+
setdirname(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of dirname.
+
+
setdoc(String) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in interface org.commonwl.lang.DocType
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in interface org.commonwl.lang.DocType
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of doc.
+
+
setdocAfter(String) - Method in interface org.commonwl.lang.DocType
+
+
This method sets the value of docAfter.
+
+
setdocAfter(String) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of docAfter.
+
+
setdocAfter(String) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of docAfter.
+
+
setdocAfter(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of docAfter.
+
+
setdocAfter(String) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of docAfter.
+
+
setdocChild(String) - Method in interface org.commonwl.lang.DocType
+
+
This method sets the value of docChild.
+
+
setdocChild(String[]) - Method in interface org.commonwl.lang.DocType
+
+
This method sets the value of docChild.
+
+
setdocChild(String) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of docChild.
+
+
setdocChild(String[]) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of docChild.
+
+
setdocChild(String) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of docChild.
+
+
setdocChild(String[]) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of docChild.
+
+
setdocChild(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of docChild.
+
+
setdocChild(String[]) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of docChild.
+
+
setdocChild(String) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of docChild.
+
+
setdocChild(String[]) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of docChild.
+
+
setdockerFile(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of dockerFile.
+
+
setdockerImageId(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of dockerImageId.
+
+
setdockerImport(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of dockerImport.
+
+
setdockerLoad(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of dockerLoad.
+
+
setdockerOutputDirectory(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of dockerOutputDirectory.
+
+
setdockerPull(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of dockerPull.
+
+
setdocParent(String) - Method in interface org.commonwl.lang.DocType
+
+
This method sets the value of docParent.
+
+
setdocParent(String) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of docParent.
+
+
setdocParent(String) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of docParent.
+
+
setdocParent(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of docParent.
+
+
setdocParent(String) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of docParent.
+
+
setdocumentRoot(Boolean) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of documentRoot.
+
+
setdocumentRoot(Boolean) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of documentRoot.
+
+
setdocumentRoot(Boolean) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of documentRoot.
+
+
setentry(String) - Method in class org.commonwl.lang.Dirent
+
+
This method sets the value of entry.
+
+
setentry(Expression) - Method in class org.commonwl.lang.Dirent
+
+
This method sets the value of entry.
+
+
setentryname(String) - Method in class org.commonwl.lang.Dirent
+
+
This method sets the value of entryname.
+
+
setentryname(Expression) - Method in class org.commonwl.lang.Dirent
+
+
This method sets the value of entryname.
+
+
setenvDef(EnvironmentDef) - Method in class org.commonwl.lang.EnvVarRequirement
+
+
This method sets the value of envDef.
+
+
setenvName(String) - Method in class org.commonwl.lang.EnvironmentDef
+
+
This method sets the value of envName.
+
+
setenvValue(String) - Method in class org.commonwl.lang.EnvironmentDef
+
+
This method sets the value of envValue.
+
+
setenvValue(Expression) - Method in class org.commonwl.lang.EnvironmentDef
+
+
This method sets the value of envValue.
+
+
setexpression(String) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of expression.
+
+
setexpression(Expression) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of expression.
+
+
setexpressionLib(String) - Method in class org.commonwl.lang.InlineJavascriptRequirement
+
+
This method sets the value of expressionLib.
+
+
setextends(String) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of extends_value.
+
+
setextends(String[]) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of extends_value.
+
+
setextends(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of extends_value.
+
+
setextends(String[]) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of extends_value.
+
+
setformat(Expression[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of format.
+
+
setformat(Expression[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of format.
+
+
setformat(Expression[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of format.
+
+
setformat(Expression[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of format.
+
+
setformat(Expression[]) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of format.
+
+
setformat(Expression[]) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of format.
+
+
setformat(Expression[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of format.
+
+
setglob(String) - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method sets the value of glob.
+
+
setglob(String[]) - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method sets the value of glob.
+
+
setglob(Expression) - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method sets the value of glob.
+
+
sethints(Any) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of hints.
+
+
sethints(Any) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of hints.
+
+
sethints(Any) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of hints.
+
+
sethints(Any) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of hints.
+
+
sethints(Any) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of hints.
+
+
setid(String) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of id.
+
+
setid(String) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.WorkflowStepOutput
+
+
This method sets the value of id.
+
+
setidentity(Boolean) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of identity.
+
+
setin(WorkflowStepInput) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of in.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.CommandInputArraySchema
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.CommandInputEnumSchema
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.InputArraySchema
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.InputEnumSchema
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of inputBinding.
+
+
setinputs(CommandInputParameter[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of inputs.
+
+
setinputs(InputParameter[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
+
+
setinputs(InputParameter[]) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of inputs.
+
+
setinputs(InputParameter[]) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of inputs.
+
+
setinputs(InputParameter[]) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of inputs.
+
+
setitemSeparator(String) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of itemSeparator.
+
+
setjsonldPredicate(String) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(JsonldPredicate) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(String) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(JsonldPredicate) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(JsonldPredicate) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(String) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(JsonldPredicate) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of jsonldPredicate.
+
+
setlabel(String) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.InputArraySchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.InputEnumSchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.InputRecordSchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in interface org.commonwl.lang.InputSchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.OutputArraySchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.OutputEnumSchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.OutputRecordSchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in interface org.commonwl.lang.OutputSchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in interface org.commonwl.lang.SchemaBase
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of label.
+
+
setlinkMerge(LinkMergeMethod) - Method in interface org.commonwl.lang.Sink
+
+
This method sets the value of linkMerge.
+
+
setlinkMerge(LinkMergeMethod) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of linkMerge.
+
+
setlinkMerge(LinkMergeMethod) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of linkMerge.
+
+
setlisting(File[]) - Method in class org.commonwl.lang.Directory
+
+
This method sets the value of listing.
+
+
setlisting(Directory[]) - Method in class org.commonwl.lang.Directory
+
+
This method sets the value of listing.
+
+
setlisting(Dirent[]) - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method sets the value of listing.
+
+
setlisting(File[]) - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method sets the value of listing.
+
+
setlisting(Directory[]) - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method sets the value of listing.
+
+
setlisting(Expression[]) - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method sets the value of listing.
+
+
setlisting(String[]) - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method sets the value of listing.
+
+
setloadContents(Boolean) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of loadContents.
+
+
setloadContents(Boolean) - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method sets the value of loadContents.
+
+
setloadContents(Boolean) - Method in interface org.commonwl.lang.InputBinding
+
+
This method sets the value of loadContents.
+
+
setlocation(String) - Method in class org.commonwl.lang.Directory
+
+
This method sets the value of location.
+
+
setlocation(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of location.
+
+
setmapPredicate(String) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of mapPredicate.
+
+
setmapSubject(String) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of mapSubject.
+
+
setname(String) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of name.
+
+
setname(String) - Method in interface org.commonwl.lang.NamedType
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of name.
+
+
setnameext(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of nameext.
+
+
setnameroot(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of nameroot.
+
+
setnoLinkCheck(Boolean) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of noLinkCheck.
+
+
setout(WorkflowStepOutput[]) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of out.
+
+
setout(String[]) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of out.
+
+
setoutdirMax(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of outdirMax.
+
+
setoutdirMax(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of outdirMax.
+
+
setoutdirMax(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of outdirMax.
+
+
setoutdirMin(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of outdirMin.
+
+
setoutdirMin(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of outdirMin.
+
+
setoutdirMin(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of outdirMin.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.CommandOutputArraySchema
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.CommandOutputEnumSchema
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.OutputArraySchema
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.OutputEnumSchema
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of outputBinding.
+
+
setoutputEval(String) - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method sets the value of outputEval.
+
+
setoutputEval(Expression) - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method sets the value of outputEval.
+
+
setoutputs(CommandOutputParameter[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of outputs.
+
+
setoutputs(OutputParameter[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
+
+
setoutputs(ExpressionToolOutputParameter[]) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of outputs.
+
+
setoutputs(OutputParameter[]) - Method in class org.commonwl.lang.ExpressionTool
+
+
This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
+
+
setoutputs(OutputParameter[]) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of outputs.
+
+
setoutputs(WorkflowOutputParameter[]) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of outputs.
+
+
setoutputs(OutputParameter[]) - Method in class org.commonwl.lang.Workflow
+
+
This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
+
+
setoutputSource(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of outputSource.
+
+
setoutputSource(String[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of outputSource.
+
+
setpackage(String) - Method in class org.commonwl.lang.SoftwarePackage
+
+
This method sets the value of package_value.
+
+
setpackages(SoftwarePackage) - Method in class org.commonwl.lang.SoftwareRequirement
+
+
This method sets the value of packages.
+
+
setpath(String) - Method in class org.commonwl.lang.Directory
+
+
This method sets the value of path.
+
+
setpath(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of path.
+
+
setpermanentFailCodes(Integer) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of permanentFailCodes.
+
+
setposition(Integer) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of position.
+
+
setprefix(String) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of prefix.
+
+
setramMax(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of ramMax.
+
+
setramMax(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of ramMax.
+
+
setramMax(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of ramMax.
+
+
setramMin(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of ramMin.
+
+
setramMin(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of ramMin.
+
+
setramMin(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of ramMin.
+
+
setrefScope(Integer) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of refScope.
+
+
setrequirements(StepInputExpressionRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(MultipleInputFeatureRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(SoftwareRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(SchemaDefRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(InitialWorkDirRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(EnvVarRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(DockerRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(ResourceRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(InlineJavascriptRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(ShellCommandRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(ScatterFeatureRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(SubworkflowFeatureRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(StepInputExpressionRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(MultipleInputFeatureRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(SoftwareRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(SchemaDefRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(InitialWorkDirRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(EnvVarRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(DockerRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(ResourceRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(InlineJavascriptRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(ShellCommandRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(ScatterFeatureRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(SubworkflowFeatureRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(StepInputExpressionRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(MultipleInputFeatureRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(SoftwareRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(SchemaDefRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(InitialWorkDirRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(EnvVarRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(DockerRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(ResourceRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(InlineJavascriptRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(ShellCommandRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(ScatterFeatureRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(SubworkflowFeatureRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(StepInputExpressionRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(MultipleInputFeatureRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(SoftwareRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(SchemaDefRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(InitialWorkDirRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(EnvVarRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(DockerRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(ResourceRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(InlineJavascriptRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(ShellCommandRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(ScatterFeatureRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(SubworkflowFeatureRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(StepInputExpressionRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(MultipleInputFeatureRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(SoftwareRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(SchemaDefRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(InitialWorkDirRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(EnvVarRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(DockerRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(ResourceRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(InlineJavascriptRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(ShellCommandRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(ScatterFeatureRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(SubworkflowFeatureRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrun(CommandLineTool) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of run.
+
+
setrun(String) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of run.
+
+
setrun(Workflow) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of run.
+
+
setrun(ExpressionTool) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of run.
+
+
setscatter(String) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of scatter.
+
+
setscatter(String[]) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of scatter.
+
+
setscatterMethod(ScatterMethod) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of scatterMethod.
+
+
setsecondaryFiles(Expression[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(File[]) - Method in class org.commonwl.lang.File
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Directory[]) - Method in class org.commonwl.lang.File
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression[]) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression[]) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setseparate(Boolean) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of separate.
+
+
setshellQuote(Boolean) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of shellQuote.
+
+
setsize(Long) - Method in class org.commonwl.lang.File
+
+
This method sets the value of size.
+
+
setsource(String) - Method in interface org.commonwl.lang.Sink
+
+
This method sets the value of source.
+
+
setsource(String[]) - Method in interface org.commonwl.lang.Sink
+
+
This method sets the value of source.
+
+
setsource(String) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of source.
+
+
setsource(String[]) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of source.
+
+
setspecialize(SpecializeDef[]) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of specialize.
+
+
setspecializeFrom(String) - Method in class org.commonwl.lang.SpecializeDef
+
+
This method sets the value of specializeFrom.
+
+
setspecializeTo(String) - Method in class org.commonwl.lang.SpecializeDef
+
+
This method sets the value of specializeTo.
+
+
setspecs(String) - Method in class org.commonwl.lang.SoftwarePackage
+
+
This method sets the value of specs.
+
+
setStandardInput(String) - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method sets the standard input String.
+
+
setStatusCode(Integer) - Method in class org.commonwl.util.SystemCommandExecution
+
 
+
setstderr(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of stderr.
+
+
setstderr(Expression) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of stderr.
+
+
setstdin(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of stdin.
+
+
setstdin(Expression) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of stdin.
+
+
setstdout(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of stdout.
+
+
setstdout(Expression) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of stdout.
+
+
setsteps(WorkflowStep[]) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of steps.
+
+
setstreamable(Boolean) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of streamable.
+
+
setstreamable(Boolean) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of streamable.
+
+
setstreamable(Boolean) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of streamable.
+
+
setstreamable(Boolean) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of streamable.
+
+
setstreamable(Boolean) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of streamable.
+
+
setstreamable(Boolean) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of streamable.
+
+
setstreamable(Boolean) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of streamable.
+
+
setsuccessCodes(Integer) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of successCodes.
+
+
settemporaryFailCodes(Integer) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of temporaryFailCodes.
+
+
settmpdirMax(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of tmpdirMax.
+
+
settmpdirMax(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of tmpdirMax.
+
+
settmpdirMax(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of tmpdirMax.
+
+
settmpdirMin(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of tmpdirMin.
+
+
settmpdirMin(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of tmpdirMin.
+
+
settmpdirMin(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of tmpdirMin.
+
+
settype(CommandInputEnumSchema[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CommandInputEnumSchema) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CommandInputRecordSchema[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CommandInputRecordSchema) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CommandInputArraySchema) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CommandInputArraySchema[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(RecordSchema) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType[]) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(RecordSchema[]) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema[]) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema[]) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(CommandOutputArraySchema) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(stderr) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CommandOutputArraySchema[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CommandOutputRecordSchema[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(stdout) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CommandOutputEnumSchema) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CommandOutputRecordSchema) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CommandOutputEnumSchema[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(RecordSchema) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType[]) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(RecordSchema[]) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema[]) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema[]) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(Object) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of type.
+
+
settype(OutputRecordSchema[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputEnumSchema[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputRecordSchema) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputEnumSchema) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputArraySchema) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputArraySchema[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(InputEnumSchema[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(InputEnumSchema) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(InputRecordSchema[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(InputRecordSchema) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(InputArraySchema) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(InputArraySchema[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(InputRecordSchema) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(InputEnumSchema) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(InputArraySchema) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(InputRecordSchema[]) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(InputArraySchema[]) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(InputEnumSchema[]) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(OutputRecordSchema) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(OutputEnumSchema) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(OutputArraySchema) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(OutputRecordSchema[]) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(OutputArraySchema[]) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(OutputEnumSchema[]) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(RecordSchema) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType[]) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(RecordSchema[]) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema[]) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema[]) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(RecordSchema) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType[]) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(RecordSchema[]) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema[]) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema[]) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(OutputRecordSchema[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputEnumSchema[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputRecordSchema) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputEnumSchema) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputArraySchema) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputArraySchema[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settypeDSL(Boolean) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of typeDSL.
+
+
settypes(InputEnumSchema[]) - Method in class org.commonwl.lang.SchemaDefRequirement
+
+
This method sets the value of types.
+
+
settypes(InputArraySchema[]) - Method in class org.commonwl.lang.SchemaDefRequirement
+
+
This method sets the value of types.
+
+
settypes(InputRecordSchema[]) - Method in class org.commonwl.lang.SchemaDefRequirement
+
+
This method sets the value of types.
+
+
setvalueFrom(String) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of valueFrom.
+
+
setvalueFrom(Expression) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of valueFrom.
+
+
setvalueFrom(String) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of valueFrom.
+
+
setvalueFrom(Expression) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of valueFrom.
+
+
setversion(String) - Method in class org.commonwl.lang.SoftwarePackage
+
+
This method sets the value of version.
+
+
setwritable(Boolean) - Method in class org.commonwl.lang.Dirent
+
+
This method sets the value of writable.
+
+
ShellCommandRequirement - Class in org.commonwl.lang
+
+
Modify the behavior of CommandLineTool to generate a single string containing a shell command line.
+
+
ShellCommandRequirement() - Constructor for class org.commonwl.lang.ShellCommandRequirement
+
 
+
shellQuote - Variable in class org.commonwl.lang.CommandLineBinding
+
+
If `ShellCommandRequirement` is in the requirements for the current command, this controls whether the value is quoted on the command line (default is true).
+
+
Sink - Interface in org.commonwl.lang
+
 
+
size - Variable in class org.commonwl.lang.File
+
+
Optional file size
+
+
SoftwarePackage - Class in org.commonwl.lang
+
 
+
SoftwarePackage() - Constructor for class org.commonwl.lang.SoftwarePackage
+
 
+
SoftwareRequirement - Class in org.commonwl.lang
+
+
A list of software packages that should be configured in the environment of the defined process.
+
+
SoftwareRequirement() - Constructor for class org.commonwl.lang.SoftwareRequirement
+
 
+
source - Static variable in interface org.commonwl.lang.Sink
+
+
Specifies one or more workflow parameters that will provide input to the underlying step parameter.
+
+
source - Variable in class org.commonwl.lang.WorkflowStepInput
+
+
Specifies one or more workflow parameters that will provide input to the underlying step parameter.
+
+
specialize - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
Only applies if `extends` is declared.
+
+
SpecializeDef - Class in org.commonwl.lang
+
 
+
SpecializeDef() - Constructor for class org.commonwl.lang.SpecializeDef
+
 
+
specializeFrom - Variable in class org.commonwl.lang.SpecializeDef
+
+
The data type to be replaced
+
+
specializeTo - Variable in class org.commonwl.lang.SpecializeDef
+
+
The new data type to replace with
+
+
specs - Variable in class org.commonwl.lang.SoftwarePackage
+
+
Must be one or more IRIs identifying resources for installing or enabling the software.
+
+
StandardError - Variable in class org.commonwl.util.SystemCommandExecution
+
+
The String used for storing the standard error.
+
+
StandardInput - Variable in class org.commonwl.util.SystemCommandExecution
+
+
The String used for storing the standard input.
+
+
StandardOutput - Variable in class org.commonwl.util.SystemCommandExecution
+
+
The String used for storing the standard output.
+
+
statusCode - Variable in class org.commonwl.util.SystemCommandExecution
+
+
The Integer used for storing the return status code.
+
+
stderr - Variable in class org.commonwl.lang.CommandLineTool
+
+
Capture the command's standard error stream to a file written to the designated output directory.
+
+
stderr - Enum in org.commonwl.lang
+
+
Only valid as a `type` for a `CommandLineTool` output with no `outputBinding` set.
+
+
stderr() - Constructor for enum org.commonwl.lang.stderr
+
 
+
stdin - Variable in class org.commonwl.lang.CommandLineTool
+
+
A path to a file whose contents must be piped into the command's standard input stream.
+
+
stdout - Variable in class org.commonwl.lang.CommandLineTool
+
+
Capture the command's standard output stream to a file written to the designated output directory.
+
+
stdout - Enum in org.commonwl.lang
+
+
Only valid as a `type` for a `CommandLineTool` output with no `outputBinding` set.
+
+
stdout() - Constructor for enum org.commonwl.lang.stdout
+
 
+
StepInputExpressionRequirement - Class in org.commonwl.lang
+
+
Indicate that the workflow platform must support the `valueFrom` field of [WorkflowStepInput](#WorkflowStepInput).
+
+
StepInputExpressionRequirement() - Constructor for class org.commonwl.lang.StepInputExpressionRequirement
+
 
+
steps - Variable in class org.commonwl.lang.Workflow
+
+
The individual steps that make up the workflow.
+
+
streamable - Variable in class org.commonwl.lang.CommandInputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
streamable - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
streamable - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
streamable - Variable in class org.commonwl.lang.InputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
streamable - Variable in class org.commonwl.lang.OutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
streamable - Static variable in interface org.commonwl.lang.Parameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
streamable - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
SubworkflowFeatureRequirement - Class in org.commonwl.lang
+
+
Indicates that the workflow platform must support nested workflows in the `run` field of [WorkflowStep](#WorkflowStep).
+
+
SubworkflowFeatureRequirement() - Constructor for class org.commonwl.lang.SubworkflowFeatureRequirement
+
 
+
successCodes - Variable in class org.commonwl.lang.CommandLineTool
+
+
Exit codes that indicate the process completed successfully.
+
+
SystemCommandExecution - Class in org.commonwl.util
+
+
This is used for executing commands on the system.
+
+
SystemCommandExecution() - Constructor for class org.commonwl.util.SystemCommandExecution
+
 
+
SystemCommandExecution(String) - Constructor for class org.commonwl.util.SystemCommandExecution
+
 
+
+ + + +

T

+
+
temporaryFailCodes - Variable in class org.commonwl.lang.CommandLineTool
+
+
Exit codes that indicate the process failed due to a possibly temporary condition, where executing the process with the same runtime environment and inputs may produce different results.
+
+
tmpdirMax - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
+
+
tmpdirMin - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
+
+
TOOL_TYPE - Variable in class org.commonwl.util.CWLJavaCodeGenerator
+
+
The String used for storing if the CWL file is a CommandLineTool or Workflow.
+
+
type - Variable in class org.commonwl.lang.CommandInputParameter
+
+
Specify valid types of data that may be assigned to this parameter.
+
+
type - Variable in class org.commonwl.lang.CommandInputRecordField
+
+
The field type
+
+
type - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
Specify valid types of data that may be assigned to this parameter.
+
+
type - Variable in class org.commonwl.lang.CommandOutputRecordField
+
+
The field type
+
+
type - Variable in class org.commonwl.lang.Documentation
+
+
Must be `documentation`
+
+
type - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
Specify valid types of data that may be assigned to this parameter.
+
+
type - Variable in class org.commonwl.lang.InputParameter
+
+
Specify valid types of data that may be assigned to this parameter.
+
+
type - Variable in class org.commonwl.lang.InputRecordField
+
+
The field type
+
+
type - Variable in class org.commonwl.lang.OutputRecordField
+
+
The field type
+
+
type - Variable in class org.commonwl.lang.RecordField
+
+
The field type
+
+
type - Variable in class org.commonwl.lang.SaladRecordField
+
+
The field type
+
+
type - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
Specify valid types of data that may be assigned to this parameter.
+
+
typeDSL - Variable in class org.commonwl.lang.JsonldPredicate
+
+
Field must be expanded based on the the Schema Salad type DSL.
+
+
types - Variable in class org.commonwl.lang.SchemaDefRequirement
+
+
The list of type definitions.
+
+
+ + + +

V

+
+
value - Variable in class org.commonwl.lang.Any
+
+
This is the value of Any.
+
+
value - Variable in class org.commonwl.lang.PrimitiveType
+
 
+
valueFrom - Variable in class org.commonwl.lang.CommandLineBinding
+
+
If `valueFrom` is a constant string value, use this as the value and apply the binding rules above.
+
+
valueFrom - Variable in class org.commonwl.lang.WorkflowStepInput
+
+
To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must be specified in the workflow or workflow step requirements.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.CWLType
+
+
Returns the enum constant of this type with the specified name.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.CWLVersion
+
+
Returns the enum constant of this type with the specified name.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.Expression
+
+
Returns the enum constant of this type with the specified name.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.LinkMergeMethod
+
+
Returns the enum constant of this type with the specified name.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.ScatterMethod
+
+
Returns the enum constant of this type with the specified name.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.stderr
+
+
Returns the enum constant of this type with the specified name.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.stdout
+
+
Returns the enum constant of this type with the specified name.
+
+
values() - Static method in enum org.commonwl.lang.CWLType
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
values() - Static method in enum org.commonwl.lang.CWLVersion
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
values() - Static method in enum org.commonwl.lang.Expression
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
values() - Static method in enum org.commonwl.lang.LinkMergeMethod
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
values() - Static method in enum org.commonwl.lang.ScatterMethod
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
values() - Static method in enum org.commonwl.lang.stderr
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
values() - Static method in enum org.commonwl.lang.stdout
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
version - Variable in class org.commonwl.lang.SoftwarePackage
+
+
The (optional) version of the software to configured.
+
+
+ + + +

W

+
+
Workflow - Class in org.commonwl.lang
+
+
A workflow describes a set of **steps** and the **dependencies** between those steps.
+
+
Workflow() - Constructor for class org.commonwl.lang.Workflow
+
 
+
WorkflowOutputParameter - Class in org.commonwl.lang
+
+
Describe an output parameter of a workflow.
+
+
WorkflowOutputParameter() - Constructor for class org.commonwl.lang.WorkflowOutputParameter
+
 
+
WorkflowStep - Class in org.commonwl.lang
+
+
A workflow step is an executable element of a workflow.
+
+
WorkflowStep() - Constructor for class org.commonwl.lang.WorkflowStep
+
 
+
WorkflowStepInput - Class in org.commonwl.lang
+
+
The input of a workflow step connects an upstream parameter (from the workflow inputs, or the outputs of other workflows steps) with the input parameters of the underlying step.
+
+
WorkflowStepInput() - Constructor for class org.commonwl.lang.WorkflowStepInput
+
 
+
WorkflowStepOutput - Class in org.commonwl.lang
+
+
Associate an output parameter of the underlying process with a workflow parameter.
+
+
WorkflowStepOutput() - Constructor for class org.commonwl.lang.WorkflowStepOutput
+
 
+
writable - Variable in class org.commonwl.lang.Dirent
+
+
If true, the file or directory must be writable by the tool.
+
+
+ + + +

_

+
+
_container - Variable in class org.commonwl.lang.JsonldPredicate
+
+
Structure hint, corresponds to JSON-LD `@container` directive.
+
+
_id - Variable in class org.commonwl.lang.JsonldPredicate
+
+
The predicate URI that this field corresponds to.
+
+
_type - Variable in class org.commonwl.lang.JsonldPredicate
+
+
The context type hint, corresponds to JSON-LD `@type` directive.
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org.commonwl.lang
+

Class Any

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.Any
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class Any
+extends java.lang.Object
    +
    The Any type validates for any non-null value.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectvalue +
      This is the value of Any.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      Any(java.lang.Object objectInstance) 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectget() +
      This method returns the value of Any.
      +
      voidset(java.lang.Object objectInstance) +
      This method sets the value of Any.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        value

        +
        java.lang.Object value
        +
        This is the value of Any.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        Any

        +
        public Any(java.lang.Object objectInstance)
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        set

        +
        public void set(java.lang.Object objectInstance)
        +
        This method sets the value of Any.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of Any, and is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        get

        +
        public java.lang.Object get()
        +
        This method returns the value of Any.
        +
        +
        Returns:
        +
        This method will return the value of Any, which is an Any type.
        +
        +
        • +
      +
      • +
    +
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+ + + diff --git a/javadoc/org/commonwl/lang/ArraySchema.html b/javadoc/org/commonwl/lang/ArraySchema.html new file mode 100644 index 00000000..ad5f46fd --- /dev/null +++ b/javadoc/org/commonwl/lang/ArraySchema.html @@ -0,0 +1,239 @@ + + + + + +ArraySchema + + + + + + + + +
+ + +
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  • Summary: 
    • +
  • Nested | 
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  • Method
    • +
+
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  • Detail: 
    • +
  • Field | 
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    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Class ArraySchema

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.ArraySchema
      • +
    +
    • +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      ArraySchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        ArraySchema

        +
        public ArraySchema()
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
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+ + + +
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    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
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  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
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  • Constr | 
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  • Method
    • +
+
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CWLType.html b/javadoc/org/commonwl/lang/CWLType.html new file mode 100644 index 00000000..a7c456e6 --- /dev/null +++ b/javadoc/org/commonwl/lang/CWLType.html @@ -0,0 +1,340 @@ + + + + + +CWLType + + + + + + + + +
+ + +
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+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Enum CWLType

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<CWLType>
      • +
    • +
        +
      • org.commonwl.lang.CWLType
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<CWLType>
    +
    +
    +
    +
    public enum CWLType
+extends java.lang.Enum<CWLType>
    +
    - Extends primitive types with the concept of a file and directory as a builtin type. - File: A File object - Directory: A Directory object
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Enum Constant Summary

      + + + + + + + + + + + +
      Enum Constants 
      Enum Constant and Description
      Directory 
      File 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Static Methods Concrete Methods 
      Modifier and TypeMethod and Description
      static CWLTypevalueOf(java.lang.String name) +
      Returns the enum constant of this type with the specified name.
      +
      static CWLType[]values() +
      Returns an array containing the constants of this enum type, in +the order they are declared.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Enum

        +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
        • +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +getClass, notify, notifyAll, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Enum Constant Detail

      + + + +
        +
      • +

        File

        +
        public static final CWLType File
        +
        • +
      + + + +
        +
      • +

        Directory

        +
        public static final CWLType Directory
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static CWLType[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (CWLType c : CWLType.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static CWLType valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CWLVersion.html b/javadoc/org/commonwl/lang/CWLVersion.html new file mode 100644 index 00000000..34e03153 --- /dev/null +++ b/javadoc/org/commonwl/lang/CWLVersion.html @@ -0,0 +1,460 @@ + + + + + +CWLVersion + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Enum CWLVersion

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<CWLVersion>
      • +
    • +
        +
      • org.commonwl.lang.CWLVersion
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<CWLVersion>
    +
    +
    +
    +
    public enum CWLVersion
+extends java.lang.Enum<CWLVersion>
    +
    Version symbols for published CWL document versions.
    +
    • +
+
+
+ +
+
+
    +
  • + + + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static CWLVersion[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (CWLVersion c : CWLVersion.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static CWLVersion valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CommandInputArraySchema.html b/javadoc/org/commonwl/lang/CommandInputArraySchema.html new file mode 100644 index 00000000..e4daeb1f --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandInputArraySchema.html @@ -0,0 +1,364 @@ + + + + + +CommandInputArraySchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandInputArraySchema

+
+
+ +
+ +
+
+ +
+
+
    +
  • + + + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandInputArraySchema

        +
        public CommandInputArraySchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Overrides:
        +
        setinputBinding in class InputArraySchema
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Overrides:
        +
        getinputBinding in class InputArraySchema
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CommandInputEnumSchema.html b/javadoc/org/commonwl/lang/CommandInputEnumSchema.html new file mode 100644 index 00000000..2ba101ba --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandInputEnumSchema.html @@ -0,0 +1,364 @@ + + + + + +CommandInputEnumSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandInputEnumSchema

+
+
+ +
+ +
+
+ +
+
+
    +
  • + + + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandInputEnumSchema

        +
        public CommandInputEnumSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Overrides:
        +
        setinputBinding in class InputEnumSchema
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Overrides:
        +
        getinputBinding in class InputEnumSchema
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CommandInputParameter.html b/javadoc/org/commonwl/lang/CommandInputParameter.html new file mode 100644 index 00000000..a9bbe0b9 --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandInputParameter.html @@ -0,0 +1,1190 @@ + + + + + +CommandInputParameter + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandInputParameter

+
+
+ +
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Parameter, SchemaBase
    +
    +
    +
    +
    public class CommandInputParameter
+extends InputParameter
    +
    An input parameter for a CommandLineTool.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) Anydefault_value +
      The default value for this parameter if not provided in the input object.
      +
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this parameter object.
      +
      (package private) CommandLineBindinginputBinding +
      Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Objecttype +
      Specify valid types of data that may be assigned to this parameter.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      Anygetdefault() +
      This method returns the value of default_value.
      +
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      CommandLineBindinggetinputBinding() +
      This method returns the value of inputBinding.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdefault(Any value) +
      This method sets the value of default_value.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetinputBinding(CommandLineBinding value) +
      This method sets the value of inputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      voidsettype(CommandInputArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(CommandInputArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(CommandInputEnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(CommandInputEnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(CommandInputRecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(CommandInputRecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(CWLType value) +
      This method sets the value of type.
      +
      voidsettype(CWLType[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      + +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        default_value

        +
        Any default_value
        +
        The default value for this parameter if not provided in the input object.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this parameter object.
        +
        • +
      + + + +
        +
      • +

        inputBinding

        +
        CommandLineBinding inputBinding
        +
        Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        Specify valid types of data that may be assigned to this parameter.
        +
        • +
      + + + +
        +
      • +

        streamable

        +
        java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandInputParameter

        +
        public CommandInputParameter()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setdefault

        +
        public void setdefault(Any value)
        +
        This method sets the value of default_value.
        +
        +
        Overrides:
        +
        setdefault in class InputParameter
        +
        Parameters:
        +
        value - will update default_value, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        getdefault

        +
        public Any getdefault()
        +
        This method returns the value of default_value.
        +
        +
        Overrides:
        +
        getdefault in class InputParameter
        +
        Returns:
        +
        This method will return the value of default_value, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Overrides:
        +
        setid in class InputParameter
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Overrides:
        +
        getid in class InputParameter
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Overrides:
        +
        setinputBinding in class InputParameter
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Overrides:
        +
        getinputBinding in class InputParameter
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandInputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputEnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandInputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputEnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class InputParameter
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandInputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputRecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandInputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputRecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class InputParameter
        +
        Parameters:
        +
        value - will update type, which is a CWLType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class InputParameter
        +
        Parameters:
        +
        value - will update type, which is a CWLType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class InputParameter
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandInputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandInputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Overrides:
        +
        gettype in class InputParameter
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setstreamable

        +
        public void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Specified by:
        +
        setstreamable in interface Parameter
        +
        Overrides:
        +
        setstreamable in class InputParameter
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        public java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Specified by:
        +
        getstreamable in interface Parameter
        +
        Overrides:
        +
        getstreamable in class InputParameter
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class InputParameter
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class InputParameter
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class InputParameter
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Specified by:
        +
        getformat in interface Parameter
        +
        Overrides:
        +
        getformat in class InputParameter
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class InputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class InputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Parameter
        +
        Overrides:
        +
        getdoc in class InputParameter
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class InputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class InputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Specified by:
        +
        getsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        getsecondaryFiles in class InputParameter
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Parameter
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Overrides:
        +
        setlabel in class InputParameter
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Parameter
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Overrides:
        +
        getlabel in class InputParameter
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
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+ + + diff --git a/javadoc/org/commonwl/lang/CommandInputRecordField.html b/javadoc/org/commonwl/lang/CommandInputRecordField.html new file mode 100644 index 00000000..d4aac6ac --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandInputRecordField.html @@ -0,0 +1,791 @@ + + + + + +CommandInputRecordField + + + + + + + + +
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+
org.commonwl.lang
+

Class CommandInputRecordField

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringdoc +
      A documentation string for this field
      +
      (package private) CommandLineBindinginputBinding 
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this process object.
      +
      (package private) java.lang.Stringname +
      The name of the field
      +
      (package private) java.lang.Objecttype +
      The field type
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetdoc() +
      This method returns the value of doc.
      +
      CommandLineBindinggetinputBinding() +
      This method returns the value of inputBinding.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      java.lang.Stringgetname() +
      This method returns the value of name.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetinputBinding(CommandLineBinding value) +
      This method sets the value of inputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetname(java.lang.String value) +
      This method sets the value of name.
      +
      voidsettype(ArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(ArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(EnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(EnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(PrimitiveType value) +
      This method sets the value of type.
      +
      voidsettype(PrimitiveType[] value) +
      This method sets the value of type.
      +
      voidsettype(RecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(RecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      + +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      + + + + + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The name of the field
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A documentation string for this field
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        The field type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandInputRecordField

        +
        public CommandInputRecordField()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Overrides:
        +
        setlabel in class InputRecordField
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Overrides:
        +
        getlabel in class InputRecordField
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Overrides:
        +
        setinputBinding in class InputRecordField
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Overrides:
        +
        getinputBinding in class InputRecordField
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Overrides:
        +
        setname in class InputRecordField
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Overrides:
        +
        getname in class InputRecordField
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Overrides:
        +
        setdoc in class InputRecordField
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Overrides:
        +
        getdoc in class InputRecordField
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class InputRecordField
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class InputRecordField
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Overrides:
        +
        gettype in class InputRecordField
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
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+ + + +
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+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CommandInputRecordSchema.html b/javadoc/org/commonwl/lang/CommandInputRecordSchema.html new file mode 100644 index 00000000..d677301d --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandInputRecordSchema.html @@ -0,0 +1,271 @@ + + + + + +CommandInputRecordSchema + + + + + + + + +
+ + +
Skip navigation links
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    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandInputRecordSchema

+
+
+ +
+ +
+
+
    +
  • + + + + + +
      +
    • + + +

      Method Summary

      + +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandInputRecordSchema

        +
        public CommandInputRecordSchema()
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ +
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CommandLineBinding.html b/javadoc/org/commonwl/lang/CommandLineBinding.html new file mode 100644 index 00000000..dd0ac4bb --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandLineBinding.html @@ -0,0 +1,700 @@ + + + + + +CommandLineBinding + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandLineBinding

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.CommandLineBinding
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    InputBinding
    +
    +
    +
    +
    public class CommandLineBinding
+extends java.lang.Object
+implements InputBinding
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.StringitemSeparator +
      Join the array elements into a single string with the elements separated by by `itemSeparator`.
      +
      (package private) java.lang.BooleanloadContents +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Integerposition +
      The sorting key.
      +
      (package private) java.lang.Stringprefix +
      Command line prefix to add before the value.
      +
      (package private) java.lang.Booleanseparate +
      If true (default), then the prefix and value must be added as separate command line arguments; if false, prefix and value must be concatenated into a single command line argument.
      +
      (package private) java.lang.BooleanshellQuote +
      If `ShellCommandRequirement` is in the requirements for the current command, this controls whether the value is quoted on the command line (default is true).
      +
      (package private) java.lang.ObjectvalueFrom +
      If `valueFrom` is a constant string value, use this as the value and apply the binding rules above.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      CommandLineBinding() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.StringgetitemSeparator() +
      This method returns the value of itemSeparator.
      +
      java.lang.BooleangetloadContents() +
      This method returns the value of loadContents.
      +
      java.lang.Integergetposition() +
      This method returns the value of position.
      +
      java.lang.Stringgetprefix() +
      This method returns the value of prefix.
      +
      java.lang.Booleangetseparate() +
      This method returns the value of separate.
      +
      java.lang.BooleangetshellQuote() +
      This method returns the value of shellQuote.
      +
      java.lang.ObjectgetvalueFrom() +
      This method returns the value of valueFrom.
      +
      voidsetitemSeparator(java.lang.String value) +
      This method sets the value of itemSeparator.
      +
      voidsetloadContents(java.lang.Boolean value) +
      This method sets the value of loadContents.
      +
      voidsetposition(java.lang.Integer value) +
      This method sets the value of position.
      +
      voidsetprefix(java.lang.String value) +
      This method sets the value of prefix.
      +
      voidsetseparate(java.lang.Boolean value) +
      This method sets the value of separate.
      +
      voidsetshellQuote(java.lang.Boolean value) +
      This method sets the value of shellQuote.
      +
      voidsetvalueFrom(Expression value) +
      This method sets the value of valueFrom.
      +
      voidsetvalueFrom(java.lang.String value) +
      This method sets the value of valueFrom.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        separate

        +
        java.lang.Boolean separate
        +
        If true (default), then the prefix and value must be added as separate command line arguments; if false, prefix and value must be concatenated into a single command line argument.
        +
        • +
      + + + +
        +
      • +

        itemSeparator

        +
        java.lang.String itemSeparator
        +
        Join the array elements into a single string with the elements separated by by `itemSeparator`.
        +
        • +
      + + + +
        +
      • +

        prefix

        +
        java.lang.String prefix
        +
        Command line prefix to add before the value.
        +
        • +
      + + + +
        +
      • +

        shellQuote

        +
        java.lang.Boolean shellQuote
        +
        If `ShellCommandRequirement` is in the requirements for the current command, this controls whether the value is quoted on the command line (default is true). Use `shellQuote: false` to inject metacharacters for operations such as pipes.
        +
        • +
      + + + +
        +
      • +

        position

        +
        java.lang.Integer position
        +
        The sorting key. Default position is 0.
        +
        • +
      + + + +
        +
      • +

        valueFrom

        +
        java.lang.Object valueFrom
        +
        If `valueFrom` is a constant string value, use this as the value and apply the binding rules above. If `valueFrom` is an expression, evaluate the expression to yield the actual value to use to build the command line and apply the binding rules above. If the inputBinding is associated with an input parameter, the value of `self` in the expression will be the value of the input parameter. When a binding is part of the `CommandLineTool.arguments` field, the `valueFrom` field is required.
        +
        • +
      + + + +
        +
      • +

        loadContents

        +
        java.lang.Boolean loadContents
        +
        Only valid when `type: File` or is an array of `items: File`. Read up to the first 64 KiB of text from the file and place it in the contents field of the file object for use by expressions.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandLineBinding

        +
        public CommandLineBinding()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setseparate

        +
        public void setseparate(java.lang.Boolean value)
        +
        This method sets the value of separate.
        +
        +
        Parameters:
        +
        value - will update separate, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getseparate

        +
        public java.lang.Boolean getseparate()
        +
        This method returns the value of separate.
        +
        +
        Returns:
        +
        This method will return the value of separate, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setitemSeparator

        +
        public void setitemSeparator(java.lang.String value)
        +
        This method sets the value of itemSeparator.
        +
        +
        Parameters:
        +
        value - will update itemSeparator, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getitemSeparator

        +
        public java.lang.String getitemSeparator()
        +
        This method returns the value of itemSeparator.
        +
        +
        Returns:
        +
        This method will return the value of itemSeparator, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setprefix

        +
        public void setprefix(java.lang.String value)
        +
        This method sets the value of prefix.
        +
        +
        Parameters:
        +
        value - will update prefix, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getprefix

        +
        public java.lang.String getprefix()
        +
        This method returns the value of prefix.
        +
        +
        Returns:
        +
        This method will return the value of prefix, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setshellQuote

        +
        public void setshellQuote(java.lang.Boolean value)
        +
        This method sets the value of shellQuote.
        +
        +
        Parameters:
        +
        value - will update shellQuote, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getshellQuote

        +
        public java.lang.Boolean getshellQuote()
        +
        This method returns the value of shellQuote.
        +
        +
        Returns:
        +
        This method will return the value of shellQuote, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setposition

        +
        public void setposition(java.lang.Integer value)
        +
        This method sets the value of position.
        +
        +
        Parameters:
        +
        value - will update position, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        getposition

        +
        public java.lang.Integer getposition()
        +
        This method returns the value of position.
        +
        +
        Returns:
        +
        This method will return the value of position, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        setvalueFrom

        +
        public void setvalueFrom(java.lang.String value)
        +
        This method sets the value of valueFrom.
        +
        +
        Parameters:
        +
        value - will update valueFrom, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setvalueFrom

        +
        public void setvalueFrom(Expression value)
        +
        This method sets the value of valueFrom.
        +
        +
        Parameters:
        +
        value - will update valueFrom, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getvalueFrom

        +
        public java.lang.Object getvalueFrom()
        +
        This method returns the value of valueFrom.
        +
        +
        Returns:
        +
        This method will return the value of valueFrom, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setloadContents

        +
        public void setloadContents(java.lang.Boolean value)
        +
        This method sets the value of loadContents.
        +
        +
        Specified by:
        +
        setloadContents in interface InputBinding
        +
        Parameters:
        +
        value - will update loadContents, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getloadContents

        +
        public java.lang.Boolean getloadContents()
        +
        This method returns the value of loadContents.
        +
        +
        Specified by:
        +
        getloadContents in interface InputBinding
        +
        Returns:
        +
        This method will return the value of loadContents, which is a Boolean type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CommandLineTool.html b/javadoc/org/commonwl/lang/CommandLineTool.html new file mode 100644 index 00000000..04ad656e --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandLineTool.html @@ -0,0 +1,1672 @@ + + + + + +CommandLineTool + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandLineTool

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.CommandLineTool
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Process
    +
    +
    +
    +
    public class CommandLineTool
+extends java.lang.Object
+implements Process
    +
    This defines the schema of the CWL Command Line Tool Description document.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectarguments +
      Command line bindings which are not directly associated with input parameters.
      +
      (package private) java.lang.ObjectbaseCommand +
      Specifies the program to execute.
      +
      (package private) java.lang.Stringclass_value 
      (package private) CWLVersioncwlVersion +
      CWL document version.
      +
      (package private) java.lang.Stringdoc +
      A long, human-readable description of this process object.
      +
      (package private) Anyhints +
      Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this process object.
      +
      (package private) CommandInputParameter[]inputs +
      Defines the input parameters of the process.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this process object.
      +
      (package private) CommandOutputParameter[]outputs +
      Defines the parameters representing the output of the process.
      +
      (package private) java.lang.IntegerpermanentFailCodes +
      Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail.
      +
      (package private) java.lang.Objectrequirements +
      Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process.
      +
      (package private) java.lang.Objectstderr +
      Capture the command's standard error stream to a file written to the designated output directory.
      +
      (package private) java.lang.Objectstdin +
      A path to a file whose contents must be piped into the command's standard input stream.
      +
      (package private) java.lang.Objectstdout +
      Capture the command's standard output stream to a file written to the designated output directory.
      +
      (package private) java.lang.IntegersuccessCodes +
      Exit codes that indicate the process completed successfully.
      +
      (package private) java.lang.IntegertemporaryFailCodes +
      Exit codes that indicate the process failed due to a possibly temporary condition, where executing the process with the same runtime environment and inputs may produce different results.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      CommandLineTool() 
      +
      • +
    + + +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        stdin

        +
        java.lang.Object stdin
        +
        A path to a file whose contents must be piped into the command's standard input stream.
        +
        • +
      + + + +
        +
      • +

        stdout

        +
        java.lang.Object stdout
        +
        Capture the command's standard output stream to a file written to the designated output directory. If `stdout` is a string, it specifies the file name to use. If `stdout` is an expression, the expression is evaluated and must return a string with the file name to use to capture stdout. If the return value is not a string, or the resulting path contains illegal characters (such as the path separator `/`) it is an error.
        +
        • +
      + + + +
        +
      • +

        successCodes

        +
        java.lang.Integer successCodes
        +
        Exit codes that indicate the process completed successfully.
        +
        • +
      + + + +
        +
      • +

        temporaryFailCodes

        +
        java.lang.Integer temporaryFailCodes
        +
        Exit codes that indicate the process failed due to a possibly temporary condition, where executing the process with the same runtime environment and inputs may produce different results.
        +
        • +
      + + + +
        +
      • +

        baseCommand

        +
        java.lang.Object baseCommand
        +
        Specifies the program to execute. If an array, the first element of the array is the command to execute, and subsequent elements are mandatory command line arguments. The elements in `baseCommand` must appear before any command line bindings from `inputBinding` or `arguments`. If `baseCommand` is not provided or is an empty array, the first element of the command line produced after processing `inputBinding` or `arguments` must be used as the program to execute. If the program includes a path separator character it must be an absolute path, otherwise it is an error. If the program does not include a path separator, search the `$PATH` variable in the runtime environment of the workflow runner find the absolute path of the executable.
        +
        • +
      + + + +
        +
      • +

        arguments

        +
        java.lang.Object arguments
        +
        Command line bindings which are not directly associated with input parameters.
        +
        • +
      + + + +
        +
      • +

        stderr

        +
        java.lang.Object stderr
        +
        Capture the command's standard error stream to a file written to the designated output directory. If `stderr` is a string, it specifies the file name to use. If `stderr` is an expression, the expression is evaluated and must return a string with the file name to use to capture stderr. If the return value is not a string, or the resulting path contains illegal characters (such as the path separator `/`) it is an error.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        • +
      + + + +
        +
      • +

        permanentFailCodes

        +
        java.lang.Integer permanentFailCodes
        +
        Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail.
        +
        • +
      + + + +
        +
      • +

        outputs

        +
        CommandOutputParameter[] outputs
        +
        Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.
        +
        • +
      + + + +
        +
      • +

        requirements

        +
        java.lang.Object requirements
        +
        Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
        +
        • +
      + + + +
        +
      • +

        cwlVersion

        +
        CWLVersion cwlVersion
        +
        CWL document version. Always required at the document root. Not required for a Process embedded inside another Process.
        +
        • +
      + + + +
        +
      • +

        inputs

        +
        CommandInputParameter[] inputs
        +
        Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object.
        +
        • +
      + + + +
        +
      • +

        hints

        +
        Any hints
        +
        Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A long, human-readable description of this process object.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this process object.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandLineTool

        +
        public CommandLineTool()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setstdin

        +
        public void setstdin(java.lang.String value)
        +
        This method sets the value of stdin.
        +
        +
        Parameters:
        +
        value - will update stdin, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstdin

        +
        public void setstdin(Expression value)
        +
        This method sets the value of stdin.
        +
        +
        Parameters:
        +
        value - will update stdin, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getstdin

        +
        public java.lang.Object getstdin()
        +
        This method returns the value of stdin.
        +
        +
        Returns:
        +
        This method will return the value of stdin, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setstdout

        +
        public void setstdout(java.lang.String value)
        +
        This method sets the value of stdout.
        +
        +
        Parameters:
        +
        value - will update stdout, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstdout

        +
        public void setstdout(Expression value)
        +
        This method sets the value of stdout.
        +
        +
        Parameters:
        +
        value - will update stdout, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getstdout

        +
        public java.lang.Object getstdout()
        +
        This method returns the value of stdout.
        +
        +
        Returns:
        +
        This method will return the value of stdout, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setsuccessCodes

        +
        public void setsuccessCodes(java.lang.Integer value)
        +
        This method sets the value of successCodes.
        +
        +
        Parameters:
        +
        value - will update successCodes, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        getsuccessCodes

        +
        public java.lang.Integer getsuccessCodes()
        +
        This method returns the value of successCodes.
        +
        +
        Returns:
        +
        This method will return the value of successCodes, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        settemporaryFailCodes

        +
        public void settemporaryFailCodes(java.lang.Integer value)
        +
        This method sets the value of temporaryFailCodes.
        +
        +
        Parameters:
        +
        value - will update temporaryFailCodes, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        gettemporaryFailCodes

        +
        public java.lang.Integer gettemporaryFailCodes()
        +
        This method returns the value of temporaryFailCodes.
        +
        +
        Returns:
        +
        This method will return the value of temporaryFailCodes, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        setbaseCommand

        +
        public void setbaseCommand(java.lang.String value)
        +
        This method sets the value of baseCommand.
        +
        +
        Parameters:
        +
        value - will update baseCommand, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setbaseCommand

        +
        public void setbaseCommand(java.lang.String[] value)
        +
        This method sets the value of baseCommand.
        +
        +
        Parameters:
        +
        value - will update baseCommand, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getbaseCommand

        +
        public java.lang.Object getbaseCommand()
        +
        This method returns the value of baseCommand.
        +
        +
        Returns:
        +
        This method will return the value of baseCommand, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setarguments

        +
        public void setarguments(Expression[] value)
        +
        This method sets the value of arguments.
        +
        +
        Parameters:
        +
        value - will update arguments, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setarguments

        +
        public void setarguments(CommandLineBinding[] value)
        +
        This method sets the value of arguments.
        +
        +
        Parameters:
        +
        value - will update arguments, which is a CommandLineBinding array.
        +
        +
        • +
      + + + +
        +
      • +

        setarguments

        +
        public void setarguments(java.lang.String[] value)
        +
        This method sets the value of arguments.
        +
        +
        Parameters:
        +
        value - will update arguments, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getarguments

        +
        public java.lang.Object getarguments()
        +
        This method returns the value of arguments.
        +
        +
        Returns:
        +
        This method will return the value of arguments, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setstderr

        +
        public void setstderr(java.lang.String value)
        +
        This method sets the value of stderr.
        +
        +
        Parameters:
        +
        value - will update stderr, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstderr

        +
        public void setstderr(Expression value)
        +
        This method sets the value of stderr.
        +
        +
        Parameters:
        +
        value - will update stderr, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getstderr

        +
        public java.lang.Object getstderr()
        +
        This method returns the value of stderr.
        +
        +
        Returns:
        +
        This method will return the value of stderr, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setpermanentFailCodes

        +
        public void setpermanentFailCodes(java.lang.Integer value)
        +
        This method sets the value of permanentFailCodes.
        +
        +
        Parameters:
        +
        value - will update permanentFailCodes, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        getpermanentFailCodes

        +
        public java.lang.Integer getpermanentFailCodes()
        +
        This method returns the value of permanentFailCodes.
        +
        +
        Returns:
        +
        This method will return the value of permanentFailCodes, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputs

        +
        public void setoutputs(CommandOutputParameter[] value)
        +
        This method sets the value of outputs.
        +
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputs

        +
        public void setoutputs(OutputParameter[] value)
        +
        This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
        +
        +
        Specified by:
        +
        setoutputs in interface Process
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputs

        +
        public CommandOutputParameter[] getoutputs()
        +
        This method returns the value of outputs.
        +
        +
        Specified by:
        +
        getoutputs in interface Process
        +
        Returns:
        +
        This method will return the value of outputs, which is a CommandOutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(StepInputExpressionRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a StepInputExpressionRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(MultipleInputFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a MultipleInputFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SoftwareRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SoftwareRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SchemaDefRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SchemaDefRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InitialWorkDirRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a InitialWorkDirRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(EnvVarRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a EnvVarRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(DockerRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a DockerRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ResourceRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ResourceRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InlineJavascriptRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a InlineJavascriptRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ShellCommandRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ShellCommandRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ScatterFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ScatterFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SubworkflowFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SubworkflowFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        getrequirements

        +
        public java.lang.Object getrequirements()
        +
        This method returns the value of requirements.
        +
        +
        Specified by:
        +
        getrequirements in interface Process
        +
        Returns:
        +
        This method will return the value of requirements, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setcwlVersion

        +
        public void setcwlVersion(CWLVersion value)
        +
        This method sets the value of cwlVersion.
        +
        +
        Specified by:
        +
        setcwlVersion in interface Process
        +
        Parameters:
        +
        value - will update cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        getcwlVersion

        +
        public CWLVersion getcwlVersion()
        +
        This method returns the value of cwlVersion.
        +
        +
        Specified by:
        +
        getcwlVersion in interface Process
        +
        Returns:
        +
        This method will return the value of cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputs

        +
        public void setinputs(CommandInputParameter[] value)
        +
        This method sets the value of inputs.
        +
        +
        Parameters:
        +
        value - will update inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setinputs

        +
        public void setinputs(InputParameter[] value)
        +
        This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
        +
        +
        Specified by:
        +
        setinputs in interface Process
        +
        Parameters:
        +
        value - will update inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getinputs

        +
        public CommandInputParameter[] getinputs()
        +
        This method returns the value of inputs.
        +
        +
        Specified by:
        +
        getinputs in interface Process
        +
        Returns:
        +
        This method will return the value of inputs, which is a CommandInputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        sethints

        +
        public void sethints(Any value)
        +
        This method sets the value of hints.
        +
        +
        Specified by:
        +
        sethints in interface Process
        +
        Parameters:
        +
        value - will update hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        gethints

        +
        public Any gethints()
        +
        This method returns the value of hints.
        +
        +
        Specified by:
        +
        gethints in interface Process
        +
        Returns:
        +
        This method will return the value of hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Process
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Process
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Specified by:
        +
        setid in interface Process
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Specified by:
        +
        getid in interface Process
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Process
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Process
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CommandOutputArraySchema.html b/javadoc/org/commonwl/lang/CommandOutputArraySchema.html new file mode 100644 index 00000000..7bb2aba9 --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandOutputArraySchema.html @@ -0,0 +1,364 @@ + + + + + +CommandOutputArraySchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandOutputArraySchema

+
+
+ +
+ +
+
+ +
+
+
    +
  • + + + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandOutputArraySchema

        +
        public CommandOutputArraySchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Overrides:
        +
        setoutputBinding in class OutputArraySchema
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Overrides:
        +
        getoutputBinding in class OutputArraySchema
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CommandOutputBinding.html b/javadoc/org/commonwl/lang/CommandOutputBinding.html new file mode 100644 index 00000000..1b03aef0 --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandOutputBinding.html @@ -0,0 +1,513 @@ + + + + + +CommandOutputBinding + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandOutputBinding

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.CommandOutputBinding
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    OutputBinding
    +
    +
    +
    +
    public class CommandOutputBinding
+extends java.lang.Object
+implements OutputBinding
    +
    Describes how to generate an output parameter based on the files produced by a CommandLineTool.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectglob +
      Find files relative to the output directory, using POSIX glob(3) pathname matching.
      +
      (package private) java.lang.BooleanloadContents +
      For each file matched in `glob`, read up to the first 64 KiB of text from the file and place it in the `contents` field of the file object for manipulation by `outputEval`.
      +
      (package private) java.lang.ObjectoutputEval +
      Evaluate an expression to generate the output value.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetglob() +
      This method returns the value of glob.
      +
      java.lang.BooleangetloadContents() +
      This method returns the value of loadContents.
      +
      java.lang.ObjectgetoutputEval() +
      This method returns the value of outputEval.
      +
      voidsetglob(Expression value) +
      This method sets the value of glob.
      +
      voidsetglob(java.lang.String value) +
      This method sets the value of glob.
      +
      voidsetglob(java.lang.String[] value) +
      This method sets the value of glob.
      +
      voidsetloadContents(java.lang.Boolean value) +
      This method sets the value of loadContents.
      +
      voidsetoutputEval(Expression value) +
      This method sets the value of outputEval.
      +
      voidsetoutputEval(java.lang.String value) +
      This method sets the value of outputEval.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        loadContents

        +
        java.lang.Boolean loadContents
        +
        For each file matched in `glob`, read up to the first 64 KiB of text from the file and place it in the `contents` field of the file object for manipulation by `outputEval`.
        +
        • +
      + + + +
        +
      • +

        outputEval

        +
        java.lang.Object outputEval
        +
        Evaluate an expression to generate the output value. If `glob` was specified, the value of `self` must be an array containing file objects that were matched. If no files were matched, `self` must be a zero length array; if a single file was matched, the value of `self` is an array of a single element. Additionally, if `loadContents` is `true`, the File objects must include up to the first 64 KiB of file contents in the `contents` field.
        +
        • +
      + + + +
        +
      • +

        glob

        +
        java.lang.Object glob
        +
        Find files relative to the output directory, using POSIX glob(3) pathname matching. If an array is provided, find files that match any pattern in the array. If an expression is provided, the expression must return a string or an array of strings, which will then be evaluated as one or more glob patterns. Must only match and return files which actually exist.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandOutputBinding

        +
        public CommandOutputBinding()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setloadContents

        +
        public void setloadContents(java.lang.Boolean value)
        +
        This method sets the value of loadContents.
        +
        +
        Parameters:
        +
        value - will update loadContents, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getloadContents

        +
        public java.lang.Boolean getloadContents()
        +
        This method returns the value of loadContents.
        +
        +
        Returns:
        +
        This method will return the value of loadContents, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputEval

        +
        public void setoutputEval(java.lang.String value)
        +
        This method sets the value of outputEval.
        +
        +
        Parameters:
        +
        value - will update outputEval, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputEval

        +
        public void setoutputEval(Expression value)
        +
        This method sets the value of outputEval.
        +
        +
        Parameters:
        +
        value - will update outputEval, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputEval

        +
        public java.lang.Object getoutputEval()
        +
        This method returns the value of outputEval.
        +
        +
        Returns:
        +
        This method will return the value of outputEval, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setglob

        +
        public void setglob(java.lang.String value)
        +
        This method sets the value of glob.
        +
        +
        Parameters:
        +
        value - will update glob, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setglob

        +
        public void setglob(java.lang.String[] value)
        +
        This method sets the value of glob.
        +
        +
        Parameters:
        +
        value - will update glob, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        setglob

        +
        public void setglob(Expression value)
        +
        This method sets the value of glob.
        +
        +
        Parameters:
        +
        value - will update glob, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getglob

        +
        public java.lang.Object getglob()
        +
        This method returns the value of glob.
        +
        +
        Returns:
        +
        This method will return the value of glob, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CommandOutputEnumSchema.html b/javadoc/org/commonwl/lang/CommandOutputEnumSchema.html new file mode 100644 index 00000000..4e619059 --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandOutputEnumSchema.html @@ -0,0 +1,364 @@ + + + + + +CommandOutputEnumSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
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+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandOutputEnumSchema

+
+
+ +
+ +
+
+ +
+
+
    +
  • + + + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandOutputEnumSchema

        +
        public CommandOutputEnumSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Overrides:
        +
        setoutputBinding in class OutputEnumSchema
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Overrides:
        +
        getoutputBinding in class OutputEnumSchema
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CommandOutputParameter.html b/javadoc/org/commonwl/lang/CommandOutputParameter.html new file mode 100644 index 00000000..5cc87fd1 --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandOutputParameter.html @@ -0,0 +1,1153 @@ + + + + + +CommandOutputParameter + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandOutputParameter

+
+
+ +
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Parameter, SchemaBase
    +
    +
    +
    +
    public class CommandOutputParameter
+extends OutputParameter
    +
    An output parameter for a CommandLineTool.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this parameter object.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) CommandOutputBindingoutputBinding +
      Describes how to handle the outputs of a process.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Objecttype +
      Specify valid types of data that may be assigned to this parameter.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      CommandOutputBindinggetoutputBinding() +
      This method returns the value of outputBinding.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetoutputBinding(CommandOutputBinding value) +
      This method sets the value of outputBinding.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      voidsettype(CommandOutputArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(CommandOutputArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(CommandOutputEnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(CommandOutputEnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(CommandOutputRecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(CommandOutputRecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(CWLType value) +
      This method sets the value of type.
      +
      voidsettype(CWLType[] value) +
      This method sets the value of type.
      +
      voidsettype(stderr value) +
      This method sets the value of type.
      +
      voidsettype(stdout value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        Specify valid types of data that may be assigned to this parameter.
        +
        • +
      + + + +
        +
      • +

        outputBinding

        +
        CommandOutputBinding outputBinding
        +
        Describes how to handle the outputs of a process.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this parameter object.
        +
        • +
      + + + +
        +
      • +

        streamable

        +
        java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandOutputParameter

        +
        public CommandOutputParameter()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        settype

        +
        public void settype(CommandOutputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CommandOutputArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(stderr value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a stderr type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandOutputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CommandOutputArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandOutputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CommandOutputRecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(stdout value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a stdout type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandOutputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CommandOutputEnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandOutputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CommandOutputRecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandOutputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CommandOutputEnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Overrides:
        +
        setoutputBinding in class OutputParameter
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Overrides:
        +
        getoutputBinding in class OutputParameter
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Overrides:
        +
        setid in class OutputParameter
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Overrides:
        +
        getid in class OutputParameter
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstreamable

        +
        public void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Specified by:
        +
        setstreamable in interface Parameter
        +
        Overrides:
        +
        setstreamable in class OutputParameter
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        public java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Specified by:
        +
        getstreamable in interface Parameter
        +
        Overrides:
        +
        getstreamable in class OutputParameter
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Specified by:
        +
        getformat in interface Parameter
        +
        Overrides:
        +
        getformat in class OutputParameter
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class OutputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class OutputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Parameter
        +
        Overrides:
        +
        getdoc in class OutputParameter
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class OutputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class OutputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Specified by:
        +
        getsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        getsecondaryFiles in class OutputParameter
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Parameter
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Overrides:
        +
        setlabel in class OutputParameter
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Parameter
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Overrides:
        +
        getlabel in class OutputParameter
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
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+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CommandOutputRecordField.html b/javadoc/org/commonwl/lang/CommandOutputRecordField.html new file mode 100644 index 00000000..c74603cf --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandOutputRecordField.html @@ -0,0 +1,731 @@ + + + + + +CommandOutputRecordField + + + + + + + + +
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+ + +
+
org.commonwl.lang
+

Class CommandOutputRecordField

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringdoc +
      A documentation string for this field
      +
      (package private) java.lang.Stringname +
      The name of the field
      +
      (package private) CommandOutputBindingoutputBinding 
      (package private) java.lang.Objecttype +
      The field type
      +
      +
      • +
    + + + + +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + + + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The name of the field
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A documentation string for this field
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        The field type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandOutputRecordField

        +
        public CommandOutputRecordField()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Overrides:
        +
        setoutputBinding in class OutputRecordField
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Overrides:
        +
        getoutputBinding in class OutputRecordField
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Overrides:
        +
        setname in class OutputRecordField
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Overrides:
        +
        getname in class OutputRecordField
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Overrides:
        +
        setdoc in class OutputRecordField
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Overrides:
        +
        getdoc in class OutputRecordField
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class OutputRecordField
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class OutputRecordField
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Overrides:
        +
        gettype in class OutputRecordField
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/CommandOutputRecordSchema.html b/javadoc/org/commonwl/lang/CommandOutputRecordSchema.html new file mode 100644 index 00000000..53878acc --- /dev/null +++ b/javadoc/org/commonwl/lang/CommandOutputRecordSchema.html @@ -0,0 +1,271 @@ + + + + + +CommandOutputRecordSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ +
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandOutputRecordSchema

+
+
+ +
+ +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandOutputRecordSchema

        +
        public CommandOutputRecordSchema()
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ +
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/Directory.html b/javadoc/org/commonwl/lang/Directory.html new file mode 100644 index 00000000..e49140fa --- /dev/null +++ b/javadoc/org/commonwl/lang/Directory.html @@ -0,0 +1,580 @@ + + + + + +Directory + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class Directory

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.Directory
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class Directory
+extends java.lang.Object
    +
    Represents a directory to present to a command line tool.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringbasename +
      The base name of the directory, that is, the name of the file without any leading directory path.
      +
      (package private) Directoryclass_value +
      Must be `Directory` to indicate this object describes a Directory.
      +
      (package private) java.lang.Objectlisting +
      List of files or subdirectories contained in this directory.
      +
      (package private) java.lang.Stringlocation +
      An IRI that identifies the directory resource.
      +
      (package private) java.lang.Stringpath +
      The local path where the Directory is made available prior to executing a CommandLineTool.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      Directory() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetbasename() +
      This method returns the value of basename.
      +
      Directorygetclass() +
      This method returns the value of class_value.
      +
      java.lang.Objectgetlisting() +
      This method returns the value of listing.
      +
      java.lang.Stringgetlocation() +
      This method returns the value of location.
      +
      java.lang.Stringgetpath() +
      This method returns the value of path.
      +
      voidsetbasename(java.lang.String value) +
      This method sets the value of basename.
      +
      voidsetclass(Directory value) +
      This method sets the value of class_value.
      +
      voidsetlisting(Directory[] value) +
      This method sets the value of listing.
      +
      voidsetlisting(File[] value) +
      This method sets the value of listing.
      +
      voidsetlocation(java.lang.String value) +
      This method sets the value of location.
      +
      voidsetpath(java.lang.String value) +
      This method sets the value of path.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        path

        +
        java.lang.String path
        +
        The local path where the Directory is made available prior to executing a CommandLineTool. This must be set by the implementation. This field must not be used in any other context. The command line tool being executed must be able to to access the directory at `path` using the POSIX `opendir(2)` syscall. If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) (`|`,`&`, `;`, `(`, `)`, `(`,`)`, `$`,`` ` ``, `\`, ``, `'`, `(space)`, `(tab)`, and `(newline)`) or characters [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) then implementations may terminate the process with a `permanentFailure`.
        +
        • +
      + + + +
        +
      • +

        basename

        +
        java.lang.String basename
        +
        The base name of the directory, that is, the name of the file without any leading directory path. The base name must not contain a slash `/`. If not provided, the implementation must set this field based on the `location` field by taking the final path component after parsing `location` as an IRI. If `basename` is provided, it is not required to match the value from `location`. When this file is made available to a CommandLineTool, it must be named with `basename`, i.e. the final component of the `path` field must match `basename`.
        +
        • +
      + + + +
        +
      • +

        location

        +
        java.lang.String location
        +
        An IRI that identifies the directory resource. This may be a relative reference, in which case it must be resolved using the base IRI of the document. The location may refer to a local or remote resource. If the `listing` field is not set, the implementation must use the location IRI to retrieve directory listing. If an implementation is unable to retrieve the directory listing stored at a remote resource (due to unsupported protocol, access denied, or other issue) it must signal an error. If the `location` field is not provided, the `listing` field must be provided. The implementation must assign a unique identifier for the `location` field. If the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, then follow the rules above.
        +
        • +
      + + + +
        +
      • +

        listing

        +
        java.lang.Object listing
        +
        List of files or subdirectories contained in this directory. The name of each file or subdirectory is determined by the `basename` field of each `File` or `Directory` object. It is an error if a `File` shares a `basename` with any other entry in `listing`. If two or more `Directory` object share the same `basename`, this must be treated as equivalent to a single subdirectory with the listings recursively merged.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        Directory class_value
        +
        Must be `Directory` to indicate this object describes a Directory.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        Directory

        +
        public Directory()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setpath

        +
        public void setpath(java.lang.String value)
        +
        This method sets the value of path.
        +
        +
        Parameters:
        +
        value - will update path, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getpath

        +
        public java.lang.String getpath()
        +
        This method returns the value of path.
        +
        +
        Returns:
        +
        This method will return the value of path, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setbasename

        +
        public void setbasename(java.lang.String value)
        +
        This method sets the value of basename.
        +
        +
        Parameters:
        +
        value - will update basename, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getbasename

        +
        public java.lang.String getbasename()
        +
        This method returns the value of basename.
        +
        +
        Returns:
        +
        This method will return the value of basename, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlocation

        +
        public void setlocation(java.lang.String value)
        +
        This method sets the value of location.
        +
        +
        Parameters:
        +
        value - will update location, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlocation

        +
        public java.lang.String getlocation()
        +
        This method returns the value of location.
        +
        +
        Returns:
        +
        This method will return the value of location, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(File[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a File array.
        +
        +
        • +
      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(Directory[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a Directory array.
        +
        +
        • +
      + + + +
        +
      • +

        getlisting

        +
        public java.lang.Object getlisting()
        +
        This method returns the value of listing.
        +
        +
        Returns:
        +
        This method will return the value of listing, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(Directory value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a Directory type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public Directory getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a Directory type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/Dirent.html b/javadoc/org/commonwl/lang/Dirent.html new file mode 100644 index 00000000..700b6834 --- /dev/null +++ b/javadoc/org/commonwl/lang/Dirent.html @@ -0,0 +1,488 @@ + + + + + +Dirent + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class Dirent

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.Dirent
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class Dirent
+extends java.lang.Object
    +
    Define a file or subdirectory that must be placed in the designated output directory prior to executing the command line tool. May be the result of executing an expression, such as building a configuration file from a template.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectentry +
      If the value is a string literal or an expression which evaluates to a string, a new file must be created with the string as the file contents.
      +
      (package private) java.lang.Objectentryname +
      The name of the file or subdirectory to create in the output directory.
      +
      (package private) java.lang.Booleanwritable +
      If true, the file or directory must be writable by the tool.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      Dirent() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetentry() +
      This method returns the value of entry.
      +
      java.lang.Objectgetentryname() +
      This method returns the value of entryname.
      +
      java.lang.Booleangetwritable() +
      This method returns the value of writable.
      +
      voidsetentry(Expression value) +
      This method sets the value of entry.
      +
      voidsetentry(java.lang.String value) +
      This method sets the value of entry.
      +
      voidsetentryname(Expression value) +
      This method sets the value of entryname.
      +
      voidsetentryname(java.lang.String value) +
      This method sets the value of entryname.
      +
      voidsetwritable(java.lang.Boolean value) +
      This method sets the value of writable.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        entry

        +
        java.lang.Object entry
        +
        If the value is a string literal or an expression which evaluates to a string, a new file must be created with the string as the file contents. If the value is an expression that evaluates to a `File` object, this indicates the referenced file should be added to the designated output directory prior to executing the tool. If the value is an expression that evaluates to a `Dirent` object, this indicates that the File or Directory in `entry` should be added to the designated output directory with the name in `entryname`. If `writable` is false, the file may be made available using a bind mount or file system link to avoid unnecessary copying of the input file.
        +
        • +
      + + + +
        +
      • +

        entryname

        +
        java.lang.Object entryname
        +
        The name of the file or subdirectory to create in the output directory. If `entry` is a File or Directory, this overrides `basename`. Optional.
        +
        • +
      + + + +
        +
      • +

        writable

        +
        java.lang.Boolean writable
        +
        If true, the file or directory must be writable by the tool. Changes to the file or directory must be isolated and not visible by any other CommandLineTool process. This may be implemented by making a copy of the original file or directory. Default false (files and directories read-only by default).
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        Dirent

        +
        public Dirent()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setentry

        +
        public void setentry(java.lang.String value)
        +
        This method sets the value of entry.
        +
        +
        Parameters:
        +
        value - will update entry, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setentry

        +
        public void setentry(Expression value)
        +
        This method sets the value of entry.
        +
        +
        Parameters:
        +
        value - will update entry, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getentry

        +
        public java.lang.Object getentry()
        +
        This method returns the value of entry.
        +
        +
        Returns:
        +
        This method will return the value of entry, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setentryname

        +
        public void setentryname(java.lang.String value)
        +
        This method sets the value of entryname.
        +
        +
        Parameters:
        +
        value - will update entryname, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setentryname

        +
        public void setentryname(Expression value)
        +
        This method sets the value of entryname.
        +
        +
        Parameters:
        +
        value - will update entryname, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getentryname

        +
        public java.lang.Object getentryname()
        +
        This method returns the value of entryname.
        +
        +
        Returns:
        +
        This method will return the value of entryname, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setwritable

        +
        public void setwritable(java.lang.Boolean value)
        +
        This method sets the value of writable.
        +
        +
        Parameters:
        +
        value - will update writable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getwritable

        +
        public java.lang.Boolean getwritable()
        +
        This method returns the value of writable.
        +
        +
        Returns:
        +
        This method will return the value of writable, which is a Boolean type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
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+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/DocType.html b/javadoc/org/commonwl/lang/DocType.html new file mode 100644 index 00000000..9c0c941c --- /dev/null +++ b/javadoc/org/commonwl/lang/DocType.html @@ -0,0 +1,501 @@ + + + + + +DocType + + + + + + + + +
+ + +
Skip navigation links
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  • Summary: 
    • +
  • Nested | 
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    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface DocType

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      static java.lang.StringdocAfter +
      Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
      +
      static java.lang.ObjectdocChild +
      Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
      +
      static java.lang.StringdocParent +
      Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.StringgetdocAfter() +
      This method returns the value of docAfter.
      +
      java.lang.ObjectgetdocChild() +
      This method returns the value of docChild.
      +
      java.lang.StringgetdocParent() +
      This method returns the value of docParent.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetdocAfter(java.lang.String value) +
      This method sets the value of docAfter.
      +
      voidsetdocChild(java.lang.String value) +
      This method sets the value of docChild.
      +
      voidsetdocChild(java.lang.String[] value) +
      This method sets the value of docChild.
      +
      voidsetdocParent(java.lang.String value) +
      This method sets the value of docParent.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        docParent

        +
        static final java.lang.String docParent
        +
        Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        static final java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        docAfter

        +
        static final java.lang.String docAfter
        +
        Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
        +
        • +
      + + + +
        +
      • +

        docChild

        +
        static final java.lang.Object docChild
        +
        Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setdocParent

        +
        void setdocParent(java.lang.String value)
        +
        This method sets the value of docParent.
        +
        +
        Parameters:
        +
        value - will update docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocParent

        +
        java.lang.String getdocParent()
        +
        This method returns the value of docParent.
        +
        +
        Returns:
        +
        This method will return the value of docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocAfter

        +
        void setdocAfter(java.lang.String value)
        +
        This method sets the value of docAfter.
        +
        +
        Parameters:
        +
        value - will update docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocAfter

        +
        java.lang.String getdocAfter()
        +
        This method returns the value of docAfter.
        +
        +
        Returns:
        +
        This method will return the value of docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        void setdocChild(java.lang.String value)
        +
        This method sets the value of docChild.
        +
        +
        Parameters:
        +
        value - will update docChild, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        void setdocChild(java.lang.String[] value)
        +
        This method sets the value of docChild.
        +
        +
        Parameters:
        +
        value - will update docChild, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdocChild

        +
        java.lang.Object getdocChild()
        +
        This method returns the value of docChild.
        +
        +
        Returns:
        +
        This method will return the value of docChild, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/DockerRequirement.html b/javadoc/org/commonwl/lang/DockerRequirement.html new file mode 100644 index 00000000..9b7ccc13 --- /dev/null +++ b/javadoc/org/commonwl/lang/DockerRequirement.html @@ -0,0 +1,677 @@ + + + + + +DockerRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
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+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class DockerRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.DockerRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class DockerRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Indicates that a workflow component should be run in a [Docker](http://docker.com) container, and specifies how to fetch or build the image.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'DockerRequirement'
      +
      (package private) java.lang.StringdockerFile +
      Supply the contents of a Dockerfile which will be built using `docker build`.
      +
      (package private) java.lang.StringdockerImageId +
      The image id that will be used for `docker run`.
      +
      (package private) java.lang.StringdockerImport +
      Provide HTTP URL to download and gunzip a Docker images using `docker import.
      +
      (package private) java.lang.StringdockerLoad +
      Specify a HTTP URL from which to download a Docker image using `docker load`.
      +
      (package private) java.lang.StringdockerOutputDirectory +
      Set the designated output directory to a specific location inside the Docker container.
      +
      (package private) java.lang.StringdockerPull +
      Specify a Docker image to retrieve using `docker pull`.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      DockerRequirement() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      java.lang.StringgetdockerFile() +
      This method returns the value of dockerFile.
      +
      java.lang.StringgetdockerImageId() +
      This method returns the value of dockerImageId.
      +
      java.lang.StringgetdockerImport() +
      This method returns the value of dockerImport.
      +
      java.lang.StringgetdockerLoad() +
      This method returns the value of dockerLoad.
      +
      java.lang.StringgetdockerOutputDirectory() +
      This method returns the value of dockerOutputDirectory.
      +
      java.lang.StringgetdockerPull() +
      This method returns the value of dockerPull.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsetdockerFile(java.lang.String value) +
      This method sets the value of dockerFile.
      +
      voidsetdockerImageId(java.lang.String value) +
      This method sets the value of dockerImageId.
      +
      voidsetdockerImport(java.lang.String value) +
      This method sets the value of dockerImport.
      +
      voidsetdockerLoad(java.lang.String value) +
      This method sets the value of dockerLoad.
      +
      voidsetdockerOutputDirectory(java.lang.String value) +
      This method sets the value of dockerOutputDirectory.
      +
      voidsetdockerPull(java.lang.String value) +
      This method sets the value of dockerPull.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        dockerFile

        +
        java.lang.String dockerFile
        +
        Supply the contents of a Dockerfile which will be built using `docker build`.
        +
        • +
      + + + +
        +
      • +

        dockerPull

        +
        java.lang.String dockerPull
        +
        Specify a Docker image to retrieve using `docker pull`.
        +
        • +
      + + + +
        +
      • +

        dockerImport

        +
        java.lang.String dockerImport
        +
        Provide HTTP URL to download and gunzip a Docker images using `docker import.
        +
        • +
      + + + +
        +
      • +

        dockerOutputDirectory

        +
        java.lang.String dockerOutputDirectory
        +
        Set the designated output directory to a specific location inside the Docker container.
        +
        • +
      + + + +
        +
      • +

        dockerLoad

        +
        java.lang.String dockerLoad
        +
        Specify a HTTP URL from which to download a Docker image using `docker load`.
        +
        • +
      + + + +
        +
      • +

        dockerImageId

        +
        java.lang.String dockerImageId
        +
        The image id that will be used for `docker run`. May be a human-readable image name or the image identifier hash. May be skipped if `dockerPull` is specified, in which case the `dockerPull` image id must be used.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'DockerRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        DockerRequirement

        +
        public DockerRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setdockerFile

        +
        public void setdockerFile(java.lang.String value)
        +
        This method sets the value of dockerFile.
        +
        +
        Parameters:
        +
        value - will update dockerFile, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdockerFile

        +
        public java.lang.String getdockerFile()
        +
        This method returns the value of dockerFile.
        +
        +
        Returns:
        +
        This method will return the value of dockerFile, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdockerPull

        +
        public void setdockerPull(java.lang.String value)
        +
        This method sets the value of dockerPull.
        +
        +
        Parameters:
        +
        value - will update dockerPull, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdockerPull

        +
        public java.lang.String getdockerPull()
        +
        This method returns the value of dockerPull.
        +
        +
        Returns:
        +
        This method will return the value of dockerPull, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdockerImport

        +
        public void setdockerImport(java.lang.String value)
        +
        This method sets the value of dockerImport.
        +
        +
        Parameters:
        +
        value - will update dockerImport, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdockerImport

        +
        public java.lang.String getdockerImport()
        +
        This method returns the value of dockerImport.
        +
        +
        Returns:
        +
        This method will return the value of dockerImport, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdockerOutputDirectory

        +
        public void setdockerOutputDirectory(java.lang.String value)
        +
        This method sets the value of dockerOutputDirectory.
        +
        +
        Parameters:
        +
        value - will update dockerOutputDirectory, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdockerOutputDirectory

        +
        public java.lang.String getdockerOutputDirectory()
        +
        This method returns the value of dockerOutputDirectory.
        +
        +
        Returns:
        +
        This method will return the value of dockerOutputDirectory, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdockerLoad

        +
        public void setdockerLoad(java.lang.String value)
        +
        This method sets the value of dockerLoad.
        +
        +
        Parameters:
        +
        value - will update dockerLoad, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdockerLoad

        +
        public java.lang.String getdockerLoad()
        +
        This method returns the value of dockerLoad.
        +
        +
        Returns:
        +
        This method will return the value of dockerLoad, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdockerImageId

        +
        public void setdockerImageId(java.lang.String value)
        +
        This method sets the value of dockerImageId.
        +
        +
        Parameters:
        +
        value - will update dockerImageId, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdockerImageId

        +
        public java.lang.String getdockerImageId()
        +
        This method returns the value of dockerImageId.
        +
        +
        Returns:
        +
        This method will return the value of dockerImageId, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
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+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/Documentation.html b/javadoc/org/commonwl/lang/Documentation.html new file mode 100644 index 00000000..2c0286be --- /dev/null +++ b/javadoc/org/commonwl/lang/Documentation.html @@ -0,0 +1,685 @@ + + + + + +Documentation + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class Documentation

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.Documentation
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    DocType, NamedType
    +
    +
    +
    +
    public class Documentation
+extends java.lang.Object
+implements NamedType, DocType
    +
    A documentation section. This type exists to facilitate self-documenting schemas but has no role in formal validation.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.StringdocAfter +
      Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
      +
      (package private) java.lang.ObjectdocChild +
      Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
      +
      (package private) java.lang.StringdocParent +
      Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
      +
      (package private) java.lang.Stringname +
      The identifier for this type
      +
      (package private) java.lang.Objecttype +
      Must be `documentation`
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      Documentation() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.StringgetdocAfter() +
      This method returns the value of docAfter.
      +
      java.lang.ObjectgetdocChild() +
      This method returns the value of docChild.
      +
      java.lang.StringgetdocParent() +
      This method returns the value of docParent.
      +
      java.lang.Stringgetname() +
      This method returns the value of name.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetdocAfter(java.lang.String value) +
      This method sets the value of docAfter.
      +
      voidsetdocChild(java.lang.String value) +
      This method sets the value of docChild.
      +
      voidsetdocChild(java.lang.String[] value) +
      This method sets the value of docChild.
      +
      voidsetdocParent(java.lang.String value) +
      This method sets the value of docParent.
      +
      voidsetname(java.lang.String value) +
      This method sets the value of name.
      +
      voidsettype(java.lang.Object value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        Must be `documentation`
        +
        • +
      + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The identifier for this type
        +
        • +
      + + + +
        +
      • +

        docParent

        +
        java.lang.String docParent
        +
        Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        docAfter

        +
        java.lang.String docAfter
        +
        Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
        +
        • +
      + + + +
        +
      • +

        docChild

        +
        java.lang.Object docChild
        +
        Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        Documentation

        +
        public Documentation()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.Object value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Specified by:
        +
        setname in interface NamedType
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Specified by:
        +
        getname in interface NamedType
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocParent

        +
        public void setdocParent(java.lang.String value)
        +
        This method sets the value of docParent.
        +
        +
        Specified by:
        +
        setdocParent in interface DocType
        +
        Parameters:
        +
        value - will update docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocParent

        +
        public java.lang.String getdocParent()
        +
        This method returns the value of docParent.
        +
        +
        Specified by:
        +
        getdocParent in interface DocType
        +
        Returns:
        +
        This method will return the value of docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface DocType
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocAfter

        +
        public void setdocAfter(java.lang.String value)
        +
        This method sets the value of docAfter.
        +
        +
        Specified by:
        +
        setdocAfter in interface DocType
        +
        Parameters:
        +
        value - will update docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocAfter

        +
        public java.lang.String getdocAfter()
        +
        This method returns the value of docAfter.
        +
        +
        Specified by:
        +
        getdocAfter in interface DocType
        +
        Returns:
        +
        This method will return the value of docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        public void setdocChild(java.lang.String value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Parameters:
        +
        value - will update docChild, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        public void setdocChild(java.lang.String[] value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Parameters:
        +
        value - will update docChild, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdocChild

        +
        public java.lang.Object getdocChild()
        +
        This method returns the value of docChild.
        +
        +
        Specified by:
        +
        getdocChild in interface DocType
        +
        Returns:
        +
        This method will return the value of docChild, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/EnumSchema.html b/javadoc/org/commonwl/lang/EnumSchema.html new file mode 100644 index 00000000..e44a3899 --- /dev/null +++ b/javadoc/org/commonwl/lang/EnumSchema.html @@ -0,0 +1,240 @@ + + + + + +EnumSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
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    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Class EnumSchema

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.EnumSchema
      • +
    +
    • +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      EnumSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        EnumSchema

        +
        public EnumSchema()
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/EnvVarRequirement.html b/javadoc/org/commonwl/lang/EnvVarRequirement.html new file mode 100644 index 00000000..18790e89 --- /dev/null +++ b/javadoc/org/commonwl/lang/EnvVarRequirement.html @@ -0,0 +1,397 @@ + + + + + +EnvVarRequirement + + + + + + + + +
+ + +
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+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class EnvVarRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.EnvVarRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class EnvVarRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Define a list of environment variables which will be set in the execution environment of the tool. See `EnvironmentDef` for details.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'EnvVarRequirement'
      +
      (package private) EnvironmentDefenvDef +
      The list of environment variables.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      EnvVarRequirement() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      EnvironmentDefgetenvDef() +
      This method returns the value of envDef.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsetenvDef(EnvironmentDef value) +
      This method sets the value of envDef.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        envDef

        +
        EnvironmentDef envDef
        +
        The list of environment variables.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'EnvVarRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        EnvVarRequirement

        +
        public EnvVarRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setenvDef

        +
        public void setenvDef(EnvironmentDef value)
        +
        This method sets the value of envDef.
        +
        +
        Parameters:
        +
        value - will update envDef, which is a EnvironmentDef type.
        +
        +
        • +
      + + + +
        +
      • +

        getenvDef

        +
        public EnvironmentDef getenvDef()
        +
        This method returns the value of envDef.
        +
        +
        Returns:
        +
        This method will return the value of envDef, which is a EnvironmentDef type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/EnvironmentDef.html b/javadoc/org/commonwl/lang/EnvironmentDef.html new file mode 100644 index 00000000..947dcaa1 --- /dev/null +++ b/javadoc/org/commonwl/lang/EnvironmentDef.html @@ -0,0 +1,412 @@ + + + + + +EnvironmentDef + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class EnvironmentDef

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.EnvironmentDef
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class EnvironmentDef
+extends java.lang.Object
    +
    Define an environment variable that will be set in the runtime environment by the workflow platform when executing the command line tool. May be the result of executing an expression, such as getting a parameter from input.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.StringenvName +
      The environment variable name
      +
      (package private) java.lang.ObjectenvValue +
      The environment variable value
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      EnvironmentDef() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.StringgetenvName() +
      This method returns the value of envName.
      +
      java.lang.ObjectgetenvValue() +
      This method returns the value of envValue.
      +
      voidsetenvName(java.lang.String value) +
      This method sets the value of envName.
      +
      voidsetenvValue(Expression value) +
      This method sets the value of envValue.
      +
      voidsetenvValue(java.lang.String value) +
      This method sets the value of envValue.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        envName

        +
        java.lang.String envName
        +
        The environment variable name
        +
        • +
      + + + +
        +
      • +

        envValue

        +
        java.lang.Object envValue
        +
        The environment variable value
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        EnvironmentDef

        +
        public EnvironmentDef()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setenvName

        +
        public void setenvName(java.lang.String value)
        +
        This method sets the value of envName.
        +
        +
        Parameters:
        +
        value - will update envName, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getenvName

        +
        public java.lang.String getenvName()
        +
        This method returns the value of envName.
        +
        +
        Returns:
        +
        This method will return the value of envName, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setenvValue

        +
        public void setenvValue(java.lang.String value)
        +
        This method sets the value of envValue.
        +
        +
        Parameters:
        +
        value - will update envValue, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setenvValue

        +
        public void setenvValue(Expression value)
        +
        This method sets the value of envValue.
        +
        +
        Parameters:
        +
        value - will update envValue, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getenvValue

        +
        public java.lang.Object getenvValue()
        +
        This method returns the value of envValue.
        +
        +
        Returns:
        +
        This method will return the value of envValue, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/Expression.html b/javadoc/org/commonwl/lang/Expression.html new file mode 100644 index 00000000..ede1ef96 --- /dev/null +++ b/javadoc/org/commonwl/lang/Expression.html @@ -0,0 +1,328 @@ + + + + + +Expression + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Enum Expression

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<Expression>
      • +
    • +
        +
      • org.commonwl.lang.Expression
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<Expression>
    +
    +
    +
    +
    public enum Expression
+extends java.lang.Enum<Expression>
    +
    'Expression' is not a real type. It indicates that a field must allow runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement) is declared and supported by the platform, the field must also allow Javascript expressions.
    +
    • +
+
+
+
    +
  • + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Static Methods Concrete Methods 
      Modifier and TypeMethod and Description
      static ExpressionvalueOf(java.lang.String name) +
      Returns the enum constant of this type with the specified name.
      +
      static Expression[]values() +
      Returns an array containing the constants of this enum type, in +the order they are declared.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Enum

        +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
        • +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +getClass, notify, notifyAll, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Enum Constant Detail

      + + + +
        +
      • +

        ExpressionPlaceholder

        +
        public static final Expression ExpressionPlaceholder
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static Expression[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (Expression c : Expression.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static Expression valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/ExpressionTool.html b/javadoc/org/commonwl/lang/ExpressionTool.html new file mode 100644 index 00000000..4a198491 --- /dev/null +++ b/javadoc/org/commonwl/lang/ExpressionTool.html @@ -0,0 +1,1158 @@ + + + + + +ExpressionTool + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class ExpressionTool

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.ExpressionTool
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Process
    +
    +
    +
    +
    public class ExpressionTool
+extends java.lang.Object
+implements Process
    +
    Execute an expression as a Workflow step.
    +
    • +
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        expression

        +
        java.lang.Object expression
        +
        The expression to execute. The expression must return a JSON object which matches the output parameters of the ExpressionTool.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        • +
      + + + +
        +
      • +

        outputs

        +
        ExpressionToolOutputParameter[] outputs
        +
        Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.
        +
        • +
      + + + +
        +
      • +

        requirements

        +
        java.lang.Object requirements
        +
        Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
        +
        • +
      + + + +
        +
      • +

        cwlVersion

        +
        CWLVersion cwlVersion
        +
        CWL document version. Always required at the document root. Not required for a Process embedded inside another Process.
        +
        • +
      + + + +
        +
      • +

        inputs

        +
        InputParameter[] inputs
        +
        Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object.
        +
        • +
      + + + +
        +
      • +

        hints

        +
        Any hints
        +
        Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A long, human-readable description of this process object.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this process object.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        ExpressionTool

        +
        public ExpressionTool()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setexpression

        +
        public void setexpression(java.lang.String value)
        +
        This method sets the value of expression.
        +
        +
        Parameters:
        +
        value - will update expression, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setexpression

        +
        public void setexpression(Expression value)
        +
        This method sets the value of expression.
        +
        +
        Parameters:
        +
        value - will update expression, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getexpression

        +
        public java.lang.Object getexpression()
        +
        This method returns the value of expression.
        +
        +
        Returns:
        +
        This method will return the value of expression, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputs

        +
        public void setoutputs(ExpressionToolOutputParameter[] value)
        +
        This method sets the value of outputs.
        +
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputs

        +
        public void setoutputs(OutputParameter[] value)
        +
        This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
        +
        +
        Specified by:
        +
        setoutputs in interface Process
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputs

        +
        public ExpressionToolOutputParameter[] getoutputs()
        +
        This method returns the value of outputs.
        +
        +
        Specified by:
        +
        getoutputs in interface Process
        +
        Returns:
        +
        This method will return the value of outputs, which is a ExpressionToolOutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(StepInputExpressionRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a StepInputExpressionRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(MultipleInputFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a MultipleInputFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SoftwareRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SoftwareRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SchemaDefRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SchemaDefRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InitialWorkDirRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a InitialWorkDirRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(EnvVarRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a EnvVarRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(DockerRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a DockerRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ResourceRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ResourceRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InlineJavascriptRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a InlineJavascriptRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ShellCommandRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ShellCommandRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ScatterFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ScatterFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SubworkflowFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SubworkflowFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        getrequirements

        +
        public java.lang.Object getrequirements()
        +
        This method returns the value of requirements.
        +
        +
        Specified by:
        +
        getrequirements in interface Process
        +
        Returns:
        +
        This method will return the value of requirements, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setcwlVersion

        +
        public void setcwlVersion(CWLVersion value)
        +
        This method sets the value of cwlVersion.
        +
        +
        Specified by:
        +
        setcwlVersion in interface Process
        +
        Parameters:
        +
        value - will update cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        getcwlVersion

        +
        public CWLVersion getcwlVersion()
        +
        This method returns the value of cwlVersion.
        +
        +
        Specified by:
        +
        getcwlVersion in interface Process
        +
        Returns:
        +
        This method will return the value of cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputs

        +
        public void setinputs(InputParameter[] value)
        +
        This method sets the value of inputs.
        +
        +
        Specified by:
        +
        setinputs in interface Process
        +
        Parameters:
        +
        value - will update inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getinputs

        +
        public InputParameter[] getinputs()
        +
        This method returns the value of inputs.
        +
        +
        Specified by:
        +
        getinputs in interface Process
        +
        Returns:
        +
        This method will return the value of inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        sethints

        +
        public void sethints(Any value)
        +
        This method sets the value of hints.
        +
        +
        Specified by:
        +
        sethints in interface Process
        +
        Parameters:
        +
        value - will update hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        gethints

        +
        public Any gethints()
        +
        This method returns the value of hints.
        +
        +
        Specified by:
        +
        gethints in interface Process
        +
        Returns:
        +
        This method will return the value of hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Process
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Process
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Specified by:
        +
        setid in interface Process
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Specified by:
        +
        getid in interface Process
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Process
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Process
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/ExpressionToolOutputParameter.html b/javadoc/org/commonwl/lang/ExpressionToolOutputParameter.html new file mode 100644 index 00000000..57a6116d --- /dev/null +++ b/javadoc/org/commonwl/lang/ExpressionToolOutputParameter.html @@ -0,0 +1,1112 @@ + + + + + +ExpressionToolOutputParameter + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class ExpressionToolOutputParameter

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this parameter object.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) CommandOutputBindingoutputBinding +
      Describes how to handle the outputs of a process.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Objecttype +
      Specify valid types of data that may be assigned to this parameter.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      CommandOutputBindinggetoutputBinding() +
      This method returns the value of outputBinding.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetoutputBinding(CommandOutputBinding value) +
      This method sets the value of outputBinding.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      voidsettype(CWLType value) +
      This method sets the value of type.
      +
      voidsettype(CWLType[] value) +
      This method sets the value of type.
      +
      voidsettype(OutputArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(OutputArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(OutputEnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(OutputEnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(OutputRecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(OutputRecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        Specify valid types of data that may be assigned to this parameter.
        +
        • +
      + + + +
        +
      • +

        outputBinding

        +
        CommandOutputBinding outputBinding
        +
        Describes how to handle the outputs of a process.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this parameter object.
        +
        • +
      + + + +
        +
      • +

        streamable

        +
        java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        ExpressionToolOutputParameter

        +
        public ExpressionToolOutputParameter()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        settype

        +
        public void settype(OutputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputRecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputEnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputRecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputEnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Overrides:
        +
        setoutputBinding in class OutputParameter
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Overrides:
        +
        getoutputBinding in class OutputParameter
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Overrides:
        +
        setid in class OutputParameter
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Overrides:
        +
        getid in class OutputParameter
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstreamable

        +
        public void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Specified by:
        +
        setstreamable in interface Parameter
        +
        Overrides:
        +
        setstreamable in class OutputParameter
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        public java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Specified by:
        +
        getstreamable in interface Parameter
        +
        Overrides:
        +
        getstreamable in class OutputParameter
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Specified by:
        +
        getformat in interface Parameter
        +
        Overrides:
        +
        getformat in class OutputParameter
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class OutputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class OutputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Parameter
        +
        Overrides:
        +
        getdoc in class OutputParameter
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class OutputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class OutputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Specified by:
        +
        getsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        getsecondaryFiles in class OutputParameter
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Parameter
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Overrides:
        +
        setlabel in class OutputParameter
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Parameter
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Overrides:
        +
        getlabel in class OutputParameter
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/File.html b/javadoc/org/commonwl/lang/File.html new file mode 100644 index 00000000..5a12d3ae --- /dev/null +++ b/javadoc/org/commonwl/lang/File.html @@ -0,0 +1,972 @@ + + + + + +File + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
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+ +
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+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class File

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.File
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class File
+extends java.lang.Object
    +
    Represents a file (or group of files if `secondaryFiles` is specified) that must be accessible by tools using standard POSIX file system call API such as open(2) and read(2).
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringbasename +
      The base name of the file, that is, the name of the file without any leading directory path.
      +
      (package private) java.lang.Stringchecksum +
      Optional hash code for validating file integrity.
      +
      (package private) Fileclass_value +
      Must be `File` to indicate this object describes a file.
      +
      (package private) java.lang.Stringcontents +
      File contents literal.
      +
      (package private) java.lang.Stringdirname +
      The name of the directory containing file, that is, the path leading up to the final slash in the path such that `dirname + '/' + basename == path`.
      +
      (package private) java.lang.Stringformat +
      The format of the file: this must be an IRI of a concept node that represents the file format, preferrably defined within an ontology.
      +
      (package private) java.lang.Stringlocation +
      An IRI that identifies the file resource.
      +
      (package private) java.lang.Stringnameext +
      The basename extension such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period.
      +
      (package private) java.lang.Stringnameroot +
      The basename root such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period.
      +
      (package private) java.lang.Stringpath +
      The local host path where the File is available when a CommandLineTool is executed.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      A list of additional files that are associated with the primary file and must be transferred alongside the primary file.
      +
      (package private) java.lang.Longsize +
      Optional file size
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      File() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetbasename() +
      This method returns the value of basename.
      +
      java.lang.Stringgetchecksum() +
      This method returns the value of checksum.
      +
      Filegetclass() +
      This method returns the value of class_value.
      +
      java.lang.Stringgetcontents() +
      This method returns the value of contents.
      +
      java.lang.Stringgetdirname() +
      This method returns the value of dirname.
      +
      java.lang.Stringgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetlocation() +
      This method returns the value of location.
      +
      java.lang.Stringgetnameext() +
      This method returns the value of nameext.
      +
      java.lang.Stringgetnameroot() +
      This method returns the value of nameroot.
      +
      java.lang.Stringgetpath() +
      This method returns the value of path.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Longgetsize() +
      This method returns the value of size.
      +
      voidsetbasename(java.lang.String value) +
      This method sets the value of basename.
      +
      voidsetchecksum(java.lang.String value) +
      This method sets the value of checksum.
      +
      voidsetclass(File value) +
      This method sets the value of class_value.
      +
      voidsetcontents(java.lang.String value) +
      This method sets the value of contents.
      +
      voidsetdirname(java.lang.String value) +
      This method sets the value of dirname.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetlocation(java.lang.String value) +
      This method sets the value of location.
      +
      voidsetnameext(java.lang.String value) +
      This method sets the value of nameext.
      +
      voidsetnameroot(java.lang.String value) +
      This method sets the value of nameroot.
      +
      voidsetpath(java.lang.String value) +
      This method sets the value of path.
      +
      voidsetsecondaryFiles(Directory[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(File[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsize(java.lang.Long value) +
      This method sets the value of size.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        path

        +
        java.lang.String path
        +
        The local host path where the File is available when a CommandLineTool is executed. This field must be set by the implementation. The final path component must match the value of `basename`. This field must not be used in any other context. The command line tool being executed must be able to to access the file at `path` using the POSIX `open(2)` syscall. As a special case, if the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, and remove the `path` field. If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) (`|`,`&`, `;`, `(`, `)`, `(`,`)`, `$`,`` ` ``, `\`, ``, `'`, `(space)`, `(tab)`, and `(newline)`) or characters [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) then implementations may terminate the process with a `permanentFailure`.
        +
        • +
      + + + +
        +
      • +

        basename

        +
        java.lang.String basename
        +
        The base name of the file, that is, the name of the file without any leading directory path. The base name must not contain a slash `/`. If not provided, the implementation must set this field based on the `location` field by taking the final path component after parsing `location` as an IRI. If `basename` is provided, it is not required to match the value from `location`. When this file is made available to a CommandLineTool, it must be named with `basename`, i.e. the final component of the `path` field must match `basename`.
        +
        • +
      + + + +
        +
      • +

        nameext

        +
        java.lang.String nameext
        +
        The basename extension such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period. Leading periods on the basename are ignored; a basename of `.cshrc` will have an empty `nameext`. The implementation must set this field automatically based on the value of `basename` prior to evaluating parameter references or expressions.
        +
        • +
      + + + +
        +
      • +

        size

        +
        java.lang.Long size
        +
        Optional file size
        +
        • +
      + + + +
        +
      • +

        contents

        +
        java.lang.String contents
        +
        File contents literal. Maximum of 64 KiB. If neither `location` nor `path` is provided, `contents` must be non-null. The implementation must assign a unique identifier for the `location` field. When the file is staged as input to CommandLineTool, the value of `contents` must be written to a file. If `loadContents` of `inputBinding` or `outputBinding` is true and `location` is valid, the implementation must read up to the first 64 KiB of text from the file and place it in the contents field.
        +
        • +
      + + + +
        +
      • +

        checksum

        +
        java.lang.String checksum
        +
        Optional hash code for validating file integrity. Currently must be in the form sha1$ + hexadecimal string using the SHA-1 algorithm.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.String format
        +
        The format of the file: this must be an IRI of a concept node that represents the file format, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. Reasoning about format compatability must be done by checking that an input file format is the same, `owl:equivalentClass` or `rdfs:subClassOf` the format required by the input parameter. `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if `(B) owl:equivalentClass (C)` and `(B) owl:subclassOf (A)` then infer `(C) owl:subclassOf (A)`. File format ontologies may be provided in the $schema metadata at the root of the document. If no ontologies are specified in `$schema`, the runtime may perform exact file format matches.
        +
        • +
      + + + +
        +
      • +

        location

        +
        java.lang.String location
        +
        An IRI that identifies the file resource. This may be a relative reference, in which case it must be resolved using the base IRI of the document. The location may refer to a local or remote resource; the implementation must use the IRI to retrieve file content. If an implementation is unable to retrieve the file content stored at a remote resource (due to unsupported protocol, access denied, or other issue) it must signal an error. If the `location` field is not provided, the `contents` field must be provided. The implementation must assign a unique identifier for the `location` field. If the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, then follow the rules above.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        A list of additional files that are associated with the primary file and must be transferred alongside the primary file. Examples include indexes of the primary file, or external references which must be included when loading primary document. A file object listed in `secondaryFiles` may itself include `secondaryFiles` for which the same rules apply.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        File class_value
        +
        Must be `File` to indicate this object describes a file.
        +
        • +
      + + + +
        +
      • +

        dirname

        +
        java.lang.String dirname
        +
        The name of the directory containing file, that is, the path leading up to the final slash in the path such that `dirname + '/' + basename == path`. The implementation must set this field based on the value of `path` prior to evaluating parameter references or expressions in a CommandLineTool document. This field must not be used in any other context.
        +
        • +
      + + + +
        +
      • +

        nameroot

        +
        java.lang.String nameroot
        +
        The basename root such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period. For the purposess of path splitting leading periods on the basename are ignored; a basename of `.cshrc` will have a nameroot of `.cshrc`. The implementation must set this field automatically based on the value of `basename` prior to evaluating parameter references or expressions.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        File

        +
        public File()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setpath

        +
        public void setpath(java.lang.String value)
        +
        This method sets the value of path.
        +
        +
        Parameters:
        +
        value - will update path, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getpath

        +
        public java.lang.String getpath()
        +
        This method returns the value of path.
        +
        +
        Returns:
        +
        This method will return the value of path, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setbasename

        +
        public void setbasename(java.lang.String value)
        +
        This method sets the value of basename.
        +
        +
        Parameters:
        +
        value - will update basename, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getbasename

        +
        public java.lang.String getbasename()
        +
        This method returns the value of basename.
        +
        +
        Returns:
        +
        This method will return the value of basename, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setnameext

        +
        public void setnameext(java.lang.String value)
        +
        This method sets the value of nameext.
        +
        +
        Parameters:
        +
        value - will update nameext, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getnameext

        +
        public java.lang.String getnameext()
        +
        This method returns the value of nameext.
        +
        +
        Returns:
        +
        This method will return the value of nameext, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsize

        +
        public void setsize(java.lang.Long value)
        +
        This method sets the value of size.
        +
        +
        Parameters:
        +
        value - will update size, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        getsize

        +
        public java.lang.Long getsize()
        +
        This method returns the value of size.
        +
        +
        Returns:
        +
        This method will return the value of size, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        setcontents

        +
        public void setcontents(java.lang.String value)
        +
        This method sets the value of contents.
        +
        +
        Parameters:
        +
        value - will update contents, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getcontents

        +
        public java.lang.String getcontents()
        +
        This method returns the value of contents.
        +
        +
        Returns:
        +
        This method will return the value of contents, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setchecksum

        +
        public void setchecksum(java.lang.String value)
        +
        This method sets the value of checksum.
        +
        +
        Parameters:
        +
        value - will update checksum, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getchecksum

        +
        public java.lang.String getchecksum()
        +
        This method returns the value of checksum.
        +
        +
        Returns:
        +
        This method will return the value of checksum, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.String getformat()
        +
        This method returns the value of format.
        +
        +
        Returns:
        +
        This method will return the value of format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlocation

        +
        public void setlocation(java.lang.String value)
        +
        This method sets the value of location.
        +
        +
        Parameters:
        +
        value - will update location, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlocation

        +
        public java.lang.String getlocation()
        +
        This method returns the value of location.
        +
        +
        Returns:
        +
        This method will return the value of location, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(File[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a File array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(Directory[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Directory array.
        +
        +
        • +
      + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(File value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a File type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public File getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a File type.
        +
        +
        • +
      + + + +
        +
      • +

        setdirname

        +
        public void setdirname(java.lang.String value)
        +
        This method sets the value of dirname.
        +
        +
        Parameters:
        +
        value - will update dirname, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdirname

        +
        public java.lang.String getdirname()
        +
        This method returns the value of dirname.
        +
        +
        Returns:
        +
        This method will return the value of dirname, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setnameroot

        +
        public void setnameroot(java.lang.String value)
        +
        This method sets the value of nameroot.
        +
        +
        Parameters:
        +
        value - will update nameroot, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getnameroot

        +
        public java.lang.String getnameroot()
        +
        This method returns the value of nameroot.
        +
        +
        Returns:
        +
        This method will return the value of nameroot, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/InitialWorkDirRequirement.html b/javadoc/org/commonwl/lang/InitialWorkDirRequirement.html new file mode 100644 index 00000000..f5198023 --- /dev/null +++ b/javadoc/org/commonwl/lang/InitialWorkDirRequirement.html @@ -0,0 +1,477 @@ + + + + + +InitialWorkDirRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InitialWorkDirRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.InitialWorkDirRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class InitialWorkDirRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Define a list of files and subdirectories that must be created by the workflow platform in the designated output directory prior to executing the command line tool.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      InitialWorkDirRequirement
      +
      (package private) java.lang.Objectlisting +
      The list of files or subdirectories that must be placed in the designated output directory prior to executing the command line tool.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      java.lang.Objectgetlisting() +
      This method returns the value of listing.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsetlisting(Directory[] value) +
      This method sets the value of listing.
      +
      voidsetlisting(Dirent[] value) +
      This method sets the value of listing.
      +
      voidsetlisting(Expression[] value) +
      This method sets the value of listing.
      +
      voidsetlisting(File[] value) +
      This method sets the value of listing.
      +
      voidsetlisting(java.lang.String[] value) +
      This method sets the value of listing.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        listing

        +
        java.lang.Object listing
        +
        The list of files or subdirectories that must be placed in the designated output directory prior to executing the command line tool. May be an expression. If so, the expression return value must validate as `{type: array, items: [File, Directory]}`.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        InitialWorkDirRequirement
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InitialWorkDirRequirement

        +
        public InitialWorkDirRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(Dirent[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a Dirent array.
        +
        +
        • +
      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(File[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a File array.
        +
        +
        • +
      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(Directory[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a Directory array.
        +
        +
        • +
      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(Expression[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(java.lang.String[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getlisting

        +
        public java.lang.Object getlisting()
        +
        This method returns the value of listing.
        +
        +
        Returns:
        +
        This method will return the value of listing, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/InlineJavascriptRequirement.html b/javadoc/org/commonwl/lang/InlineJavascriptRequirement.html new file mode 100644 index 00000000..96d08d8f --- /dev/null +++ b/javadoc/org/commonwl/lang/InlineJavascriptRequirement.html @@ -0,0 +1,397 @@ + + + + + +InlineJavascriptRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InlineJavascriptRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.InlineJavascriptRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class InlineJavascriptRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Indicates that the workflow platform must support inline Javascript expressions. If this requirement is not present, the workflow platform must not perform expression interpolatation.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'InlineJavascriptRequirement'
      +
      (package private) java.lang.StringexpressionLib +
      Additional code fragments that will also be inserted before executing the expression code.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      java.lang.StringgetexpressionLib() +
      This method returns the value of expressionLib.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsetexpressionLib(java.lang.String value) +
      This method sets the value of expressionLib.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        expressionLib

        +
        java.lang.String expressionLib
        +
        Additional code fragments that will also be inserted before executing the expression code. Allows for function definitions that may be called from CWL expressions.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'InlineJavascriptRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InlineJavascriptRequirement

        +
        public InlineJavascriptRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setexpressionLib

        +
        public void setexpressionLib(java.lang.String value)
        +
        This method sets the value of expressionLib.
        +
        +
        Parameters:
        +
        value - will update expressionLib, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getexpressionLib

        +
        public java.lang.String getexpressionLib()
        +
        This method returns the value of expressionLib.
        +
        +
        Returns:
        +
        This method will return the value of expressionLib, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/InputArraySchema.html b/javadoc/org/commonwl/lang/InputArraySchema.html new file mode 100644 index 00000000..b7b72bdd --- /dev/null +++ b/javadoc/org/commonwl/lang/InputArraySchema.html @@ -0,0 +1,410 @@ + + + + + +InputArraySchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InputArraySchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) CommandLineBindinginputBinding 
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      InputArraySchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      CommandLineBindinggetinputBinding() +
      This method returns the value of inputBinding.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetinputBinding(CommandLineBinding value) +
      This method sets the value of inputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + + + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InputArraySchema

        +
        public InputArraySchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface InputSchema
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface InputSchema
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
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+ + + +
+ +
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+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/InputBinding.html b/javadoc/org/commonwl/lang/InputBinding.html new file mode 100644 index 00000000..7c039bb9 --- /dev/null +++ b/javadoc/org/commonwl/lang/InputBinding.html @@ -0,0 +1,289 @@ + + + + + +InputBinding + + + + + + + + +
+ + +
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+ + + + +
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+ + + +
+ +
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+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface InputBinding

+
+
+
+
    +
  • +
    +
    All Known Implementing Classes:
    +
    CommandLineBinding
    +
    +
    +
    +
    public interface InputBinding
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.BooleanloadContents +
      Only valid when `type: File` or is an array of `items: File`.
      +
      +
      • +
    + + +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        loadContents

        +
        static final java.lang.Boolean loadContents
        +
        Only valid when `type: File` or is an array of `items: File`. Read up to the first 64 KiB of text from the file and place it in the contents field of the file object for use by expressions.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setloadContents

        +
        void setloadContents(java.lang.Boolean value)
        +
        This method sets the value of loadContents.
        +
        +
        Parameters:
        +
        value - will update loadContents, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getloadContents

        +
        java.lang.Boolean getloadContents()
        +
        This method returns the value of loadContents.
        +
        +
        Returns:
        +
        This method will return the value of loadContents, which is a Boolean type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/InputEnumSchema.html b/javadoc/org/commonwl/lang/InputEnumSchema.html new file mode 100644 index 00000000..bfc8c1ef --- /dev/null +++ b/javadoc/org/commonwl/lang/InputEnumSchema.html @@ -0,0 +1,410 @@ + + + + + +InputEnumSchema + + + + + + + + +
+ + +
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+ + + +
+ +
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+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InputEnumSchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) CommandLineBindinginputBinding 
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      InputEnumSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      CommandLineBindinggetinputBinding() +
      This method returns the value of inputBinding.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetinputBinding(CommandLineBinding value) +
      This method sets the value of inputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + + + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InputEnumSchema

        +
        public InputEnumSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface InputSchema
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface InputSchema
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/InputParameter.html b/javadoc/org/commonwl/lang/InputParameter.html new file mode 100644 index 00000000..4fc7ee6d --- /dev/null +++ b/javadoc/org/commonwl/lang/InputParameter.html @@ -0,0 +1,1128 @@ + + + + + +InputParameter + + + + + + + + +
+ + +
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+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InputParameter

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.InputParameter
      • +
    +
    • +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) Anydefault_value +
      The default value for this parameter if not provided in the input object.
      +
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this parameter object.
      +
      (package private) CommandLineBindinginputBinding +
      Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Objecttype +
      Specify valid types of data that may be assigned to this parameter.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      InputParameter() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      Anygetdefault() +
      This method returns the value of default_value.
      +
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      CommandLineBindinggetinputBinding() +
      This method returns the value of inputBinding.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdefault(Any value) +
      This method sets the value of default_value.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetinputBinding(CommandLineBinding value) +
      This method sets the value of inputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      voidsettype(CWLType value) +
      This method sets the value of type.
      +
      voidsettype(CWLType[] value) +
      This method sets the value of type.
      +
      voidsettype(InputArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(InputArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(InputEnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(InputEnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(InputRecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(InputRecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        default_value

        +
        Any default_value
        +
        The default value for this parameter if not provided in the input object.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this parameter object.
        +
        • +
      + + + +
        +
      • +

        inputBinding

        +
        CommandLineBinding inputBinding
        +
        Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        Specify valid types of data that may be assigned to this parameter.
        +
        • +
      + + + +
        +
      • +

        streamable

        +
        java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InputParameter

        +
        public InputParameter()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setdefault

        +
        public void setdefault(Any value)
        +
        This method sets the value of default_value.
        +
        +
        Parameters:
        +
        value - will update default_value, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        getdefault

        +
        public Any getdefault()
        +
        This method returns the value of default_value.
        +
        +
        Returns:
        +
        This method will return the value of default_value, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputEnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputEnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputRecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputRecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setstreamable

        +
        public void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Specified by:
        +
        setstreamable in interface Parameter
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        public java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Specified by:
        +
        getstreamable in interface Parameter
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Specified by:
        +
        getformat in interface Parameter
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Parameter
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(Expression[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(Expression value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Specified by:
        +
        getsecondaryFiles in interface Parameter
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Parameter
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Parameter
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/InputRecordField.html b/javadoc/org/commonwl/lang/InputRecordField.html new file mode 100644 index 00000000..b65ce7ed --- /dev/null +++ b/javadoc/org/commonwl/lang/InputRecordField.html @@ -0,0 +1,766 @@ + + + + + +InputRecordField + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InputRecordField

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringdoc +
      A documentation string for this field
      +
      (package private) CommandLineBindinginputBinding 
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this process object.
      +
      (package private) java.lang.Stringname +
      The name of the field
      +
      (package private) java.lang.Objecttype +
      The field type
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      InputRecordField() 
      +
      • +
    + + +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      + + + + + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The name of the field
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A documentation string for this field
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        The field type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InputRecordField

        +
        public InputRecordField()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Overrides:
        +
        setname in class RecordField
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Overrides:
        +
        getname in class RecordField
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Overrides:
        +
        setdoc in class RecordField
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Overrides:
        +
        getdoc in class RecordField
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Overrides:
        +
        gettype in class RecordField
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/InputRecordSchema.html b/javadoc/org/commonwl/lang/InputRecordSchema.html new file mode 100644 index 00000000..ef08c1a6 --- /dev/null +++ b/javadoc/org/commonwl/lang/InputRecordSchema.html @@ -0,0 +1,357 @@ + + + + + +InputRecordSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InputRecordSchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      InputRecordSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InputRecordSchema

        +
        public InputRecordSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface InputSchema
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface InputSchema
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/InputSchema.html b/javadoc/org/commonwl/lang/InputSchema.html new file mode 100644 index 00000000..662cc9b2 --- /dev/null +++ b/javadoc/org/commonwl/lang/InputSchema.html @@ -0,0 +1,298 @@ + + + + + +InputSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface InputSchema

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        static final java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/JsonldPredicate.html b/javadoc/org/commonwl/lang/JsonldPredicate.html new file mode 100644 index 00000000..017c4429 --- /dev/null +++ b/javadoc/org/commonwl/lang/JsonldPredicate.html @@ -0,0 +1,784 @@ + + + + + +JsonldPredicate + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class JsonldPredicate

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.JsonldPredicate
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class JsonldPredicate
+extends java.lang.Object
    +
    Attached to a record field to define how the parent record field is handled for URI resolution and JSON-LD context generation.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.String_container +
      Structure hint, corresponds to JSON-LD `@container` directive.
      +
      (package private) java.lang.String_id +
      The predicate URI that this field corresponds to.
      +
      (package private) java.lang.String_type +
      The context type hint, corresponds to JSON-LD `@type` directive.
      +
      (package private) java.lang.Booleanidentity +
      If true and `_type` is `@id` this indicates that the parent field must be resolved according to identity resolution rules instead of link resolution rules.
      +
      (package private) java.lang.StringmapPredicate +
      Only applies if `mapSubject` is also provided.
      +
      (package private) java.lang.StringmapSubject +
      If the value of the field is a JSON object, it must be transformed into an array of JSON objects, where each key-value pair from the source JSON object is a list item, the list items must be JSON objects, and the key is assigned to the field specified by `mapSubject`.
      +
      (package private) java.lang.BooleannoLinkCheck +
      If true, this indicates that link validation traversal must stop at this field.
      +
      (package private) java.lang.IntegerrefScope +
      If the field contains a relative reference, it must be resolved by searching for valid document references in each successive parent scope in the document fragment.
      +
      (package private) java.lang.BooleantypeDSL +
      Field must be expanded based on the the Schema Salad type DSL.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      JsonldPredicate() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringget_container() +
      This method returns the value of _container.
      +
      java.lang.Stringget_id() +
      This method returns the value of _id.
      +
      java.lang.Stringget_type() +
      This method returns the value of _type.
      +
      java.lang.Booleangetidentity() +
      This method returns the value of identity.
      +
      java.lang.StringgetmapPredicate() +
      This method returns the value of mapPredicate.
      +
      java.lang.StringgetmapSubject() +
      This method returns the value of mapSubject.
      +
      java.lang.BooleangetnoLinkCheck() +
      This method returns the value of noLinkCheck.
      +
      java.lang.IntegergetrefScope() +
      This method returns the value of refScope.
      +
      java.lang.BooleangettypeDSL() +
      This method returns the value of typeDSL.
      +
      voidset_container(java.lang.String value) +
      This method sets the value of _container.
      +
      voidset_id(java.lang.String value) +
      This method sets the value of _id.
      +
      voidset_type(java.lang.String value) +
      This method sets the value of _type.
      +
      voidsetidentity(java.lang.Boolean value) +
      This method sets the value of identity.
      +
      voidsetmapPredicate(java.lang.String value) +
      This method sets the value of mapPredicate.
      +
      voidsetmapSubject(java.lang.String value) +
      This method sets the value of mapSubject.
      +
      voidsetnoLinkCheck(java.lang.Boolean value) +
      This method sets the value of noLinkCheck.
      +
      voidsetrefScope(java.lang.Integer value) +
      This method sets the value of refScope.
      +
      voidsettypeDSL(java.lang.Boolean value) +
      This method sets the value of typeDSL.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        _container

        +
        java.lang.String _container
        +
        Structure hint, corresponds to JSON-LD `@container` directive.
        +
        • +
      + + + +
        +
      • +

        noLinkCheck

        +
        java.lang.Boolean noLinkCheck
        +
        If true, this indicates that link validation traversal must stop at this field. This field (it is is a URI) or any fields under it (if it is an object or array) are not subject to link checking.
        +
        • +
      + + + +
        +
      • +

        typeDSL

        +
        java.lang.Boolean typeDSL
        +
        Field must be expanded based on the the Schema Salad type DSL.
        +
        • +
      + + + +
        +
      • +

        identity

        +
        java.lang.Boolean identity
        +
        If true and `_type` is `@id` this indicates that the parent field must be resolved according to identity resolution rules instead of link resolution rules. In addition, the field value is considered an assertion that the linked value exists; absence of an object in the loaded document with the URI is not an error.
        +
        • +
      + + + +
        +
      • +

        _type

        +
        java.lang.String _type
        +
        The context type hint, corresponds to JSON-LD `@type` directive. * If the value of this field is `@id` and `identity` is false or unspecified, the parent field must be resolved using the link resolution rules. If `identity` is true, the parent field must be resolved using the identifier expansion rules. * If the value of this field is `@vocab`, the parent field must be resolved using the vocabulary resolution rules.
        +
        • +
      + + + +
        +
      • +

        refScope

        +
        java.lang.Integer refScope
        +
        If the field contains a relative reference, it must be resolved by searching for valid document references in each successive parent scope in the document fragment. For example, a reference of `foo` in the context `#foo/bar/baz` will first check for the existence of `#foo/bar/baz/foo`, followed by `#foo/bar/foo`, then `#foo/foo` and then finally `#foo`. The first valid URI in the search order shall be used as the fully resolved value of the identifier. The value of the refScope field is the specified number of levels from the containing identifer scope before starting the search, so if `refScope: 2` then baz and bar must be stripped to get the base `#foo` and search `#foo/foo` and the `#foo`. The last scope searched must be the top level scope before determining if the identifier cannot be resolved.
        +
        • +
      + + + +
        +
      • +

        mapSubject

        +
        java.lang.String mapSubject
        +
        If the value of the field is a JSON object, it must be transformed into an array of JSON objects, where each key-value pair from the source JSON object is a list item, the list items must be JSON objects, and the key is assigned to the field specified by `mapSubject`.
        +
        • +
      + + + +
        +
      • +

        _id

        +
        java.lang.String _id
        +
        The predicate URI that this field corresponds to. Corresponds to JSON-LD `@id` directive.
        +
        • +
      + + + +
        +
      • +

        mapPredicate

        +
        java.lang.String mapPredicate
        +
        Only applies if `mapSubject` is also provided. If the value of the field is a JSON object, it is transformed as described in `mapSubject`, with the addition that when the value of a map item is not an object, the item is transformed to a JSON object with the key assigned to the field specified by `mapSubject` and the value assigned to the field specified by `mapPredicate`.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        JsonldPredicate

        +
        public JsonldPredicate()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        set_container

        +
        public void set_container(java.lang.String value)
        +
        This method sets the value of _container.
        +
        +
        Parameters:
        +
        value - will update _container, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        get_container

        +
        public java.lang.String get_container()
        +
        This method returns the value of _container.
        +
        +
        Returns:
        +
        This method will return the value of _container, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setnoLinkCheck

        +
        public void setnoLinkCheck(java.lang.Boolean value)
        +
        This method sets the value of noLinkCheck.
        +
        +
        Parameters:
        +
        value - will update noLinkCheck, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getnoLinkCheck

        +
        public java.lang.Boolean getnoLinkCheck()
        +
        This method returns the value of noLinkCheck.
        +
        +
        Returns:
        +
        This method will return the value of noLinkCheck, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        settypeDSL

        +
        public void settypeDSL(java.lang.Boolean value)
        +
        This method sets the value of typeDSL.
        +
        +
        Parameters:
        +
        value - will update typeDSL, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        gettypeDSL

        +
        public java.lang.Boolean gettypeDSL()
        +
        This method returns the value of typeDSL.
        +
        +
        Returns:
        +
        This method will return the value of typeDSL, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setidentity

        +
        public void setidentity(java.lang.Boolean value)
        +
        This method sets the value of identity.
        +
        +
        Parameters:
        +
        value - will update identity, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getidentity

        +
        public java.lang.Boolean getidentity()
        +
        This method returns the value of identity.
        +
        +
        Returns:
        +
        This method will return the value of identity, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        set_type

        +
        public void set_type(java.lang.String value)
        +
        This method sets the value of _type.
        +
        +
        Parameters:
        +
        value - will update _type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        get_type

        +
        public java.lang.String get_type()
        +
        This method returns the value of _type.
        +
        +
        Returns:
        +
        This method will return the value of _type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setrefScope

        +
        public void setrefScope(java.lang.Integer value)
        +
        This method sets the value of refScope.
        +
        +
        Parameters:
        +
        value - will update refScope, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        getrefScope

        +
        public java.lang.Integer getrefScope()
        +
        This method returns the value of refScope.
        +
        +
        Returns:
        +
        This method will return the value of refScope, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        setmapSubject

        +
        public void setmapSubject(java.lang.String value)
        +
        This method sets the value of mapSubject.
        +
        +
        Parameters:
        +
        value - will update mapSubject, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getmapSubject

        +
        public java.lang.String getmapSubject()
        +
        This method returns the value of mapSubject.
        +
        +
        Returns:
        +
        This method will return the value of mapSubject, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        set_id

        +
        public void set_id(java.lang.String value)
        +
        This method sets the value of _id.
        +
        +
        Parameters:
        +
        value - will update _id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        get_id

        +
        public java.lang.String get_id()
        +
        This method returns the value of _id.
        +
        +
        Returns:
        +
        This method will return the value of _id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setmapPredicate

        +
        public void setmapPredicate(java.lang.String value)
        +
        This method sets the value of mapPredicate.
        +
        +
        Parameters:
        +
        value - will update mapPredicate, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getmapPredicate

        +
        public java.lang.String getmapPredicate()
        +
        This method returns the value of mapPredicate.
        +
        +
        Returns:
        +
        This method will return the value of mapPredicate, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/LinkMergeMethod.html b/javadoc/org/commonwl/lang/LinkMergeMethod.html new file mode 100644 index 00000000..60e4d37c --- /dev/null +++ b/javadoc/org/commonwl/lang/LinkMergeMethod.html @@ -0,0 +1,340 @@ + + + + + +LinkMergeMethod + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Enum LinkMergeMethod

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<LinkMergeMethod>
      • +
    • +
        +
      • org.commonwl.lang.LinkMergeMethod
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<LinkMergeMethod>
    +
    +
    +
    +
    public enum LinkMergeMethod
+extends java.lang.Enum<LinkMergeMethod>
    +
    The input link merge method, described in [WorkflowStepInput](#WorkflowStepInput).
    +
    • +
+
+
+
    +
  • + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Static Methods Concrete Methods 
      Modifier and TypeMethod and Description
      static LinkMergeMethodvalueOf(java.lang.String name) +
      Returns the enum constant of this type with the specified name.
      +
      static LinkMergeMethod[]values() +
      Returns an array containing the constants of this enum type, in +the order they are declared.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Enum

        +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
        • +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +getClass, notify, notifyAll, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + + + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static LinkMergeMethod[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (LinkMergeMethod c : LinkMergeMethod.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static LinkMergeMethod valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/MultipleInputFeatureRequirement.html b/javadoc/org/commonwl/lang/MultipleInputFeatureRequirement.html new file mode 100644 index 00000000..babbf79b --- /dev/null +++ b/javadoc/org/commonwl/lang/MultipleInputFeatureRequirement.html @@ -0,0 +1,341 @@ + + + + + +MultipleInputFeatureRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class MultipleInputFeatureRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.MultipleInputFeatureRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class MultipleInputFeatureRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Indicates that the workflow platform must support multiple inbound data links listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'MultipleInputFeatureRequirement'
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'MultipleInputFeatureRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        MultipleInputFeatureRequirement

        +
        public MultipleInputFeatureRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/NamedType.html b/javadoc/org/commonwl/lang/NamedType.html new file mode 100644 index 00000000..bb09cce9 --- /dev/null +++ b/javadoc/org/commonwl/lang/NamedType.html @@ -0,0 +1,289 @@ + + + + + +NamedType + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface NamedType

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Stringname +
      The identifier for this type
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetname() +
      This method returns the value of name.
      +
      voidsetname(java.lang.String value) +
      This method sets the value of name.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        name

        +
        static final java.lang.String name
        +
        The identifier for this type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setname

        +
        void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/OutputArraySchema.html b/javadoc/org/commonwl/lang/OutputArraySchema.html new file mode 100644 index 00000000..89a85053 --- /dev/null +++ b/javadoc/org/commonwl/lang/OutputArraySchema.html @@ -0,0 +1,410 @@ + + + + + +OutputArraySchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class OutputArraySchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) CommandOutputBindingoutputBinding 
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      OutputArraySchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      CommandOutputBindinggetoutputBinding() +
      This method returns the value of outputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetoutputBinding(CommandOutputBinding value) +
      This method sets the value of outputBinding.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + + + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        OutputArraySchema

        +
        public OutputArraySchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface OutputSchema
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface OutputSchema
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/OutputBinding.html b/javadoc/org/commonwl/lang/OutputBinding.html new file mode 100644 index 00000000..5f8eacb6 --- /dev/null +++ b/javadoc/org/commonwl/lang/OutputBinding.html @@ -0,0 +1,169 @@ + + + + + +OutputBinding + + + + + + + + +
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+ + +
+
org.commonwl.lang
+

Interface OutputBinding

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+
    +
  • +
    +
    All Known Implementing Classes:
    +
    CommandOutputBinding
    +
    +
    +
    +
    public interface OutputBinding
    +
    • +
+
+
+ + +
+ + +
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    +
  • Summary: 
    • +
  • Nested | 
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    • +
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    • +
  • Method
    • +
+
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  • Detail: 
    • +
  • Field | 
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    • +
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+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/OutputEnumSchema.html b/javadoc/org/commonwl/lang/OutputEnumSchema.html new file mode 100644 index 00000000..3a3edfc6 --- /dev/null +++ b/javadoc/org/commonwl/lang/OutputEnumSchema.html @@ -0,0 +1,410 @@ + + + + + +OutputEnumSchema + + + + + + + + +
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org.commonwl.lang
+

Class OutputEnumSchema

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+ +
+ +
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    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) CommandOutputBindingoutputBinding 
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      OutputEnumSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      CommandOutputBindinggetoutputBinding() +
      This method returns the value of outputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetoutputBinding(CommandOutputBinding value) +
      This method sets the value of outputBinding.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
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    +
  • + +
      +
    • + + +

      Field Detail

      + + + + + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        OutputEnumSchema

        +
        public OutputEnumSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface OutputSchema
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface OutputSchema
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
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+ + +
+ + +
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+ + + diff --git a/javadoc/org/commonwl/lang/OutputParameter.html b/javadoc/org/commonwl/lang/OutputParameter.html new file mode 100644 index 00000000..9960303f --- /dev/null +++ b/javadoc/org/commonwl/lang/OutputParameter.html @@ -0,0 +1,836 @@ + + + + + +OutputParameter + + + + + + + + +
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+ + + +
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+ + +
+ + +
+
org.commonwl.lang
+

Class OutputParameter

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.OutputParameter
      • +
    +
    • +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this parameter object.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) CommandOutputBindingoutputBinding +
      Describes how to handle the outputs of a process.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      OutputParameter() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      CommandOutputBindinggetoutputBinding() +
      This method returns the value of outputBinding.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetoutputBinding(CommandOutputBinding value) +
      This method sets the value of outputBinding.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        outputBinding

        +
        CommandOutputBinding outputBinding
        +
        Describes how to handle the outputs of a process.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this parameter object.
        +
        • +
      + + + +
        +
      • +

        streamable

        +
        java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        OutputParameter

        +
        public OutputParameter()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstreamable

        +
        public void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Specified by:
        +
        setstreamable in interface Parameter
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        public java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Specified by:
        +
        getstreamable in interface Parameter
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Specified by:
        +
        getformat in interface Parameter
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Parameter
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(Expression[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(Expression value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Specified by:
        +
        getsecondaryFiles in interface Parameter
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Parameter
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Parameter
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/OutputRecordField.html b/javadoc/org/commonwl/lang/OutputRecordField.html new file mode 100644 index 00000000..d9d56dbb --- /dev/null +++ b/javadoc/org/commonwl/lang/OutputRecordField.html @@ -0,0 +1,710 @@ + + + + + +OutputRecordField + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class OutputRecordField

+
+
+ +
+ +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + + + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The name of the field
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A documentation string for this field
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        The field type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        OutputRecordField

        +
        public OutputRecordField()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Overrides:
        +
        setname in class RecordField
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Overrides:
        +
        getname in class RecordField
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Overrides:
        +
        setdoc in class RecordField
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Overrides:
        +
        getdoc in class RecordField
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Overrides:
        +
        gettype in class RecordField
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/OutputRecordSchema.html b/javadoc/org/commonwl/lang/OutputRecordSchema.html new file mode 100644 index 00000000..4223270c --- /dev/null +++ b/javadoc/org/commonwl/lang/OutputRecordSchema.html @@ -0,0 +1,357 @@ + + + + + +OutputRecordSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class OutputRecordSchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      OutputRecordSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        OutputRecordSchema

        +
        public OutputRecordSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface OutputSchema
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface OutputSchema
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/OutputSchema.html b/javadoc/org/commonwl/lang/OutputSchema.html new file mode 100644 index 00000000..7ce7e130 --- /dev/null +++ b/javadoc/org/commonwl/lang/OutputSchema.html @@ -0,0 +1,298 @@ + + + + + +OutputSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface OutputSchema

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        static final java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/Parameter.html b/javadoc/org/commonwl/lang/Parameter.html new file mode 100644 index 00000000..40bc2504 --- /dev/null +++ b/javadoc/org/commonwl/lang/Parameter.html @@ -0,0 +1,643 @@ + + + + + +Parameter + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface Parameter

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      static java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      static java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      static java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      static java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        streamable

        +
        static final java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        static final java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        static final java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        static final java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        static final java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setstreamable

        +
        void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        void setsecondaryFiles(Expression[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        void setsecondaryFiles(Expression value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getsecondaryFiles

        +
        java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/PrimitiveType.html b/javadoc/org/commonwl/lang/PrimitiveType.html new file mode 100644 index 00000000..426d6ee4 --- /dev/null +++ b/javadoc/org/commonwl/lang/PrimitiveType.html @@ -0,0 +1,442 @@ + + + + + +PrimitiveType + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class PrimitiveType

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.PrimitiveType
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class PrimitiveType
+extends java.lang.Object
    +
    Salad data types are based on Avro schema declarations. Refer to the + [Avro schema declaration documentation](https://avro.apache.org/docs/current/spec.html#schemas) for + detailed information. + The types are: 1) null: no value, + 2) boolean: a binary value, + 3) int: 32-bit signed integer, + 4) long: 64-bit signed integer, + 5) float: single precision (32-bit) IEEE 754 floating-point number, + 6) double: double precision (64-bit) IEEE 754 floating-point number, and + 7) string: Unicode character sequence.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectvalue 
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      PrimitiveType(java.lang.Object objectInstance) 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectget() +
      This method returns the value of PrimitiveType.
      +
      voidset(java.lang.Boolean objectInstance) +
      This method sets the value of PrimitiveType.
      +
      voidset(java.lang.Double objectInstance) +
      This method sets the value of PrimitiveType.
      +
      voidset(java.lang.Float objectInstance) +
      This method sets the value of PrimitiveType.
      +
      voidset(java.lang.Integer objectInstance) +
      This method sets the value of PrimitiveType.
      +
      voidset(java.lang.Long objectInstance) +
      This method sets the value of PrimitiveType.
      +
      voidset(java.lang.String objectInstance) +
      This method sets the value of PrimitiveType.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        value

        +
        java.lang.Object value
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        PrimitiveType

        +
        public PrimitiveType(java.lang.Object objectInstance)
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        set

        +
        public void set(java.lang.Boolean objectInstance)
        +
        This method sets the value of PrimitiveType.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of PrimitiveType, and is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        set

        +
        public void set(java.lang.Integer objectInstance)
        +
        This method sets the value of PrimitiveType.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of PrimitiveType, and is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        set

        +
        public void set(java.lang.Long objectInstance)
        +
        This method sets the value of PrimitiveType.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of PrimitiveType, and is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        set

        +
        public void set(java.lang.Float objectInstance)
        +
        This method sets the value of PrimitiveType.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of PrimitiveType, and is a Float type.
        +
        +
        • +
      + + + +
        +
      • +

        set

        +
        public void set(java.lang.Double objectInstance)
        +
        This method sets the value of PrimitiveType.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of PrimitiveType, and is a Double type.
        +
        +
        • +
      + + + +
        +
      • +

        set

        +
        public void set(java.lang.String objectInstance)
        +
        This method sets the value of PrimitiveType.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of PrimitiveType, and is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        get

        +
        public java.lang.Object get()
        +
        This method returns the value of PrimitiveType.
        +
        +
        Returns:
        +
        This method will return the value of PrimitiveType, which is an Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/Process.html b/javadoc/org/commonwl/lang/Process.html new file mode 100644 index 00000000..ceda44f4 --- /dev/null +++ b/javadoc/org/commonwl/lang/Process.html @@ -0,0 +1,901 @@ + + + + + +Process + + + + + + + + +
+ + +
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+ + + + +
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+ + + +
+ +
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+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface Process

+
+
+
+ +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        outputs

        +
        static final OutputParameter[] outputs
        +
        Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.
        +
        • +
      + + + +
        +
      • +

        requirements

        +
        static final java.lang.Object requirements
        +
        Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
        +
        • +
      + + + +
        +
      • +

        cwlVersion

        +
        static final CWLVersion cwlVersion
        +
        CWL document version. Always required at the document root. Not required for a Process embedded inside another Process.
        +
        • +
      + + + +
        +
      • +

        inputs

        +
        static final InputParameter[] inputs
        +
        Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object.
        +
        • +
      + + + +
        +
      • +

        hints

        +
        static final Any hints
        +
        Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        static final java.lang.String doc
        +
        A long, human-readable description of this process object.
        +
        • +
      + + + +
        +
      • +

        id

        +
        static final java.lang.String id
        +
        The unique identifier for this process object.
        +
        • +
      + + + +
        +
      • +

        label

        +
        static final java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputs

        +
        void setoutputs(OutputParameter[] value)
        +
        This method sets the value of outputs.
        +
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputs

        +
        OutputParameter[] getoutputs()
        +
        This method returns the value of outputs.
        +
        +
        Returns:
        +
        This method will return the value of outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(StepInputExpressionRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a StepInputExpressionRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(MultipleInputFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a MultipleInputFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(SoftwareRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a SoftwareRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(SchemaDefRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a SchemaDefRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(InitialWorkDirRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a InitialWorkDirRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(EnvVarRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a EnvVarRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(DockerRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a DockerRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(ResourceRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a ResourceRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(InlineJavascriptRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a InlineJavascriptRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(ShellCommandRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a ShellCommandRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(ScatterFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a ScatterFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(SubworkflowFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a SubworkflowFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        getrequirements

        +
        java.lang.Object getrequirements()
        +
        This method returns the value of requirements.
        +
        +
        Returns:
        +
        This method will return the value of requirements, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setcwlVersion

        +
        void setcwlVersion(CWLVersion value)
        +
        This method sets the value of cwlVersion.
        +
        +
        Parameters:
        +
        value - will update cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        getcwlVersion

        +
        CWLVersion getcwlVersion()
        +
        This method returns the value of cwlVersion.
        +
        +
        Returns:
        +
        This method will return the value of cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputs

        +
        void setinputs(InputParameter[] value)
        +
        This method sets the value of inputs.
        +
        +
        Parameters:
        +
        value - will update inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getinputs

        +
        InputParameter[] getinputs()
        +
        This method returns the value of inputs.
        +
        +
        Returns:
        +
        This method will return the value of inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        sethints

        +
        void sethints(Any value)
        +
        This method sets the value of hints.
        +
        +
        Parameters:
        +
        value - will update hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        gethints

        +
        Any gethints()
        +
        This method returns the value of hints.
        +
        +
        Returns:
        +
        This method will return the value of hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
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    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/ProcessRequirement.html b/javadoc/org/commonwl/lang/ProcessRequirement.html new file mode 100644 index 00000000..7c38a9b4 --- /dev/null +++ b/javadoc/org/commonwl/lang/ProcessRequirement.html @@ -0,0 +1,170 @@ + + + + + +ProcessRequirement + + + + + + + + +
+ + +
Skip navigation links
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+ + + +
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    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
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  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Interface ProcessRequirement

+
+
+
+ +
+
+ + +
+ + +
Skip navigation links
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    +
  • Summary: 
    • +
  • Nested | 
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+
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  • Detail: 
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    • +
+
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/RecordField.html b/javadoc/org/commonwl/lang/RecordField.html new file mode 100644 index 00000000..d8711e09 --- /dev/null +++ b/javadoc/org/commonwl/lang/RecordField.html @@ -0,0 +1,632 @@ + + + + + +RecordField + + + + + + + + +
+ + +
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+ + + +
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+ + +
+ + +
+
org.commonwl.lang
+

Class RecordField

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.RecordField
      • +
    +
    • +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringdoc +
      A documentation string for this field
      +
      (package private) java.lang.Stringname +
      The name of the field
      +
      (package private) java.lang.Objecttype +
      The field type
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      RecordField() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Stringgetname() +
      This method returns the value of name.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetname(java.lang.String value) +
      This method sets the value of name.
      +
      voidsettype(ArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(ArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(EnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(EnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(PrimitiveType value) +
      This method sets the value of type.
      +
      voidsettype(PrimitiveType[] value) +
      This method sets the value of type.
      +
      voidsettype(RecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(RecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The name of the field
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A documentation string for this field
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        The field type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        RecordField

        +
        public RecordField()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
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+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/RecordSchema.html b/javadoc/org/commonwl/lang/RecordSchema.html new file mode 100644 index 00000000..eb36db2b --- /dev/null +++ b/javadoc/org/commonwl/lang/RecordSchema.html @@ -0,0 +1,239 @@ + + + + + +RecordSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Class RecordSchema

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.RecordSchema
      • +
    +
    • +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      RecordSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        RecordSchema

        +
        public RecordSchema()
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/ResourceRequirement.html b/javadoc/org/commonwl/lang/ResourceRequirement.html new file mode 100644 index 00000000..bea01659 --- /dev/null +++ b/javadoc/org/commonwl/lang/ResourceRequirement.html @@ -0,0 +1,1109 @@ + + + + + +ResourceRequirement + + + + + + + + +
+ + +
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+ + + + +
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+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class ResourceRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.ResourceRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class ResourceRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Specify basic hardware resource requirements.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'ResourceRequirement'
      +
      (package private) java.lang.ObjectcoresMax +
      Maximum reserved number of CPU cores
      +
      (package private) java.lang.ObjectcoresMin +
      Minimum reserved number of CPU cores
      +
      (package private) java.lang.ObjectoutdirMax +
      Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
      +
      (package private) java.lang.ObjectoutdirMin +
      Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
      +
      (package private) java.lang.ObjectramMax +
      Maximum reserved RAM in mebibytes (2**20)
      +
      (package private) java.lang.ObjectramMin +
      Minimum reserved RAM in mebibytes (2**20)
      +
      (package private) java.lang.ObjecttmpdirMax +
      Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
      +
      (package private) java.lang.ObjecttmpdirMin +
      Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      java.lang.ObjectgetcoresMax() +
      This method returns the value of coresMax.
      +
      java.lang.ObjectgetcoresMin() +
      This method returns the value of coresMin.
      +
      java.lang.ObjectgetoutdirMax() +
      This method returns the value of outdirMax.
      +
      java.lang.ObjectgetoutdirMin() +
      This method returns the value of outdirMin.
      +
      java.lang.ObjectgetramMax() +
      This method returns the value of ramMax.
      +
      java.lang.ObjectgetramMin() +
      This method returns the value of ramMin.
      +
      java.lang.ObjectgettmpdirMax() +
      This method returns the value of tmpdirMax.
      +
      java.lang.ObjectgettmpdirMin() +
      This method returns the value of tmpdirMin.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsetcoresMax(Expression value) +
      This method sets the value of coresMax.
      +
      voidsetcoresMax(java.lang.Integer value) +
      This method sets the value of coresMax.
      +
      voidsetcoresMax(java.lang.String value) +
      This method sets the value of coresMax.
      +
      voidsetcoresMin(Expression value) +
      This method sets the value of coresMin.
      +
      voidsetcoresMin(java.lang.Long value) +
      This method sets the value of coresMin.
      +
      voidsetcoresMin(java.lang.String value) +
      This method sets the value of coresMin.
      +
      voidsetoutdirMax(Expression value) +
      This method sets the value of outdirMax.
      +
      voidsetoutdirMax(java.lang.Long value) +
      This method sets the value of outdirMax.
      +
      voidsetoutdirMax(java.lang.String value) +
      This method sets the value of outdirMax.
      +
      voidsetoutdirMin(Expression value) +
      This method sets the value of outdirMin.
      +
      voidsetoutdirMin(java.lang.Long value) +
      This method sets the value of outdirMin.
      +
      voidsetoutdirMin(java.lang.String value) +
      This method sets the value of outdirMin.
      +
      voidsetramMax(Expression value) +
      This method sets the value of ramMax.
      +
      voidsetramMax(java.lang.Long value) +
      This method sets the value of ramMax.
      +
      voidsetramMax(java.lang.String value) +
      This method sets the value of ramMax.
      +
      voidsetramMin(Expression value) +
      This method sets the value of ramMin.
      +
      voidsetramMin(java.lang.Long value) +
      This method sets the value of ramMin.
      +
      voidsetramMin(java.lang.String value) +
      This method sets the value of ramMin.
      +
      voidsettmpdirMax(Expression value) +
      This method sets the value of tmpdirMax.
      +
      voidsettmpdirMax(java.lang.Long value) +
      This method sets the value of tmpdirMax.
      +
      voidsettmpdirMax(java.lang.String value) +
      This method sets the value of tmpdirMax.
      +
      voidsettmpdirMin(Expression value) +
      This method sets the value of tmpdirMin.
      +
      voidsettmpdirMin(java.lang.Long value) +
      This method sets the value of tmpdirMin.
      +
      voidsettmpdirMin(java.lang.String value) +
      This method sets the value of tmpdirMin.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        tmpdirMin

        +
        java.lang.Object tmpdirMin
        +
        Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
        +
        • +
      + + + +
        +
      • +

        tmpdirMax

        +
        java.lang.Object tmpdirMax
        +
        Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
        +
        • +
      + + + +
        +
      • +

        ramMax

        +
        java.lang.Object ramMax
        +
        Maximum reserved RAM in mebibytes (2**20)
        +
        • +
      + + + +
        +
      • +

        coresMax

        +
        java.lang.Object coresMax
        +
        Maximum reserved number of CPU cores
        +
        • +
      + + + +
        +
      • +

        ramMin

        +
        java.lang.Object ramMin
        +
        Minimum reserved RAM in mebibytes (2**20)
        +
        • +
      + + + +
        +
      • +

        outdirMin

        +
        java.lang.Object outdirMin
        +
        Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
        +
        • +
      + + + +
        +
      • +

        coresMin

        +
        java.lang.Object coresMin
        +
        Minimum reserved number of CPU cores
        +
        • +
      + + + +
        +
      • +

        outdirMax

        +
        java.lang.Object outdirMax
        +
        Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'ResourceRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        ResourceRequirement

        +
        public ResourceRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        settmpdirMin

        +
        public void settmpdirMin(Expression value)
        +
        This method sets the value of tmpdirMin.
        +
        +
        Parameters:
        +
        value - will update tmpdirMin, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        settmpdirMin

        +
        public void settmpdirMin(java.lang.String value)
        +
        This method sets the value of tmpdirMin.
        +
        +
        Parameters:
        +
        value - will update tmpdirMin, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settmpdirMin

        +
        public void settmpdirMin(java.lang.Long value)
        +
        This method sets the value of tmpdirMin.
        +
        +
        Parameters:
        +
        value - will update tmpdirMin, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        gettmpdirMin

        +
        public java.lang.Object gettmpdirMin()
        +
        This method returns the value of tmpdirMin.
        +
        +
        Returns:
        +
        This method will return the value of tmpdirMin, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        settmpdirMax

        +
        public void settmpdirMax(Expression value)
        +
        This method sets the value of tmpdirMax.
        +
        +
        Parameters:
        +
        value - will update tmpdirMax, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        settmpdirMax

        +
        public void settmpdirMax(java.lang.String value)
        +
        This method sets the value of tmpdirMax.
        +
        +
        Parameters:
        +
        value - will update tmpdirMax, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settmpdirMax

        +
        public void settmpdirMax(java.lang.Long value)
        +
        This method sets the value of tmpdirMax.
        +
        +
        Parameters:
        +
        value - will update tmpdirMax, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        gettmpdirMax

        +
        public java.lang.Object gettmpdirMax()
        +
        This method returns the value of tmpdirMax.
        +
        +
        Returns:
        +
        This method will return the value of tmpdirMax, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setramMax

        +
        public void setramMax(Expression value)
        +
        This method sets the value of ramMax.
        +
        +
        Parameters:
        +
        value - will update ramMax, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        setramMax

        +
        public void setramMax(java.lang.String value)
        +
        This method sets the value of ramMax.
        +
        +
        Parameters:
        +
        value - will update ramMax, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setramMax

        +
        public void setramMax(java.lang.Long value)
        +
        This method sets the value of ramMax.
        +
        +
        Parameters:
        +
        value - will update ramMax, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        getramMax

        +
        public java.lang.Object getramMax()
        +
        This method returns the value of ramMax.
        +
        +
        Returns:
        +
        This method will return the value of ramMax, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setcoresMax

        +
        public void setcoresMax(Expression value)
        +
        This method sets the value of coresMax.
        +
        +
        Parameters:
        +
        value - will update coresMax, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        setcoresMax

        +
        public void setcoresMax(java.lang.String value)
        +
        This method sets the value of coresMax.
        +
        +
        Parameters:
        +
        value - will update coresMax, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setcoresMax

        +
        public void setcoresMax(java.lang.Integer value)
        +
        This method sets the value of coresMax.
        +
        +
        Parameters:
        +
        value - will update coresMax, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        getcoresMax

        +
        public java.lang.Object getcoresMax()
        +
        This method returns the value of coresMax.
        +
        +
        Returns:
        +
        This method will return the value of coresMax, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setramMin

        +
        public void setramMin(Expression value)
        +
        This method sets the value of ramMin.
        +
        +
        Parameters:
        +
        value - will update ramMin, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        setramMin

        +
        public void setramMin(java.lang.String value)
        +
        This method sets the value of ramMin.
        +
        +
        Parameters:
        +
        value - will update ramMin, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setramMin

        +
        public void setramMin(java.lang.Long value)
        +
        This method sets the value of ramMin.
        +
        +
        Parameters:
        +
        value - will update ramMin, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        getramMin

        +
        public java.lang.Object getramMin()
        +
        This method returns the value of ramMin.
        +
        +
        Returns:
        +
        This method will return the value of ramMin, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutdirMin

        +
        public void setoutdirMin(Expression value)
        +
        This method sets the value of outdirMin.
        +
        +
        Parameters:
        +
        value - will update outdirMin, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutdirMin

        +
        public void setoutdirMin(java.lang.String value)
        +
        This method sets the value of outdirMin.
        +
        +
        Parameters:
        +
        value - will update outdirMin, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutdirMin

        +
        public void setoutdirMin(java.lang.Long value)
        +
        This method sets the value of outdirMin.
        +
        +
        Parameters:
        +
        value - will update outdirMin, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutdirMin

        +
        public java.lang.Object getoutdirMin()
        +
        This method returns the value of outdirMin.
        +
        +
        Returns:
        +
        This method will return the value of outdirMin, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setcoresMin

        +
        public void setcoresMin(Expression value)
        +
        This method sets the value of coresMin.
        +
        +
        Parameters:
        +
        value - will update coresMin, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        setcoresMin

        +
        public void setcoresMin(java.lang.String value)
        +
        This method sets the value of coresMin.
        +
        +
        Parameters:
        +
        value - will update coresMin, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setcoresMin

        +
        public void setcoresMin(java.lang.Long value)
        +
        This method sets the value of coresMin.
        +
        +
        Parameters:
        +
        value - will update coresMin, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        getcoresMin

        +
        public java.lang.Object getcoresMin()
        +
        This method returns the value of coresMin.
        +
        +
        Returns:
        +
        This method will return the value of coresMin, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutdirMax

        +
        public void setoutdirMax(Expression value)
        +
        This method sets the value of outdirMax.
        +
        +
        Parameters:
        +
        value - will update outdirMax, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutdirMax

        +
        public void setoutdirMax(java.lang.String value)
        +
        This method sets the value of outdirMax.
        +
        +
        Parameters:
        +
        value - will update outdirMax, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutdirMax

        +
        public void setoutdirMax(java.lang.Long value)
        +
        This method sets the value of outdirMax.
        +
        +
        Parameters:
        +
        value - will update outdirMax, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutdirMax

        +
        public java.lang.Object getoutdirMax()
        +
        This method returns the value of outdirMax.
        +
        +
        Returns:
        +
        This method will return the value of outdirMax, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/SaladEnumSchema.html b/javadoc/org/commonwl/lang/SaladEnumSchema.html new file mode 100644 index 00000000..2f788db3 --- /dev/null +++ b/javadoc/org/commonwl/lang/SaladEnumSchema.html @@ -0,0 +1,812 @@ + + + + + +SaladEnumSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SaladEnumSchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.StringdocAfter +
      Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
      +
      (package private) java.lang.ObjectdocChild +
      Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
      +
      (package private) java.lang.StringdocParent +
      Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
      +
      (package private) java.lang.BooleandocumentRoot +
      If true, indicates that the type is a valid at the document root.
      +
      (package private) java.lang.Objectextends_value +
      Indicates that this enum inherits symbols from a base enum.
      +
      (package private) java.lang.ObjectjsonldPredicate +
      Annotate this type with linked data context.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      SaladEnumSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.StringgetdocAfter() +
      This method returns the value of docAfter.
      +
      java.lang.ObjectgetdocChild() +
      This method returns the value of docChild.
      +
      java.lang.StringgetdocParent() +
      This method returns the value of docParent.
      +
      java.lang.BooleangetdocumentRoot() +
      This method returns the value of documentRoot.
      +
      java.lang.Objectgetextends() +
      This method returns the value of extends_value.
      +
      java.lang.ObjectgetjsonldPredicate() +
      This method returns the value of jsonldPredicate.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetdocAfter(java.lang.String value) +
      This method sets the value of docAfter.
      +
      voidsetdocChild(java.lang.String value) +
      This method sets the value of docChild.
      +
      voidsetdocChild(java.lang.String[] value) +
      This method sets the value of docChild.
      +
      voidsetdocParent(java.lang.String value) +
      This method sets the value of docParent.
      +
      voidsetdocumentRoot(java.lang.Boolean value) +
      This method sets the value of documentRoot.
      +
      voidsetextends(java.lang.String value) +
      This method sets the value of extends_value.
      +
      voidsetextends(java.lang.String[] value) +
      This method sets the value of extends_value.
      +
      voidsetjsonldPredicate(JsonldPredicate value) +
      This method sets the value of jsonldPredicate.
      +
      voidsetjsonldPredicate(java.lang.String value) +
      This method sets the value of jsonldPredicate.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        extends_value

        +
        java.lang.Object extends_value
        +
        Indicates that this enum inherits symbols from a base enum.
        +
        • +
      + + + +
        +
      • +

        documentRoot

        +
        java.lang.Boolean documentRoot
        +
        If true, indicates that the type is a valid at the document root. At least one type in a schema must be tagged with `documentRoot: true`.
        +
        • +
      + + + +
        +
      • +

        jsonldPredicate

        +
        java.lang.Object jsonldPredicate
        +
        Annotate this type with linked data context.
        +
        • +
      + + + +
        +
      • +

        docParent

        +
        java.lang.String docParent
        +
        Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        docAfter

        +
        java.lang.String docAfter
        +
        Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
        +
        • +
      + + + +
        +
      • +

        docChild

        +
        java.lang.Object docChild
        +
        Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SaladEnumSchema

        +
        public SaladEnumSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setextends

        +
        public void setextends(java.lang.String value)
        +
        This method sets the value of extends_value.
        +
        +
        Parameters:
        +
        value - will update extends_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setextends

        +
        public void setextends(java.lang.String[] value)
        +
        This method sets the value of extends_value.
        +
        +
        Parameters:
        +
        value - will update extends_value, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getextends

        +
        public java.lang.Object getextends()
        +
        This method returns the value of extends_value.
        +
        +
        Returns:
        +
        This method will return the value of extends_value, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocumentRoot

        +
        public void setdocumentRoot(java.lang.Boolean value)
        +
        This method sets the value of documentRoot.
        +
        +
        Specified by:
        +
        setdocumentRoot in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update documentRoot, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocumentRoot

        +
        public java.lang.Boolean getdocumentRoot()
        +
        This method returns the value of documentRoot.
        +
        +
        Specified by:
        +
        getdocumentRoot in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of documentRoot, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        public void setjsonldPredicate(java.lang.String value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Specified by:
        +
        setjsonldPredicate in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        public void setjsonldPredicate(JsonldPredicate value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Specified by:
        +
        setjsonldPredicate in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a JsonldPredicate type.
        +
        +
        • +
      + + + +
        +
      • +

        getjsonldPredicate

        +
        public java.lang.Object getjsonldPredicate()
        +
        This method returns the value of jsonldPredicate.
        +
        +
        Specified by:
        +
        getjsonldPredicate in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of jsonldPredicate, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocParent

        +
        public void setdocParent(java.lang.String value)
        +
        This method sets the value of docParent.
        +
        +
        Specified by:
        +
        setdocParent in interface DocType
        +
        Specified by:
        +
        setdocParent in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocParent

        +
        public java.lang.String getdocParent()
        +
        This method returns the value of docParent.
        +
        +
        Specified by:
        +
        getdocParent in interface DocType
        +
        Specified by:
        +
        getdocParent in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Specified by:
        +
        setdoc in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Specified by:
        +
        setdoc in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface DocType
        +
        Specified by:
        +
        getdoc in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocAfter

        +
        public void setdocAfter(java.lang.String value)
        +
        This method sets the value of docAfter.
        +
        +
        Specified by:
        +
        setdocAfter in interface DocType
        +
        Specified by:
        +
        setdocAfter in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocAfter

        +
        public java.lang.String getdocAfter()
        +
        This method returns the value of docAfter.
        +
        +
        Specified by:
        +
        getdocAfter in interface DocType
        +
        Specified by:
        +
        getdocAfter in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        public void setdocChild(java.lang.String value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Specified by:
        +
        setdocChild in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docChild, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        public void setdocChild(java.lang.String[] value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Specified by:
        +
        setdocChild in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docChild, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdocChild

        +
        public java.lang.Object getdocChild()
        +
        This method returns the value of docChild.
        +
        +
        Specified by:
        +
        getdocChild in interface DocType
        +
        Specified by:
        +
        getdocChild in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of docChild, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/SaladRecordField.html b/javadoc/org/commonwl/lang/SaladRecordField.html new file mode 100644 index 00000000..9d47b60a --- /dev/null +++ b/javadoc/org/commonwl/lang/SaladRecordField.html @@ -0,0 +1,739 @@ + + + + + +SaladRecordField + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SaladRecordField

+
+
+ +
+
    +
  • +
    +
    +
    public class SaladRecordField
+extends RecordField
    +
    A field of a record.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringdoc +
      A documentation string for this field
      +
      (package private) java.lang.ObjectjsonldPredicate +
      Annotate this type with linked data context.
      +
      (package private) java.lang.Stringname +
      The name of the field
      +
      (package private) java.lang.Objecttype +
      The field type
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      SaladRecordField() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetdoc() +
      This method returns the value of doc.
      +
      java.lang.ObjectgetjsonldPredicate() +
      This method returns the value of jsonldPredicate.
      +
      java.lang.Stringgetname() +
      This method returns the value of name.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetjsonldPredicate(JsonldPredicate value) +
      This method sets the value of jsonldPredicate.
      +
      voidsetjsonldPredicate(java.lang.String value) +
      This method sets the value of jsonldPredicate.
      +
      voidsetname(java.lang.String value) +
      This method sets the value of name.
      +
      voidsettype(ArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(ArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(EnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(EnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(PrimitiveType value) +
      This method sets the value of type.
      +
      voidsettype(PrimitiveType[] value) +
      This method sets the value of type.
      +
      voidsettype(RecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(RecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        jsonldPredicate

        +
        java.lang.Object jsonldPredicate
        +
        Annotate this type with linked data context.
        +
        • +
      + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The name of the field
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A documentation string for this field
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        The field type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SaladRecordField

        +
        public SaladRecordField()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setjsonldPredicate

        +
        public void setjsonldPredicate(java.lang.String value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        public void setjsonldPredicate(JsonldPredicate value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a JsonldPredicate type.
        +
        +
        • +
      + + + +
        +
      • +

        getjsonldPredicate

        +
        public java.lang.Object getjsonldPredicate()
        +
        This method returns the value of jsonldPredicate.
        +
        +
        Returns:
        +
        This method will return the value of jsonldPredicate, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Overrides:
        +
        setname in class RecordField
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Overrides:
        +
        getname in class RecordField
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Overrides:
        +
        setdoc in class RecordField
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Overrides:
        +
        getdoc in class RecordField
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Overrides:
        +
        gettype in class RecordField
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/SaladRecordSchema.html b/javadoc/org/commonwl/lang/SaladRecordSchema.html new file mode 100644 index 00000000..7129723d --- /dev/null +++ b/javadoc/org/commonwl/lang/SaladRecordSchema.html @@ -0,0 +1,983 @@ + + + + + +SaladRecordSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SaladRecordSchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Booleanabstract_value +
      If true, this record is abstract and may be used as a base for other records, but is not valid on its own.
      +
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.StringdocAfter +
      Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
      +
      (package private) java.lang.ObjectdocChild +
      Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
      +
      (package private) java.lang.StringdocParent +
      Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
      +
      (package private) java.lang.BooleandocumentRoot +
      If true, indicates that the type is a valid at the document root.
      +
      (package private) java.lang.Objectextends_value +
      Indicates that this record inherits fields from one or more base records.
      +
      (package private) java.lang.ObjectjsonldPredicate +
      Annotate this type with linked data context.
      +
      (package private) java.lang.Stringname +
      The identifier for this type
      +
      (package private) SpecializeDef[]specialize +
      Only applies if `extends` is declared.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      SaladRecordSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Booleangetabstract() +
      This method returns the value of abstract_value.
      +
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.StringgetdocAfter() +
      This method returns the value of docAfter.
      +
      java.lang.ObjectgetdocChild() +
      This method returns the value of docChild.
      +
      java.lang.StringgetdocParent() +
      This method returns the value of docParent.
      +
      java.lang.BooleangetdocumentRoot() +
      This method returns the value of documentRoot.
      +
      java.lang.Objectgetextends() +
      This method returns the value of extends_value.
      +
      java.lang.ObjectgetjsonldPredicate() +
      This method returns the value of jsonldPredicate.
      +
      java.lang.Stringgetname() +
      This method returns the value of name.
      +
      SpecializeDef[]getspecialize() +
      This method returns the value of specialize.
      +
      voidsetabstract(java.lang.Boolean value) +
      This method sets the value of abstract_value.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetdocAfter(java.lang.String value) +
      This method sets the value of docAfter.
      +
      voidsetdocChild(java.lang.String value) +
      This method sets the value of docChild.
      +
      voidsetdocChild(java.lang.String[] value) +
      This method sets the value of docChild.
      +
      voidsetdocParent(java.lang.String value) +
      This method sets the value of docParent.
      +
      voidsetdocumentRoot(java.lang.Boolean value) +
      This method sets the value of documentRoot.
      +
      voidsetextends(java.lang.String value) +
      This method sets the value of extends_value.
      +
      voidsetextends(java.lang.String[] value) +
      This method sets the value of extends_value.
      +
      voidsetjsonldPredicate(JsonldPredicate value) +
      This method sets the value of jsonldPredicate.
      +
      voidsetjsonldPredicate(java.lang.String value) +
      This method sets the value of jsonldPredicate.
      +
      voidsetname(java.lang.String value) +
      This method sets the value of name.
      +
      voidsetspecialize(SpecializeDef[] value) +
      This method sets the value of specialize.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        extends_value

        +
        java.lang.Object extends_value
        +
        Indicates that this record inherits fields from one or more base records.
        +
        • +
      + + + +
        +
      • +

        abstract_value

        +
        java.lang.Boolean abstract_value
        +
        If true, this record is abstract and may be used as a base for other records, but is not valid on its own.
        +
        • +
      + + + +
        +
      • +

        specialize

        +
        SpecializeDef[] specialize
        +
        Only applies if `extends` is declared. Apply type specialization using the base record as a template. For each field inherited from the base record, replace any instance of the type `specializeFrom` with `specializeTo`.
        +
        • +
      + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The identifier for this type
        +
        • +
      + + + +
        +
      • +

        documentRoot

        +
        java.lang.Boolean documentRoot
        +
        If true, indicates that the type is a valid at the document root. At least one type in a schema must be tagged with `documentRoot: true`.
        +
        • +
      + + + +
        +
      • +

        jsonldPredicate

        +
        java.lang.Object jsonldPredicate
        +
        Annotate this type with linked data context.
        +
        • +
      + + + +
        +
      • +

        docParent

        +
        java.lang.String docParent
        +
        Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        docAfter

        +
        java.lang.String docAfter
        +
        Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
        +
        • +
      + + + +
        +
      • +

        docChild

        +
        java.lang.Object docChild
        +
        Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SaladRecordSchema

        +
        public SaladRecordSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setextends

        +
        public void setextends(java.lang.String value)
        +
        This method sets the value of extends_value.
        +
        +
        Parameters:
        +
        value - will update extends_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setextends

        +
        public void setextends(java.lang.String[] value)
        +
        This method sets the value of extends_value.
        +
        +
        Parameters:
        +
        value - will update extends_value, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getextends

        +
        public java.lang.Object getextends()
        +
        This method returns the value of extends_value.
        +
        +
        Returns:
        +
        This method will return the value of extends_value, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setabstract

        +
        public void setabstract(java.lang.Boolean value)
        +
        This method sets the value of abstract_value.
        +
        +
        Parameters:
        +
        value - will update abstract_value, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getabstract

        +
        public java.lang.Boolean getabstract()
        +
        This method returns the value of abstract_value.
        +
        +
        Returns:
        +
        This method will return the value of abstract_value, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setspecialize

        +
        public void setspecialize(SpecializeDef[] value)
        +
        This method sets the value of specialize.
        +
        +
        Parameters:
        +
        value - will update specialize, which is a SpecializeDef array.
        +
        +
        • +
      + + + +
        +
      • +

        getspecialize

        +
        public SpecializeDef[] getspecialize()
        +
        This method returns the value of specialize.
        +
        +
        Returns:
        +
        This method will return the value of specialize, which is a SpecializeDef array.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Specified by:
        +
        setname in interface NamedType
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Specified by:
        +
        getname in interface NamedType
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocumentRoot

        +
        public void setdocumentRoot(java.lang.Boolean value)
        +
        This method sets the value of documentRoot.
        +
        +
        Specified by:
        +
        setdocumentRoot in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update documentRoot, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocumentRoot

        +
        public java.lang.Boolean getdocumentRoot()
        +
        This method returns the value of documentRoot.
        +
        +
        Specified by:
        +
        getdocumentRoot in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of documentRoot, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        public void setjsonldPredicate(java.lang.String value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Specified by:
        +
        setjsonldPredicate in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        public void setjsonldPredicate(JsonldPredicate value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Specified by:
        +
        setjsonldPredicate in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a JsonldPredicate type.
        +
        +
        • +
      + + + +
        +
      • +

        getjsonldPredicate

        +
        public java.lang.Object getjsonldPredicate()
        +
        This method returns the value of jsonldPredicate.
        +
        +
        Specified by:
        +
        getjsonldPredicate in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of jsonldPredicate, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocParent

        +
        public void setdocParent(java.lang.String value)
        +
        This method sets the value of docParent.
        +
        +
        Specified by:
        +
        setdocParent in interface DocType
        +
        Specified by:
        +
        setdocParent in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocParent

        +
        public java.lang.String getdocParent()
        +
        This method returns the value of docParent.
        +
        +
        Specified by:
        +
        getdocParent in interface DocType
        +
        Specified by:
        +
        getdocParent in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Specified by:
        +
        setdoc in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Specified by:
        +
        setdoc in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface DocType
        +
        Specified by:
        +
        getdoc in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocAfter

        +
        public void setdocAfter(java.lang.String value)
        +
        This method sets the value of docAfter.
        +
        +
        Specified by:
        +
        setdocAfter in interface DocType
        +
        Specified by:
        +
        setdocAfter in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocAfter

        +
        public java.lang.String getdocAfter()
        +
        This method returns the value of docAfter.
        +
        +
        Specified by:
        +
        getdocAfter in interface DocType
        +
        Specified by:
        +
        getdocAfter in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        public void setdocChild(java.lang.String value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Specified by:
        +
        setdocChild in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docChild, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        public void setdocChild(java.lang.String[] value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Specified by:
        +
        setdocChild in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docChild, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdocChild

        +
        public java.lang.Object getdocChild()
        +
        This method returns the value of docChild.
        +
        +
        Specified by:
        +
        getdocChild in interface DocType
        +
        Specified by:
        +
        getdocChild in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of docChild, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/ScatterFeatureRequirement.html b/javadoc/org/commonwl/lang/ScatterFeatureRequirement.html new file mode 100644 index 00000000..6b8b7002 --- /dev/null +++ b/javadoc/org/commonwl/lang/ScatterFeatureRequirement.html @@ -0,0 +1,341 @@ + + + + + +ScatterFeatureRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class ScatterFeatureRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.ScatterFeatureRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class ScatterFeatureRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Indicates that the workflow platform must support the `scatter` and `scatterMethod` fields of [WorkflowStep](#WorkflowStep).
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'ScatterFeatureRequirement'
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'ScatterFeatureRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        ScatterFeatureRequirement

        +
        public ScatterFeatureRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/ScatterMethod.html b/javadoc/org/commonwl/lang/ScatterMethod.html new file mode 100644 index 00000000..88d0da42 --- /dev/null +++ b/javadoc/org/commonwl/lang/ScatterMethod.html @@ -0,0 +1,352 @@ + + + + + +ScatterMethod + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Enum ScatterMethod

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<ScatterMethod>
      • +
    • +
        +
      • org.commonwl.lang.ScatterMethod
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<ScatterMethod>
    +
    +
    +
    +
    public enum ScatterMethod
+extends java.lang.Enum<ScatterMethod>
    +
    The scatter method, as described in [workflow step scatter](#WorkflowStep).
    +
    • +
+
+
+
    +
  • + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Static Methods Concrete Methods 
      Modifier and TypeMethod and Description
      static ScatterMethodvalueOf(java.lang.String name) +
      Returns the enum constant of this type with the specified name.
      +
      static ScatterMethod[]values() +
      Returns an array containing the constants of this enum type, in +the order they are declared.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Enum

        +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
        • +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +getClass, notify, notifyAll, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Enum Constant Detail

      + + + +
        +
      • +

        dotproduct

        +
        public static final ScatterMethod dotproduct
        +
        • +
      + + + +
        +
      • +

        nested_crossproduct

        +
        public static final ScatterMethod nested_crossproduct
        +
        • +
      + + + +
        +
      • +

        flat_crossproduct

        +
        public static final ScatterMethod flat_crossproduct
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static ScatterMethod[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (ScatterMethod c : ScatterMethod.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static ScatterMethod valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/SchemaBase.html b/javadoc/org/commonwl/lang/SchemaBase.html new file mode 100644 index 00000000..99ad6bba --- /dev/null +++ b/javadoc/org/commonwl/lang/SchemaBase.html @@ -0,0 +1,293 @@ + + + + + +SchemaBase + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface SchemaBase

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        static final java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/SchemaDefRequirement.html b/javadoc/org/commonwl/lang/SchemaDefRequirement.html new file mode 100644 index 00000000..83ca8426 --- /dev/null +++ b/javadoc/org/commonwl/lang/SchemaDefRequirement.html @@ -0,0 +1,437 @@ + + + + + +SchemaDefRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SchemaDefRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.SchemaDefRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class SchemaDefRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    This field consists of an array of type definitions which must be used when interpreting the `inputs` and `outputs` fields. When a `type` field contain a IRI, the implementation must check if the type is defined in `schemaDefs` and use that definition. If the type is not found in `schemaDefs`, it is an error. The entries in `schemaDefs` must be processed in the order listed such that later schema definitions may refer to earlier schema definitions.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'SchemaDefRequirement'
      +
      (package private) java.lang.Objecttypes +
      The list of type definitions.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      java.lang.Objectgettypes() +
      This method returns the value of types.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsettypes(InputArraySchema[] value) +
      This method sets the value of types.
      +
      voidsettypes(InputEnumSchema[] value) +
      This method sets the value of types.
      +
      voidsettypes(InputRecordSchema[] value) +
      This method sets the value of types.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        types

        +
        java.lang.Object types
        +
        The list of type definitions.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'SchemaDefRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SchemaDefRequirement

        +
        public SchemaDefRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        settypes

        +
        public void settypes(InputEnumSchema[] value)
        +
        This method sets the value of types.
        +
        +
        Parameters:
        +
        value - will update types, which is a InputEnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settypes

        +
        public void settypes(InputArraySchema[] value)
        +
        This method sets the value of types.
        +
        +
        Parameters:
        +
        value - will update types, which is a InputArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settypes

        +
        public void settypes(InputRecordSchema[] value)
        +
        This method sets the value of types.
        +
        +
        Parameters:
        +
        value - will update types, which is a InputRecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettypes

        +
        public java.lang.Object gettypes()
        +
        This method returns the value of types.
        +
        +
        Returns:
        +
        This method will return the value of types, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/SchemaDefinedType.html b/javadoc/org/commonwl/lang/SchemaDefinedType.html new file mode 100644 index 00000000..d6fa1180 --- /dev/null +++ b/javadoc/org/commonwl/lang/SchemaDefinedType.html @@ -0,0 +1,655 @@ + + + + + +SchemaDefinedType + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface SchemaDefinedType

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      static java.lang.StringdocAfter +
      Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
      +
      static java.lang.ObjectdocChild +
      Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
      +
      static java.lang.StringdocParent +
      Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
      +
      static java.lang.BooleandocumentRoot +
      If true, indicates that the type is a valid at the document root.
      +
      static java.lang.ObjectjsonldPredicate +
      Annotate this type with linked data context.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.StringgetdocAfter() +
      This method returns the value of docAfter.
      +
      java.lang.ObjectgetdocChild() +
      This method returns the value of docChild.
      +
      java.lang.StringgetdocParent() +
      This method returns the value of docParent.
      +
      java.lang.BooleangetdocumentRoot() +
      This method returns the value of documentRoot.
      +
      java.lang.ObjectgetjsonldPredicate() +
      This method returns the value of jsonldPredicate.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetdocAfter(java.lang.String value) +
      This method sets the value of docAfter.
      +
      voidsetdocChild(java.lang.String value) +
      This method sets the value of docChild.
      +
      voidsetdocChild(java.lang.String[] value) +
      This method sets the value of docChild.
      +
      voidsetdocParent(java.lang.String value) +
      This method sets the value of docParent.
      +
      voidsetdocumentRoot(java.lang.Boolean value) +
      This method sets the value of documentRoot.
      +
      voidsetjsonldPredicate(JsonldPredicate value) +
      This method sets the value of jsonldPredicate.
      +
      voidsetjsonldPredicate(java.lang.String value) +
      This method sets the value of jsonldPredicate.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        documentRoot

        +
        static final java.lang.Boolean documentRoot
        +
        If true, indicates that the type is a valid at the document root. At least one type in a schema must be tagged with `documentRoot: true`.
        +
        • +
      + + + +
        +
      • +

        jsonldPredicate

        +
        static final java.lang.Object jsonldPredicate
        +
        Annotate this type with linked data context.
        +
        • +
      + + + +
        +
      • +

        docParent

        +
        static final java.lang.String docParent
        +
        Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        static final java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        docAfter

        +
        static final java.lang.String docAfter
        +
        Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
        +
        • +
      + + + +
        +
      • +

        docChild

        +
        static final java.lang.Object docChild
        +
        Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setdocumentRoot

        +
        void setdocumentRoot(java.lang.Boolean value)
        +
        This method sets the value of documentRoot.
        +
        +
        Parameters:
        +
        value - will update documentRoot, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocumentRoot

        +
        java.lang.Boolean getdocumentRoot()
        +
        This method returns the value of documentRoot.
        +
        +
        Returns:
        +
        This method will return the value of documentRoot, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        void setjsonldPredicate(java.lang.String value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        void setjsonldPredicate(JsonldPredicate value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a JsonldPredicate type.
        +
        +
        • +
      + + + +
        +
      • +

        getjsonldPredicate

        +
        java.lang.Object getjsonldPredicate()
        +
        This method returns the value of jsonldPredicate.
        +
        +
        Returns:
        +
        This method will return the value of jsonldPredicate, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocParent

        +
        void setdocParent(java.lang.String value)
        +
        This method sets the value of docParent.
        +
        +
        Specified by:
        +
        setdocParent in interface DocType
        +
        Parameters:
        +
        value - will update docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocParent

        +
        java.lang.String getdocParent()
        +
        This method returns the value of docParent.
        +
        +
        Specified by:
        +
        getdocParent in interface DocType
        +
        Returns:
        +
        This method will return the value of docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface DocType
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocAfter

        +
        void setdocAfter(java.lang.String value)
        +
        This method sets the value of docAfter.
        +
        +
        Specified by:
        +
        setdocAfter in interface DocType
        +
        Parameters:
        +
        value - will update docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocAfter

        +
        java.lang.String getdocAfter()
        +
        This method returns the value of docAfter.
        +
        +
        Specified by:
        +
        getdocAfter in interface DocType
        +
        Returns:
        +
        This method will return the value of docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        void setdocChild(java.lang.String value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Parameters:
        +
        value - will update docChild, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        void setdocChild(java.lang.String[] value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Parameters:
        +
        value - will update docChild, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdocChild

        +
        java.lang.Object getdocChild()
        +
        This method returns the value of docChild.
        +
        +
        Specified by:
        +
        getdocChild in interface DocType
        +
        Returns:
        +
        This method will return the value of docChild, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/ShellCommandRequirement.html b/javadoc/org/commonwl/lang/ShellCommandRequirement.html new file mode 100644 index 00000000..61423e28 --- /dev/null +++ b/javadoc/org/commonwl/lang/ShellCommandRequirement.html @@ -0,0 +1,341 @@ + + + + + +ShellCommandRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class ShellCommandRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.ShellCommandRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class ShellCommandRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Modify the behavior of CommandLineTool to generate a single string containing a shell command line. Each item in the argument list must be joined into a string separated by single spaces and quoted to prevent intepretation by the shell, unless `CommandLineBinding` for that argument contains `shellQuote: false`. If `shellQuote: false` is specified, the argument is joined into the command string without quoting, which allows the use of shell metacharacters such as `|` for pipes.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'ShellCommandRequirement'
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'ShellCommandRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        ShellCommandRequirement

        +
        public ShellCommandRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/Sink.html b/javadoc/org/commonwl/lang/Sink.html new file mode 100644 index 00000000..bf77ff26 --- /dev/null +++ b/javadoc/org/commonwl/lang/Sink.html @@ -0,0 +1,365 @@ + + + + + +Sink + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface Sink

+
+
+
+
    +
  • +
    +
    All Known Implementing Classes:
    +
    WorkflowStepInput
    +
    +
    +
    +
    public interface Sink
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static LinkMergeMethodlinkMerge +
      The method to use to merge multiple inbound links into a single array.
      +
      static java.lang.Objectsource +
      Specifies one or more workflow parameters that will provide input to the underlying step parameter.
      +
      +
      • +
    + + +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        linkMerge

        +
        static final LinkMergeMethod linkMerge
        +
        The method to use to merge multiple inbound links into a single array. If not specified, the default method is merge_nested.
        +
        • +
      + + + +
        +
      • +

        source

        +
        static final java.lang.Object source
        +
        Specifies one or more workflow parameters that will provide input to the underlying step parameter.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlinkMerge

        +
        void setlinkMerge(LinkMergeMethod value)
        +
        This method sets the value of linkMerge.
        +
        +
        Parameters:
        +
        value - will update linkMerge, which is a LinkMergeMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        getlinkMerge

        +
        LinkMergeMethod getlinkMerge()
        +
        This method returns the value of linkMerge.
        +
        +
        Returns:
        +
        This method will return the value of linkMerge, which is a LinkMergeMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        setsource

        +
        void setsource(java.lang.String value)
        +
        This method sets the value of source.
        +
        +
        Parameters:
        +
        value - will update source, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsource

        +
        void setsource(java.lang.String[] value)
        +
        This method sets the value of source.
        +
        +
        Parameters:
        +
        value - will update source, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getsource

        +
        java.lang.Object getsource()
        +
        This method returns the value of source.
        +
        +
        Returns:
        +
        This method will return the value of source, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/SoftwarePackage.html b/javadoc/org/commonwl/lang/SoftwarePackage.html new file mode 100644 index 00000000..016d2cd3 --- /dev/null +++ b/javadoc/org/commonwl/lang/SoftwarePackage.html @@ -0,0 +1,447 @@ + + + + + +SoftwarePackage + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SoftwarePackage

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.SoftwarePackage
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class SoftwarePackage
+extends java.lang.Object
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringpackage_value +
      The common name of the software to be configured.
      +
      (package private) java.lang.Stringspecs +
      Must be one or more IRIs identifying resources for installing or enabling the software.
      +
      (package private) java.lang.Stringversion +
      The (optional) version of the software to configured.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      SoftwarePackage() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetpackage() +
      This method returns the value of package_value.
      +
      java.lang.Stringgetspecs() +
      This method returns the value of specs.
      +
      java.lang.Stringgetversion() +
      This method returns the value of version.
      +
      voidsetpackage(java.lang.String value) +
      This method sets the value of package_value.
      +
      voidsetspecs(java.lang.String value) +
      This method sets the value of specs.
      +
      voidsetversion(java.lang.String value) +
      This method sets the value of version.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        specs

        +
        java.lang.String specs
        +
        Must be one or more IRIs identifying resources for installing or enabling the software. Implementations may provide resolvers which map well-known software spec IRIs to some configuration action. For example, an IRI `https://packages.debian.org/jessie/bowtie` could be resolved with `apt-get install bowtie`. An IRI `https://anaconda.org/bioconda/bowtie` could be resolved with `conda install -c bioconda bowtie`. Tools may also provide IRIs to index entries such as [RRID](http://www.identifiers.org/rrid/), such as `http://identifiers.org/rrid/RRID:SCR_005476`
        +
        • +
      + + + +
        +
      • +

        package_value

        +
        java.lang.String package_value
        +
        The common name of the software to be configured.
        +
        • +
      + + + +
        +
      • +

        version

        +
        java.lang.String version
        +
        The (optional) version of the software to configured.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SoftwarePackage

        +
        public SoftwarePackage()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setspecs

        +
        public void setspecs(java.lang.String value)
        +
        This method sets the value of specs.
        +
        +
        Parameters:
        +
        value - will update specs, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getspecs

        +
        public java.lang.String getspecs()
        +
        This method returns the value of specs.
        +
        +
        Returns:
        +
        This method will return the value of specs, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setpackage

        +
        public void setpackage(java.lang.String value)
        +
        This method sets the value of package_value.
        +
        +
        Parameters:
        +
        value - will update package_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getpackage

        +
        public java.lang.String getpackage()
        +
        This method returns the value of package_value.
        +
        +
        Returns:
        +
        This method will return the value of package_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setversion

        +
        public void setversion(java.lang.String value)
        +
        This method sets the value of version.
        +
        +
        Parameters:
        +
        value - will update version, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getversion

        +
        public java.lang.String getversion()
        +
        This method returns the value of version.
        +
        +
        Returns:
        +
        This method will return the value of version, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/SoftwareRequirement.html b/javadoc/org/commonwl/lang/SoftwareRequirement.html new file mode 100644 index 00000000..9905c532 --- /dev/null +++ b/javadoc/org/commonwl/lang/SoftwareRequirement.html @@ -0,0 +1,397 @@ + + + + + +SoftwareRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SoftwareRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.SoftwareRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class SoftwareRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    A list of software packages that should be configured in the environment of the defined process.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'SoftwareRequirement'
      +
      (package private) SoftwarePackagepackages +
      The list of software to be configured.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      SoftwarePackagegetpackages() +
      This method returns the value of packages.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsetpackages(SoftwarePackage value) +
      This method sets the value of packages.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        packages

        +
        SoftwarePackage packages
        +
        The list of software to be configured.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'SoftwareRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SoftwareRequirement

        +
        public SoftwareRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setpackages

        +
        public void setpackages(SoftwarePackage value)
        +
        This method sets the value of packages.
        +
        +
        Parameters:
        +
        value - will update packages, which is a SoftwarePackage type.
        +
        +
        • +
      + + + +
        +
      • +

        getpackages

        +
        public SoftwarePackage getpackages()
        +
        This method returns the value of packages.
        +
        +
        Returns:
        +
        This method will return the value of packages, which is a SoftwarePackage type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/SpecializeDef.html b/javadoc/org/commonwl/lang/SpecializeDef.html new file mode 100644 index 00000000..ded42823 --- /dev/null +++ b/javadoc/org/commonwl/lang/SpecializeDef.html @@ -0,0 +1,391 @@ + + + + + +SpecializeDef + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SpecializeDef

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.SpecializeDef
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class SpecializeDef
+extends java.lang.Object
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.StringspecializeFrom +
      The data type to be replaced
      +
      (package private) java.lang.StringspecializeTo +
      The new data type to replace with
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      SpecializeDef() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.StringgetspecializeFrom() +
      This method returns the value of specializeFrom.
      +
      java.lang.StringgetspecializeTo() +
      This method returns the value of specializeTo.
      +
      voidsetspecializeFrom(java.lang.String value) +
      This method sets the value of specializeFrom.
      +
      voidsetspecializeTo(java.lang.String value) +
      This method sets the value of specializeTo.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        specializeFrom

        +
        java.lang.String specializeFrom
        +
        The data type to be replaced
        +
        • +
      + + + +
        +
      • +

        specializeTo

        +
        java.lang.String specializeTo
        +
        The new data type to replace with
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SpecializeDef

        +
        public SpecializeDef()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setspecializeFrom

        +
        public void setspecializeFrom(java.lang.String value)
        +
        This method sets the value of specializeFrom.
        +
        +
        Parameters:
        +
        value - will update specializeFrom, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getspecializeFrom

        +
        public java.lang.String getspecializeFrom()
        +
        This method returns the value of specializeFrom.
        +
        +
        Returns:
        +
        This method will return the value of specializeFrom, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setspecializeTo

        +
        public void setspecializeTo(java.lang.String value)
        +
        This method sets the value of specializeTo.
        +
        +
        Parameters:
        +
        value - will update specializeTo, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getspecializeTo

        +
        public java.lang.String getspecializeTo()
        +
        This method returns the value of specializeTo.
        +
        +
        Returns:
        +
        This method will return the value of specializeTo, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/StepInputExpressionRequirement.html b/javadoc/org/commonwl/lang/StepInputExpressionRequirement.html new file mode 100644 index 00000000..5f18fb92 --- /dev/null +++ b/javadoc/org/commonwl/lang/StepInputExpressionRequirement.html @@ -0,0 +1,341 @@ + + + + + +StepInputExpressionRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class StepInputExpressionRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.StepInputExpressionRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class StepInputExpressionRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Indicate that the workflow platform must support the `valueFrom` field of [WorkflowStepInput](#WorkflowStepInput).
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'StepInputExpressionRequirement'
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'StepInputExpressionRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        StepInputExpressionRequirement

        +
        public StepInputExpressionRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/SubworkflowFeatureRequirement.html b/javadoc/org/commonwl/lang/SubworkflowFeatureRequirement.html new file mode 100644 index 00000000..872ea6d6 --- /dev/null +++ b/javadoc/org/commonwl/lang/SubworkflowFeatureRequirement.html @@ -0,0 +1,341 @@ + + + + + +SubworkflowFeatureRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SubworkflowFeatureRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.SubworkflowFeatureRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class SubworkflowFeatureRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Indicates that the workflow platform must support nested workflows in the `run` field of [WorkflowStep](#WorkflowStep).
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'SubworkflowFeatureRequirement'
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'SubworkflowFeatureRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SubworkflowFeatureRequirement

        +
        public SubworkflowFeatureRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/Workflow.html b/javadoc/org/commonwl/lang/Workflow.html new file mode 100644 index 00000000..fce0d399 --- /dev/null +++ b/javadoc/org/commonwl/lang/Workflow.html @@ -0,0 +1,1138 @@ + + + + + +Workflow + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class Workflow

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.Workflow
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Process
    +
    +
    +
    +
    public class Workflow
+extends java.lang.Object
+implements Process
    +
    A workflow describes a set of **steps** and the **dependencies** between those steps. When a step produces output that will be consumed by a second step, the first step is a dependency of the second step.
    +
    • +
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        • +
      + + + +
        +
      • +

        steps

        +
        WorkflowStep[] steps
        +
        The individual steps that make up the workflow. Each step is executed when all of its input data links are fufilled. An implementation may choose to execute the steps in a different order than listed and/or execute steps concurrently, provided that dependencies between steps are met.
        +
        • +
      + + + +
        +
      • +

        outputs

        +
        WorkflowOutputParameter[] outputs
        +
        Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.
        +
        • +
      + + + +
        +
      • +

        requirements

        +
        java.lang.Object requirements
        +
        Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
        +
        • +
      + + + +
        +
      • +

        cwlVersion

        +
        CWLVersion cwlVersion
        +
        CWL document version. Always required at the document root. Not required for a Process embedded inside another Process.
        +
        • +
      + + + +
        +
      • +

        inputs

        +
        InputParameter[] inputs
        +
        Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object.
        +
        • +
      + + + +
        +
      • +

        hints

        +
        Any hints
        +
        Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A long, human-readable description of this process object.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this process object.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        Workflow

        +
        public Workflow()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsteps

        +
        public void setsteps(WorkflowStep[] value)
        +
        This method sets the value of steps.
        +
        +
        Parameters:
        +
        value - will update steps, which is a WorkflowStep array.
        +
        +
        • +
      + + + +
        +
      • +

        getsteps

        +
        public WorkflowStep[] getsteps()
        +
        This method returns the value of steps.
        +
        +
        Returns:
        +
        This method will return the value of steps, which is a WorkflowStep array.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputs

        +
        public void setoutputs(WorkflowOutputParameter[] value)
        +
        This method sets the value of outputs.
        +
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputs

        +
        public void setoutputs(OutputParameter[] value)
        +
        This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
        +
        +
        Specified by:
        +
        setoutputs in interface Process
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputs

        +
        public WorkflowOutputParameter[] getoutputs()
        +
        This method returns the value of outputs.
        +
        +
        Specified by:
        +
        getoutputs in interface Process
        +
        Returns:
        +
        This method will return the value of outputs, which is a WorkflowOutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(StepInputExpressionRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a StepInputExpressionRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(MultipleInputFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a MultipleInputFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SoftwareRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SoftwareRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SchemaDefRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SchemaDefRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InitialWorkDirRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a InitialWorkDirRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(EnvVarRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a EnvVarRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(DockerRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a DockerRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ResourceRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ResourceRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InlineJavascriptRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a InlineJavascriptRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ShellCommandRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ShellCommandRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ScatterFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ScatterFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SubworkflowFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SubworkflowFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        getrequirements

        +
        public java.lang.Object getrequirements()
        +
        This method returns the value of requirements.
        +
        +
        Specified by:
        +
        getrequirements in interface Process
        +
        Returns:
        +
        This method will return the value of requirements, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setcwlVersion

        +
        public void setcwlVersion(CWLVersion value)
        +
        This method sets the value of cwlVersion.
        +
        +
        Specified by:
        +
        setcwlVersion in interface Process
        +
        Parameters:
        +
        value - will update cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        getcwlVersion

        +
        public CWLVersion getcwlVersion()
        +
        This method returns the value of cwlVersion.
        +
        +
        Specified by:
        +
        getcwlVersion in interface Process
        +
        Returns:
        +
        This method will return the value of cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputs

        +
        public void setinputs(InputParameter[] value)
        +
        This method sets the value of inputs.
        +
        +
        Specified by:
        +
        setinputs in interface Process
        +
        Parameters:
        +
        value - will update inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getinputs

        +
        public InputParameter[] getinputs()
        +
        This method returns the value of inputs.
        +
        +
        Specified by:
        +
        getinputs in interface Process
        +
        Returns:
        +
        This method will return the value of inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        sethints

        +
        public void sethints(Any value)
        +
        This method sets the value of hints.
        +
        +
        Specified by:
        +
        sethints in interface Process
        +
        Parameters:
        +
        value - will update hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        gethints

        +
        public Any gethints()
        +
        This method returns the value of hints.
        +
        +
        Specified by:
        +
        gethints in interface Process
        +
        Returns:
        +
        This method will return the value of hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Process
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Process
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Specified by:
        +
        setid in interface Process
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Specified by:
        +
        getid in interface Process
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Process
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Process
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/WorkflowOutputParameter.html b/javadoc/org/commonwl/lang/WorkflowOutputParameter.html new file mode 100644 index 00000000..387b41f9 --- /dev/null +++ b/javadoc/org/commonwl/lang/WorkflowOutputParameter.html @@ -0,0 +1,1245 @@ + + + + + +WorkflowOutputParameter + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class WorkflowOutputParameter

+
+
+ +
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Parameter, SchemaBase
    +
    +
    +
    +
    public class WorkflowOutputParameter
+extends OutputParameter
    +
    Describe an output parameter of a workflow. The parameter must be connected to one or more parameters defined in the workflow that will provide the value of the output parameter.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this parameter object.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) LinkMergeMethodlinkMerge +
      The method to use to merge multiple sources into a single array.
      +
      (package private) CommandOutputBindingoutputBinding +
      Describes how to handle the outputs of a process.
      +
      (package private) java.lang.ObjectoutputSource +
      Specifies one or more workflow parameters that supply the value of to the output parameter.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Objecttype +
      Specify valid types of data that may be assigned to this parameter.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      LinkMergeMethodgetlinkMerge() +
      This method returns the value of linkMerge.
      +
      CommandOutputBindinggetoutputBinding() +
      This method returns the value of outputBinding.
      +
      java.lang.ObjectgetoutputSource() +
      This method returns the value of outputSource.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetlinkMerge(LinkMergeMethod value) +
      This method sets the value of linkMerge.
      +
      voidsetoutputBinding(CommandOutputBinding value) +
      This method sets the value of outputBinding.
      +
      voidsetoutputSource(java.lang.String value) +
      This method sets the value of outputSource.
      +
      voidsetoutputSource(java.lang.String[] value) +
      This method sets the value of outputSource.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      voidsettype(CWLType value) +
      This method sets the value of type.
      +
      voidsettype(CWLType[] value) +
      This method sets the value of type.
      +
      voidsettype(OutputArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(OutputArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(OutputEnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(OutputEnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(OutputRecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(OutputRecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        linkMerge

        +
        LinkMergeMethod linkMerge
        +
        The method to use to merge multiple sources into a single array. If not specified, the default method is merge_nested.
        +
        • +
      + + + +
        +
      • +

        outputSource

        +
        java.lang.Object outputSource
        +
        Specifies one or more workflow parameters that supply the value of to the output parameter.
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        Specify valid types of data that may be assigned to this parameter.
        +
        • +
      + + + +
        +
      • +

        outputBinding

        +
        CommandOutputBinding outputBinding
        +
        Describes how to handle the outputs of a process.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this parameter object.
        +
        • +
      + + + +
        +
      • +

        streamable

        +
        java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        WorkflowOutputParameter

        +
        public WorkflowOutputParameter()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlinkMerge

        +
        public void setlinkMerge(LinkMergeMethod value)
        +
        This method sets the value of linkMerge.
        +
        +
        Parameters:
        +
        value - will update linkMerge, which is a LinkMergeMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        getlinkMerge

        +
        public LinkMergeMethod getlinkMerge()
        +
        This method returns the value of linkMerge.
        +
        +
        Returns:
        +
        This method will return the value of linkMerge, which is a LinkMergeMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputSource

        +
        public void setoutputSource(java.lang.String value)
        +
        This method sets the value of outputSource.
        +
        +
        Parameters:
        +
        value - will update outputSource, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputSource

        +
        public void setoutputSource(java.lang.String[] value)
        +
        This method sets the value of outputSource.
        +
        +
        Parameters:
        +
        value - will update outputSource, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputSource

        +
        public java.lang.Object getoutputSource()
        +
        This method returns the value of outputSource.
        +
        +
        Returns:
        +
        This method will return the value of outputSource, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputRecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputEnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputRecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputEnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Overrides:
        +
        setoutputBinding in class OutputParameter
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Overrides:
        +
        getoutputBinding in class OutputParameter
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Overrides:
        +
        setid in class OutputParameter
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Overrides:
        +
        getid in class OutputParameter
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstreamable

        +
        public void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Specified by:
        +
        setstreamable in interface Parameter
        +
        Overrides:
        +
        setstreamable in class OutputParameter
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        public java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Specified by:
        +
        getstreamable in interface Parameter
        +
        Overrides:
        +
        getstreamable in class OutputParameter
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Specified by:
        +
        getformat in interface Parameter
        +
        Overrides:
        +
        getformat in class OutputParameter
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class OutputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class OutputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Parameter
        +
        Overrides:
        +
        getdoc in class OutputParameter
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class OutputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class OutputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Specified by:
        +
        getsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        getsecondaryFiles in class OutputParameter
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Parameter
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Overrides:
        +
        setlabel in class OutputParameter
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Parameter
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Overrides:
        +
        getlabel in class OutputParameter
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
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+ + + +
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+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/WorkflowStep.html b/javadoc/org/commonwl/lang/WorkflowStep.html new file mode 100644 index 00000000..d7689d4b --- /dev/null +++ b/javadoc/org/commonwl/lang/WorkflowStep.html @@ -0,0 +1,1157 @@ + + + + + +WorkflowStep + + + + + + + + +
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+ + +
+
org.commonwl.lang
+

Class WorkflowStep

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.WorkflowStep
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class WorkflowStep
+extends java.lang.Object
    +
    A workflow step is an executable element of a workflow. It specifies the underlying process implementation (such as `CommandLineTool` or another `Workflow`) in the `run` field and connects the input and output parameters of the underlying process to workflow parameters.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringdoc +
      A long, human-readable description of this process object.
      +
      (package private) Anyhints +
      Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this workflow step.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this workflow step.
      +
      (package private) WorkflowStepInputin +
      Defines the input parameters of the workflow step.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this process object.
      +
      (package private) java.lang.Objectout +
      Defines the parameters representing the output of the process.
      +
      (package private) java.lang.Objectrequirements +
      Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this workflow step.
      +
      (package private) java.lang.Objectrun +
      Specifies the process to run.
      +
      (package private) java.lang.Objectscatter 
      (package private) ScatterMethodscatterMethod +
      Required if `scatter` is an array of more than one element.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      WorkflowStep() 
      +
      • +
    + + +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        requirements

        +
        java.lang.Object requirements
        +
        Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this workflow step. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
        +
        • +
      + + + +
        +
      • +

        in

        +
        WorkflowStepInput in
        +
        Defines the input parameters of the workflow step. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used build a user interface for constructing the input object.
        +
        • +
      + + + +
        +
      • +

        hints

        +
        Any hints
        +
        Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this workflow step. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning.
        +
        • +
      + + + +
        +
      • +

        scatter

        +
        java.lang.Object scatter
        +
        • +
      + + + +
        +
      • +

        scatterMethod

        +
        ScatterMethod scatterMethod
        +
        Required if `scatter` is an array of more than one element.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A long, human-readable description of this process object.
        +
        • +
      + + + +
        +
      • +

        run

        +
        java.lang.Object run
        +
        Specifies the process to run.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this workflow step.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      + + + +
        +
      • +

        out

        +
        java.lang.Object out
        +
        Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        WorkflowStep

        +
        public WorkflowStep()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(StepInputExpressionRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a StepInputExpressionRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(MultipleInputFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a MultipleInputFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SoftwareRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a SoftwareRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SchemaDefRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a SchemaDefRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InitialWorkDirRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a InitialWorkDirRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(EnvVarRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a EnvVarRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(DockerRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a DockerRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ResourceRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a ResourceRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InlineJavascriptRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a InlineJavascriptRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ShellCommandRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a ShellCommandRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ScatterFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a ScatterFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SubworkflowFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a SubworkflowFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        getrequirements

        +
        public java.lang.Object getrequirements()
        +
        This method returns the value of requirements.
        +
        +
        Returns:
        +
        This method will return the value of requirements, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setin

        +
        public void setin(WorkflowStepInput value)
        +
        This method sets the value of in.
        +
        +
        Parameters:
        +
        value - will update in, which is a WorkflowStepInput type.
        +
        +
        • +
      + + + +
        +
      • +

        getin

        +
        public WorkflowStepInput getin()
        +
        This method returns the value of in.
        +
        +
        Returns:
        +
        This method will return the value of in, which is a WorkflowStepInput type.
        +
        +
        • +
      + + + +
        +
      • +

        sethints

        +
        public void sethints(Any value)
        +
        This method sets the value of hints.
        +
        +
        Parameters:
        +
        value - will update hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        gethints

        +
        public Any gethints()
        +
        This method returns the value of hints.
        +
        +
        Returns:
        +
        This method will return the value of hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setscatter

        +
        public void setscatter(java.lang.String value)
        +
        This method sets the value of scatter.
        +
        +
        Parameters:
        +
        value - will update scatter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setscatter

        +
        public void setscatter(java.lang.String[] value)
        +
        This method sets the value of scatter.
        +
        +
        Parameters:
        +
        value - will update scatter, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getscatter

        +
        public java.lang.Object getscatter()
        +
        This method returns the value of scatter.
        +
        +
        Returns:
        +
        This method will return the value of scatter, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setscatterMethod

        +
        public void setscatterMethod(ScatterMethod value)
        +
        This method sets the value of scatterMethod.
        +
        +
        Parameters:
        +
        value - will update scatterMethod, which is a ScatterMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        getscatterMethod

        +
        public ScatterMethod getscatterMethod()
        +
        This method returns the value of scatterMethod.
        +
        +
        Returns:
        +
        This method will return the value of scatterMethod, which is a ScatterMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setrun

        +
        public void setrun(CommandLineTool value)
        +
        This method sets the value of run.
        +
        +
        Parameters:
        +
        value - will update run, which is a CommandLineTool type.
        +
        +
        • +
      + + + +
        +
      • +

        setrun

        +
        public void setrun(java.lang.String value)
        +
        This method sets the value of run.
        +
        +
        Parameters:
        +
        value - will update run, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setrun

        +
        public void setrun(Workflow value)
        +
        This method sets the value of run.
        +
        +
        Parameters:
        +
        value - will update run, which is a Workflow type.
        +
        +
        • +
      + + + +
        +
      • +

        setrun

        +
        public void setrun(ExpressionTool value)
        +
        This method sets the value of run.
        +
        +
        Parameters:
        +
        value - will update run, which is a ExpressionTool type.
        +
        +
        • +
      + + + +
        +
      • +

        getrun

        +
        public java.lang.Object getrun()
        +
        This method returns the value of run.
        +
        +
        Returns:
        +
        This method will return the value of run, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setout

        +
        public void setout(WorkflowStepOutput[] value)
        +
        This method sets the value of out.
        +
        +
        Parameters:
        +
        value - will update out, which is a WorkflowStepOutput array.
        +
        +
        • +
      + + + +
        +
      • +

        setout

        +
        public void setout(java.lang.String[] value)
        +
        This method sets the value of out.
        +
        +
        Parameters:
        +
        value - will update out, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getout

        +
        public java.lang.Object getout()
        +
        This method returns the value of out.
        +
        +
        Returns:
        +
        This method will return the value of out, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/WorkflowStepInput.html b/javadoc/org/commonwl/lang/WorkflowStepInput.html new file mode 100644 index 00000000..a75bf66e --- /dev/null +++ b/javadoc/org/commonwl/lang/WorkflowStepInput.html @@ -0,0 +1,615 @@ + + + + + +WorkflowStepInput + + + + + + + + +
+ + +
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+ + +
+ + +
+
org.commonwl.lang
+

Class WorkflowStepInput

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.WorkflowStepInput
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Sink
    +
    +
    +
    +
    public class WorkflowStepInput
+extends java.lang.Object
+implements Sink
    +
    The input of a workflow step connects an upstream parameter (from the workflow inputs, or the outputs of other workflows steps) with the input parameters of the underlying step.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) Anydefault_value +
      The default value for this parameter if there is no `source` field.
      +
      (package private) java.lang.Stringid +
      A unique identifier for this workflow input parameter.
      +
      (package private) LinkMergeMethodlinkMerge +
      The method to use to merge multiple inbound links into a single array.
      +
      (package private) java.lang.Objectsource +
      Specifies one or more workflow parameters that will provide input to the underlying step parameter.
      +
      (package private) java.lang.ObjectvalueFrom +
      To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must be specified in the workflow or workflow step requirements.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      WorkflowStepInput() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      Anygetdefault() +
      This method returns the value of default_value.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      LinkMergeMethodgetlinkMerge() +
      This method returns the value of linkMerge.
      +
      java.lang.Objectgetsource() +
      This method returns the value of source.
      +
      java.lang.ObjectgetvalueFrom() +
      This method returns the value of valueFrom.
      +
      voidsetdefault(Any value) +
      This method sets the value of default_value.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetlinkMerge(LinkMergeMethod value) +
      This method sets the value of linkMerge.
      +
      voidsetsource(java.lang.String value) +
      This method sets the value of source.
      +
      voidsetsource(java.lang.String[] value) +
      This method sets the value of source.
      +
      voidsetvalueFrom(Expression value) +
      This method sets the value of valueFrom.
      +
      voidsetvalueFrom(java.lang.String value) +
      This method sets the value of valueFrom.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        default_value

        +
        Any default_value
        +
        The default value for this parameter if there is no `source` field.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        A unique identifier for this workflow input parameter.
        +
        • +
      + + + +
        +
      • +

        valueFrom

        +
        java.lang.Object valueFrom
        +
        To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must be specified in the workflow or workflow step requirements. If `valueFrom` is a constant string value, use this as the value for this input parameter. If `valueFrom` is a parameter reference or expression, it must be evaluated to yield the actual value to be assiged to the input field. The `self` value of in the parameter reference or expression must be the value of the parameter(s) specified in the `source` field, or null if there is no `source` field. The value of `inputs` in the parameter reference or expression must be the input object to the workflow step after assigning the `source` values and then scattering. The order of evaluating `valueFrom` among step input parameters is undefined and the result of evaluating `valueFrom` on a parameter must not be visible to evaluation of `valueFrom` on other parameters.
        +
        • +
      + + + +
        +
      • +

        linkMerge

        +
        LinkMergeMethod linkMerge
        +
        The method to use to merge multiple inbound links into a single array. If not specified, the default method is merge_nested.
        +
        • +
      + + + +
        +
      • +

        source

        +
        java.lang.Object source
        +
        Specifies one or more workflow parameters that will provide input to the underlying step parameter.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        WorkflowStepInput

        +
        public WorkflowStepInput()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setdefault

        +
        public void setdefault(Any value)
        +
        This method sets the value of default_value.
        +
        +
        Parameters:
        +
        value - will update default_value, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        getdefault

        +
        public Any getdefault()
        +
        This method returns the value of default_value.
        +
        +
        Returns:
        +
        This method will return the value of default_value, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setvalueFrom

        +
        public void setvalueFrom(java.lang.String value)
        +
        This method sets the value of valueFrom.
        +
        +
        Parameters:
        +
        value - will update valueFrom, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setvalueFrom

        +
        public void setvalueFrom(Expression value)
        +
        This method sets the value of valueFrom.
        +
        +
        Parameters:
        +
        value - will update valueFrom, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getvalueFrom

        +
        public java.lang.Object getvalueFrom()
        +
        This method returns the value of valueFrom.
        +
        +
        Returns:
        +
        This method will return the value of valueFrom, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlinkMerge

        +
        public void setlinkMerge(LinkMergeMethod value)
        +
        This method sets the value of linkMerge.
        +
        +
        Specified by:
        +
        setlinkMerge in interface Sink
        +
        Parameters:
        +
        value - will update linkMerge, which is a LinkMergeMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        getlinkMerge

        +
        public LinkMergeMethod getlinkMerge()
        +
        This method returns the value of linkMerge.
        +
        +
        Specified by:
        +
        getlinkMerge in interface Sink
        +
        Returns:
        +
        This method will return the value of linkMerge, which is a LinkMergeMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        setsource

        +
        public void setsource(java.lang.String value)
        +
        This method sets the value of source.
        +
        +
        Specified by:
        +
        setsource in interface Sink
        +
        Parameters:
        +
        value - will update source, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsource

        +
        public void setsource(java.lang.String[] value)
        +
        This method sets the value of source.
        +
        +
        Specified by:
        +
        setsource in interface Sink
        +
        Parameters:
        +
        value - will update source, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getsource

        +
        public java.lang.Object getsource()
        +
        This method returns the value of source.
        +
        +
        Specified by:
        +
        getsource in interface Sink
        +
        Returns:
        +
        This method will return the value of source, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
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+ + + +
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+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/WorkflowStepOutput.html b/javadoc/org/commonwl/lang/WorkflowStepOutput.html new file mode 100644 index 00000000..f97d266a --- /dev/null +++ b/javadoc/org/commonwl/lang/WorkflowStepOutput.html @@ -0,0 +1,336 @@ + + + + + +WorkflowStepOutput + + + + + + + + +
+ + +
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+
org.commonwl.lang
+

Class WorkflowStepOutput

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.WorkflowStepOutput
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class WorkflowStepOutput
+extends java.lang.Object
    +
    Associate an output parameter of the underlying process with a workflow parameter. The workflow parameter (given in the `id` field) be may be used as a `source` to connect with input parameters of other workflow steps, or with an output parameter of the process.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringid +
      A unique identifier for this workflow output parameter.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      WorkflowStepOutput() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        A unique identifier for this workflow output parameter. This is the identifier to use in the `source` field of `WorkflowStepInput` to connect the output value to downstream parameters.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        WorkflowStepOutput

        +
        public WorkflowStepOutput()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
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org.commonwl.lang

+
+

Interfaces

+ +

Classes

+ +

Enums

+ +
+ + diff --git a/javadoc/org/commonwl/lang/package-summary.html b/javadoc/org/commonwl/lang/package-summary.html new file mode 100644 index 00000000..15a5562c --- /dev/null +++ b/javadoc/org/commonwl/lang/package-summary.html @@ -0,0 +1,558 @@ + + + + + +org.commonwl.lang + + + + + + + + +
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Package org.commonwl.lang

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Hierarchy For Package org.commonwl.lang

+Package Hierarchies: + +
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Class Hierarchy

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Interface Hierarchy

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  • Summary: 
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org.commonwl.lang
+

Enum stderr

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<stderr>
      • +
    • +
        +
      • org.commonwl.lang.stderr
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<stderr>
    +
    +
    +
    +
    public enum stderr
+extends java.lang.Enum<stderr>
    +
    Only valid as a `type` for a `CommandLineTool` output with no `outputBinding` set.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Static Methods Concrete Methods 
      Modifier and TypeMethod and Description
      static stderrvalueOf(java.lang.String name) +
      Returns the enum constant of this type with the specified name.
      +
      static stderr[]values() +
      Returns an array containing the constants of this enum type, in +the order they are declared.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Enum

        +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
        • +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +getClass, notify, notifyAll, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static stderr[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (stderr c : stderr.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static stderr valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/javadoc/org/commonwl/lang/stdout.html b/javadoc/org/commonwl/lang/stdout.html new file mode 100644 index 00000000..c0caf5a9 --- /dev/null +++ b/javadoc/org/commonwl/lang/stdout.html @@ -0,0 +1,294 @@ + + + + + +stdout + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Enum stdout

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<stdout>
      • +
    • +
        +
      • org.commonwl.lang.stdout
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<stdout>
    +
    +
    +
    +
    public enum stdout
+extends java.lang.Enum<stdout>
    +
    Only valid as a `type` for a `CommandLineTool` output with no `outputBinding` set.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Static Methods Concrete Methods 
      Modifier and TypeMethod and Description
      static stdoutvalueOf(java.lang.String name) +
      Returns the enum constant of this type with the specified name.
      +
      static stdout[]values() +
      Returns an array containing the constants of this enum type, in +the order they are declared.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Enum

        +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
        • +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +getClass, notify, notifyAll, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static stdout[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (stdout c : stdout.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static stdout valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/javadoc/org/commonwl/util/CWLJavaCodeGenerator.html b/javadoc/org/commonwl/util/CWLJavaCodeGenerator.html new file mode 100644 index 00000000..391502f0 --- /dev/null +++ b/javadoc/org/commonwl/util/CWLJavaCodeGenerator.html @@ -0,0 +1,514 @@ + + + + + +CWLJavaCodeGenerator + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.util
+

Class CWLJavaCodeGenerator

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.util.CWLJavaCodeGenerator
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class CWLJavaCodeGenerator
+extends java.lang.Object
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.StringCWL_FILE +
      The String used for storing CWL filename.
      +
      (package private) java.lang.StringCWL_JAVA_CLASS_NAME +
      The String used for storing CWL Java code-generated class name.
      +
      (package private) java.lang.StringCWL_JAVA_FILE +
      The String used for storing CWL Java code-generated filename.
      +
      (package private) java.lang.StringCWL_OBJECT +
      The String used for storing CWL Java code-generated filename.
      +
      (package private) java.lang.StringTOOL_TYPE +
      The String used for storing if the CWL file is a CommandLineTool or Workflow.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      CWLJavaCodeGenerator(java.lang.String cwlFile) +
      The CommandOutputParameter used for storing outputs in the CWL file.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      private java.lang.StringaddIndentedNewline(java.lang.String text) +
      This method adds a newline character to a string of text.
      +
      private java.lang.StringaddNewline(java.lang.String text) +
      This method adds a newline character to a string of text.
      +
      (package private) java.lang.StringcleanStandardInput(java.lang.String reference) +
      Purpose: To remove the paranthesis "()" and dollar sign ($) + standard input.
      +
      (package private) java.lang.StringgetFirstElementOfArrayList(java.util.ArrayList arrayList) +
      Purpose: Returns the first element of an ArrayList as a String.
      +
      private voidprocessContents(java.util.Map contents) +
      This method processing of the contents of a CWL file for populating a CommandLineTool instance.
      +
      voidprocessFile() +
      This method starts the processing of the CWL file for populating the contents in a CommandLineTool.
      +
      (package private) java.lang.StringremoveBrackets(java.lang.String reference) +
      Purpose: To remove the brackets ([]) in a baseCommand.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        CWL_FILE

        +
        java.lang.String CWL_FILE
        +
        The String used for storing CWL filename.
        +
        • +
      + + + +
        +
      • +

        CWL_JAVA_CLASS_NAME

        +
        java.lang.String CWL_JAVA_CLASS_NAME
        +
        The String used for storing CWL Java code-generated class name.
        +
        • +
      + + + +
        +
      • +

        CWL_JAVA_FILE

        +
        java.lang.String CWL_JAVA_FILE
        +
        The String used for storing CWL Java code-generated filename.
        +
        • +
      + + + +
        +
      • +

        CWL_OBJECT

        +
        java.lang.String CWL_OBJECT
        +
        The String used for storing CWL Java code-generated filename.
        +
        • +
      + + + +
        +
      • +

        TOOL_TYPE

        +
        java.lang.String TOOL_TYPE
        +
        The String used for storing if the CWL file is a CommandLineTool or Workflow.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CWLJavaCodeGenerator

        +
        public CWLJavaCodeGenerator(java.lang.String cwlFile)
        +
        The CommandOutputParameter used for storing outputs in the CWL file.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        processFile

        +
        public void processFile()
+                 throws java.lang.Exception
        +
        This method starts the processing of the CWL file for populating the contents in a CommandLineTool.
        +
        +
        Throws:
        +
        java.lang.Exception - is thrown if there issues with reading the file.
        +
        +
        • +
      + + + +
        +
      • +

        addNewline

        +
        private java.lang.String addNewline(java.lang.String text)
        +
        This method adds a newline character to a string of text.
        +
        +
        Parameters:
        +
        text - is a String of text.
        +
        +
        • +
      + + + +
        +
      • +

        addIndentedNewline

        +
        private java.lang.String addIndentedNewline(java.lang.String text)
        +
        This method adds a newline character to a string of text.
        +
        +
        Parameters:
        +
        text - is a String of text.
        +
        +
        • +
      + + + +
        +
      • +

        processContents

        +
        private void processContents(java.util.Map contents)
+                      throws java.lang.Exception
        +
        This method processing of the contents of a CWL file for populating a CommandLineTool instance.
        +
        +
        Parameters:
        +
        contents - is a Map of the CWL YAML file.
        +
        Throws:
        +
        java.lang.Exception
        +
        +
        • +
      + + + +
        +
      • +

        removeBrackets

        +
        java.lang.String removeBrackets(java.lang.String reference)
        +
        Purpose: To remove the brackets ([]) in a baseCommand.
        +
        +
        Parameters:
        +
        reference - a String to be updated.
        +
        Returns:
        +
        an updated String.
        +
        +
        • +
      + + + +
        +
      • +

        cleanStandardInput

        +
        java.lang.String cleanStandardInput(java.lang.String reference)
        +
        Purpose: To remove the paranthesis "()" and dollar sign ($) + standard input.
        +
        +
        Parameters:
        +
        reference - a String to be updated.
        +
        Returns:
        +
        an updated String.
        +
        +
        • +
      + + + +
        +
      • +

        getFirstElementOfArrayList

        +
        java.lang.String getFirstElementOfArrayList(java.util.ArrayList arrayList)
        +
        Purpose: Returns the first element of an ArrayList as a String.
        +
        +
        Parameters:
        +
        arrayList - which is an ArrayList for retrieving its first element.
        +
        Returns:
        +
        an updated String.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/util/CWLReader.html b/javadoc/org/commonwl/util/CWLReader.html new file mode 100644 index 00000000..20140dda --- /dev/null +++ b/javadoc/org/commonwl/util/CWLReader.html @@ -0,0 +1,535 @@ + + + + + +CWLReader + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.util
+

Class CWLReader

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.util.CWLReader
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class CWLReader
+extends java.lang.Object
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) CommandLineToolCOMMAND_LINE_TOOL +
      The CommandLineTool used for storing class in the CWL file.
      +
      (package private) java.lang.StringCWL_FILE +
      The String used for storing CWL filename.
      +
      (package private) CommandInputParameter[]INPUTS +
      The CommandInputParameter used for storing inputs in the CWL file.
      +
      (package private) CommandOutputParameter[]OUTPUTS +
      The CommandOutputParameter used for storing outputs in the CWL file.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      CWLReader(java.lang.String cwlFile) 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      (package private) java.lang.StringcleanStandardInput(java.lang.String reference) +
      Purpose: To remove the paranthesis "()" and dollar sign ($) + standard input.
      +
      CommandLineToolgetCommandLineToolInstance() +
      Purpose: Returns the populated CommandLineTool instance.
      +
      (package private) java.lang.StringgetFirstElementOfArrayList(java.util.ArrayList arrayList) +
      Purpose: Returns the first element of an ArrayList as a String.
      +
      private voidprocessClass(java.lang.String classType) +
      This method processes the class in a CWL file, and updates the CommandLineTool contents.
      +
      private voidprocessContents(java.lang.String key, + java.lang.Object value) +
      This method processing of the contents of a CWL file for populating a CommandLineTool instance.
      +
      voidprocessFile() +
      This method starts the processing of the CWL file for populating the contents in a CommandLineTool.
      +
      private voidprocessInputs(java.util.Map inputs) +
      This method processes the intputs in a CWL file, and updates the CommandLineTool contents.
      +
      private voidprocessOutputs(java.util.Map outputs) +
      This method processes the outputs in a CWL file, and updates the CommandLineTool contents.
      +
      (package private) java.lang.StringremoveBrackets(java.lang.String reference) +
      Purpose: To remove the brackets ([]) in a baseCommand.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        CWL_FILE

        +
        java.lang.String CWL_FILE
        +
        The String used for storing CWL filename.
        +
        • +
      + + + +
        +
      • +

        COMMAND_LINE_TOOL

        +
        CommandLineTool COMMAND_LINE_TOOL
        +
        The CommandLineTool used for storing class in the CWL file.
        +
        • +
      + + + +
        +
      • +

        INPUTS

        +
        CommandInputParameter[] INPUTS
        +
        The CommandInputParameter used for storing inputs in the CWL file.
        +
        • +
      + + + +
        +
      • +

        OUTPUTS

        +
        CommandOutputParameter[] OUTPUTS
        +
        The CommandOutputParameter used for storing outputs in the CWL file.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CWLReader

        +
        public CWLReader(java.lang.String cwlFile)
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        processFile

        +
        public void processFile()
+                 throws java.lang.Exception
        +
        This method starts the processing of the CWL file for populating the contents in a CommandLineTool.
        +
        +
        Throws:
        +
        java.lang.Exception - is thrown if there issues with reading the file.
        +
        +
        • +
      + + + +
        +
      • +

        processContents

        +
        private void processContents(java.lang.String key,
+                             java.lang.Object value)
        +
        This method processing of the contents of a CWL file for populating a CommandLineTool instance.
        +
        +
        Parameters:
        +
        key - is a String denoting the key of the element in the CWL file.
        +
        value - is an Object denoting the value of the element in the CWL file.
        +
        +
        • +
      + + + +
        +
      • +

        processClass

        +
        private void processClass(java.lang.String classType)
        +
        This method processes the class in a CWL file, and updates the CommandLineTool contents.
        +
        +
        Parameters:
        +
        classType - is a String of the type of the class (i.e. CommandLineTool).
        +
        +
        • +
      + + + +
        +
      • +

        processInputs

        +
        private void processInputs(java.util.Map inputs)
        +
        This method processes the intputs in a CWL file, and updates the CommandLineTool contents.
        +
        +
        Parameters:
        +
        inputs - is a key-value pair Map of the inputs.
        +
        +
        • +
      + + + +
        +
      • +

        processOutputs

        +
        private void processOutputs(java.util.Map outputs)
        +
        This method processes the outputs in a CWL file, and updates the CommandLineTool contents.
        +
        +
        Parameters:
        +
        outputs - is a key-value pair Map of the outputs.
        +
        +
        • +
      + + + +
        +
      • +

        removeBrackets

        +
        java.lang.String removeBrackets(java.lang.String reference)
        +
        Purpose: To remove the brackets ([]) in a baseCommand.
        +
        +
        Parameters:
        +
        reference - a String to be updated.
        +
        Returns:
        +
        an updated String.
        +
        +
        • +
      + + + +
        +
      • +

        cleanStandardInput

        +
        java.lang.String cleanStandardInput(java.lang.String reference)
        +
        Purpose: To remove the paranthesis "()" and dollar sign ($) + standard input.
        +
        +
        Parameters:
        +
        reference - a String to be updated.
        +
        Returns:
        +
        an updated String.
        +
        +
        • +
      + + + +
        +
      • +

        getFirstElementOfArrayList

        +
        java.lang.String getFirstElementOfArrayList(java.util.ArrayList arrayList)
        +
        Purpose: Returns the first element of an ArrayList as a String.
        +
        +
        Parameters:
        +
        arrayList - which is an ArrayList for retrieving its first element.
        +
        Returns:
        +
        an updated String.
        +
        +
        • +
      + + + +
        +
      • +

        getCommandLineToolInstance

        +
        public CommandLineTool getCommandLineToolInstance()
        +
        Purpose: Returns the populated CommandLineTool instance.
        +
        +
        Returns:
        +
        an CommandLineTool instance.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/javadoc/org/commonwl/util/JSONReader.html b/javadoc/org/commonwl/util/JSONReader.html new file mode 100644 index 00000000..a2912712 --- /dev/null +++ b/javadoc/org/commonwl/util/JSONReader.html @@ -0,0 +1,371 @@ + + + + + +JSONReader + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.util
+

Class JSONReader

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.util.JSONReader
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class JSONReader
+extends java.lang.Object
    +
    This is used reading and processing a JSON file.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.StringJSON_FILE +
      The String used for storing the JSON filename.
      +
      (package private) java.util.Map<java.lang.String,java.lang.String>jsonMap +
      The key-value pairs in a JSON file that sit underneath the root key in a JSON file.
      +
      (package private) java.lang.StringROOT_KEY +
      The String used for storing the key of the root of a JSON file's contents.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      JSONReader(java.lang.String jsonFile) 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.StringgetValue(java.lang.String key) +
      This method is used to request the value using a key in the processed JSON file.
      +
      voidprocessFile() +
      This method will process a JSON file an store it's contents.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        JSON_FILE

        +
        java.lang.String JSON_FILE
        +
        The String used for storing the JSON filename.
        +
        • +
      + + + +
        +
      • +

        ROOT_KEY

        +
        java.lang.String ROOT_KEY
        +
        The String used for storing the key of the root of a JSON file's contents.
        +
        • +
      + + + +
        +
      • +

        jsonMap

        +
        java.util.Map<java.lang.String,java.lang.String> jsonMap
        +
        The key-value pairs in a JSON file that sit underneath the root key in a JSON file.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        JSONReader

        +
        public JSONReader(java.lang.String jsonFile)
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        processFile

        +
        public void processFile()
+                 throws java.lang.Exception
        +
        This method will process a JSON file an store it's contents.
        +
        +
        Throws:
        +
        java.lang.Exception - is thrown if there issues with reading the file.
        +
        +
        • +
      + + + +
        +
      • +

        getValue

        +
        public java.lang.String getValue(java.lang.String key)
        +
        This method is used to request the value using a key in the processed JSON file.
        +
        +
        Parameters:
        +
        key - is a particular key, which is a String.
        +
        Returns:
        +
        a String value for a particular key.
        +
        +
        • +
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+
org.commonwl.util
+

Class SystemCommandExecution

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.util.SystemCommandExecution
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class SystemCommandExecution
+extends java.lang.Object
    +
    This is used for executing commands on the system.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      private java.lang.StringStandardError +
      The String used for storing the standard error.
      +
      private java.lang.StringStandardInput +
      The String used for storing the standard input.
      +
      private java.lang.StringStandardOutput +
      The String used for storing the standard output.
      +
      private java.lang.IntegerstatusCode +
      The Integer used for storing the return status code.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.StringcleanupClassName(java.lang.String className) +
      This method removes the "class" string from the class name, produced by the getClass() method.
      +
      java.lang.String[]executeCommand() +
      This method executes the command and returns a String array of the standard input, + standard output, and standard error.
      +
      voidextendExecutionCommand(java.lang.Object command) +
      This method is a helper method to process any object being requested to be run, such as + the ones returned by getbaseCommand() which are actually a String type.
      +
      voidextendExecutionCommand(java.lang.String command) +
      This method is a method to process a String command being requested to be run.
      +
      java.lang.StringgetStandardError() +
      This method returns the last value of the standard error.
      +
      java.lang.StringgetStandardInput() +
      This method returns the last value of the standard input.
      +
      java.lang.StringgetStandardOutput() +
      This method returns the last value of the standard output.
      +
      java.lang.IntegergetStatusCode() 
      voidnewExecutionCommand() +
      This method resets the standard input String.
      +
      voidsetStandardInput(java.lang.String inputText) +
      This method sets the standard input String.
      +
      voidsetStatusCode(java.lang.Integer statusCode) 
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        StandardInput

        +
        private java.lang.String StandardInput
        +
        The String used for storing the standard input.
        +
        • +
      + + + +
        +
      • +

        StandardError

        +
        private java.lang.String StandardError
        +
        The String used for storing the standard error.
        +
        • +
      + + + +
        +
      • +

        StandardOutput

        +
        private java.lang.String StandardOutput
        +
        The String used for storing the standard output.
        +
        • +
      + + + +
        +
      • +

        statusCode

        +
        private java.lang.Integer statusCode
        +
        The Integer used for storing the return status code.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SystemCommandExecution

        +
        public SystemCommandExecution()
        +
        • +
      + + + +
        +
      • +

        SystemCommandExecution

        +
        public SystemCommandExecution(java.lang.String StandardInput)
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        getStatusCode

        +
        public java.lang.Integer getStatusCode()
        +
        • +
      + + + +
        +
      • +

        setStatusCode

        +
        public void setStatusCode(java.lang.Integer statusCode)
        +
        • +
      + + + +
        +
      • +

        executeCommand

        +
        public java.lang.String[] executeCommand()
        +
        This method executes the command and returns a String array of the standard input, + standard output, and standard error.
        +
        +
        Returns:
        +
        a String array of the standard input, standard output, and standard error.
        +
        +
        • +
      + + + +
        +
      • +

        getStandardInput

        +
        public java.lang.String getStandardInput()
        +
        This method returns the last value of the standard input.
        +
        +
        Returns:
        +
        a String of the standard input.
        +
        +
        • +
      + + + +
        +
      • +

        getStandardError

        +
        public java.lang.String getStandardError()
        +
        This method returns the last value of the standard error.
        +
        +
        Returns:
        +
        a String of the standard error.
        +
        +
        • +
      + + + +
        +
      • +

        getStandardOutput

        +
        public java.lang.String getStandardOutput()
        +
        This method returns the last value of the standard output.
        +
        +
        Returns:
        +
        a String of the standard output.
        +
        +
        • +
      + + + +
        +
      • +

        cleanupClassName

        +
        public java.lang.String cleanupClassName(java.lang.String className)
        +
        This method removes the "class" string from the class name, produced by the getClass() method.
        +
        +
        Parameters:
        +
        className - a String of the class name.
        +
        Returns:
        +
        an updated String of the class name.
        +
        +
        • +
      + + + +
        +
      • +

        extendExecutionCommand

        +
        public void extendExecutionCommand(java.lang.Object command)
        +
        This method is a helper method to process any object being requested to be run, such as + the ones returned by getbaseCommand() which are actually a String type. The value is cast + String and added to the standard input string.
        +
        +
        Parameters:
        +
        command - a String of the standard input.
        +
        +
        • +
      + + + +
        +
      • +

        extendExecutionCommand

        +
        public void extendExecutionCommand(java.lang.String command)
        +
        This method is a method to process a String command being requested to be run. The value is + added to the standard input string.
        +
        +
        Parameters:
        +
        command - a String of the standard input.
        +
        +
        • +
      + + + +
        +
      • +

        newExecutionCommand

        +
        public void newExecutionCommand()
        +
        This method resets the standard input String.
        +
        • +
      + + + +
        +
      • +

        setStandardInput

        +
        public void setStandardInput(java.lang.String inputText)
        +
        This method sets the standard input String.
        +
        +
        Parameters:
        +
        inputText - is a String of the standard input.
        +
        +
        • +
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Crusoe - mrc@commonwl.org - Common Workflow Language, a member project of Software Freedom Conservancy, Inc. - - - - scm:git:git://github.com/common-workflow-language/cwljava.git - scm:git:ssh://github.com/common-workflow-language/cwljava.git - https://github.com/common-workflow-language/cwljava/tree/cwl-1.2.0/ - - - - - - org.apache.maven.plugins - maven-deploy-plugin - 3.1.4 - - - org.apache.maven.plugins - maven-compiler-plugin - 3.15.0 - - 11 - true - - - - - - - org.apache.maven.plugins - maven-release-plugin - 3.3.1 - - - org.apache.maven.plugins - maven-surefire-plugin - 3.5.4 - - - org.apache.maven.plugins - maven-javadoc-plugin - 3.12.0 - attach-javadocsjar - - - org.apache.maven.plugins - maven-source-plugin - 3.4.0 - attach-sourcesjar-no-fork - - - org.apache.maven.plugins - maven-jar-plugin - 3.5.0 - - - src/main/resources/META-INF/MANIFEST.MF - - - - - maven-assembly-plugin - - - - org.commonwl.cwlsdk.cwl1_2.utils.Validator - - - - jar-with-dependencies - - - - - - - - - org.apache.commons - commons-lang3 - ${commonslang.version} - - - - - - junit - junit - 4.13.2 - - - org.snakeyaml - snakeyaml-engine - 3.0.1 - - - com.fasterxml.jackson.core - jackson-databind - 2.21.0 - - - - - deployment - - - - org.apache.maven.plugins - maven-javadoc-plugin - 3.12.0 - - - attach-javadocs - - jar - - - - - - org.apache.maven.plugins - maven-source-plugin - 3.4.0 - - - attach-sources - - jar-no-fork - - - - - - org.apache.maven.plugins - maven-gpg-plugin - 3.2.8 - - - ${gpg.keyname} - - - --pinentry-mode - loopback - - - - - sign-artifacts - verify - - sign - - - - - - org.sonatype.central - central-publishing-maven-plugin - 0.10.0 - true - - central - true - uploaded - - - - - - - github - - - env.CI - true - - - - - - org.jacoco - jacoco-maven-plugin - 0.8.14 - - - prepare-agent - - prepare-agent - - - - - - org.eluder.coveralls - coveralls-maven-plugin - 4.3.0 - - - javax.xml.bind - jaxb-api - 2.3.1 - - - - - - - - diff --git a/sdk-and-javadoc-generation/AUTHORS.TXT b/sdk-and-javadoc-generation/AUTHORS.TXT new file mode 100755 index 00000000..81294e06 --- /dev/null +++ b/sdk-and-javadoc-generation/AUTHORS.TXT @@ -0,0 +1,24 @@ + + Java SDK for CWL + + @author Paul Grosu (pgrosu@gmail.com), Northeastern University + @version 0.20 + @since April 28, 2016 + +

Alternate SDK (via Avro): + + Denis Yuen (denis.yuen@gmail.com) + +CWL Draft: + + Peter Amstutz (peter.amstutz@curoverse.com), Curoverse + Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics + + Contributors: + + Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics + John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University + Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis + Herve Menager (herve.menager@gmail.com), Institut Pasteur + Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics + Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester diff --git a/sdk-and-javadoc-generation/CWLSDKBuilder.java b/sdk-and-javadoc-generation/CWLSDKBuilder.java new file mode 100755 index 00000000..6209cbb8 --- /dev/null +++ b/sdk-and-javadoc-generation/CWLSDKBuilder.java @@ -0,0 +1,1430 @@ + +/************************************************************************* +* +* Authors: +* +* * Paul Grosu , Northeastern University +* +* Purpose: +* +* To generate a Java SDK using the results of YAMLParser. +* +* Requirements: +* +* * Java SDK +* * CommandLineTool.yml +* * Process.yml +* * Workflow.yml +* * metaschema.yml +* * cwl-sdk-config.txt +* * CreateCWLJavaSDK.java +* * YAMLParser.java +* * CWLSDKBuilder.java +* * Creating a directory called sdk, into which the +* CWL Java SDK will be generated +* +* Below is the command-line on how to compile and run the collection of +* programs: +* +* To compile and run: +* +* ./step1-generate_sdk.sh +* +* To compile: +* +* javac CreateCWLJavaSDK.java +* javac YAMLParser.java +* javac CWLSDKBuilder.java +* +* To run: +* +* java CreateCWLJavaSDK cwl-yaml-specs/CommandLineTool.yml cwl-yaml-specs/Process.yml cwl-yaml-specs/Workflow.yml cwl-yaml-specs/metaschema.yml +* +* +* Output of the program: +* +* The program will generate the CWL Java SDK in the sdk folder. +* +* +*************************************************************************/ + +// ******************** Load the appropriate packages ******************** + +import java.util.*; +import java.io.*; + +public class CWLSDKBuilder { + + // *************** Initialize the required variables *************** + + public YAMLParser yamlParser; + public Map objects; + public Map objectInformation; + public Map config_override = new HashMap(); + public Map config_namespace = new HashMap(); + public ArrayList config_skip = new ArrayList(); + public Map variableTypes = new HashMap(); + public ArrayList authors = new ArrayList(); + + Map fields; + Map fieldsDocumentation; + + String SDK_PACKAGE = "package org.commonwl.lang;"; + String SDK_DIRECTORY = "org/commonwl/lang/"; + String CONFIG_FILE = "cwl-sdk-config.txt"; + String AUTHORS_FILE = "AUTHORS.TXT"; + + String NAME = "name"; + String TYPE = "type"; + String DOCUMENTATION = "documentation"; + String EXTENDS = "extends"; + String SPECIALIZE = "specialize"; + String SYMBOLS = "symbols"; + String FIELDS = "fields"; + String FIELDS_DOCUMENTATION = "fieldsDocumentation"; + String RECORD = "record"; + String ENUM = "enum"; + String ABSTRACT = "abstract"; + + String COLON = ":"; + String COMMA = ","; + + String PUBLIC_CLASS = "public class "; + String PUBLIC_INTERFACE = "public interface "; + String CONSTRUCTOR = " public "; + String INTERFACE = "interface"; + + + /************************************************************************* + * + * Purpose: Get the processed YAML file as a Map for + * generating the SDK class files. + * + */ + public CWLSDKBuilder( Map objectsInstance ) { + + objects = objectsInstance; + + } + + /************************************************************************* + * + * Purpose: An alias method to print a String. + * + */ + public void print( String text ) { + System.out.println( text ); + } + + /************************************************************************* + * + * Purpose: This method intiates the generation of the SDK by calling + * other methods. + * + */ + public void generateSDK() throws Exception { + + print( "" ); + print( "Building SDK..."); + print( "" ); + print( "Reading config..."); + print( "" ); + + readConfig(); + readAuthors(); + + print( "Writing classes..." ); + print(""); + + writeClasses(); + + print(""); + print( "SDK creation complete!" ); + + } + + /************************************************************************* + * + * Purpose: Get the key portion of a line the cwl-sdk-config.txt file. + * + */ + String getConfigKey( String text ) { + Integer indexOfColon = text.indexOf(COLON); + return text.substring(0, indexOfColon - 1).trim(); + } + + /************************************************************************* + * + * Purpose: Get the value portion of a line the cwl-sdk-config.txt file. + * + */ + String getConfigValue( String text ) { + Integer indexOfColon = text.indexOf(COLON); + return text.substring( indexOfColon + 1 ).trim(); + } + + /************************************************************************* + * + * Purpose: Read the cwl-sdk-config.txt file and store the information + * as keys or key-value pairs in: + * + * config_override : override definition + * config_namespace : namespaces for variables + * config_skip : class auto-generation to skip + * + */ + public void readConfig() throws Exception { + + FileReader configFileDescriptor = new FileReader(new File(CONFIG_FILE)); + BufferedReader bufferedReader = new BufferedReader(configFileDescriptor); + + String configLine; + String configValue; + + while((configLine = bufferedReader.readLine()) != null) { + + if( getConfigKey( configLine ).equals("override") ) { + configValue = castToString( getConfigValue(configLine) ); + config_override.put( getConfigKey( configValue ), getConfigValue(configValue) ); + } else if( getConfigKey( configLine ).equals("namespace") ) { + configValue = castToString( getConfigValue(configLine) ); + config_namespace.put( getConfigKey( configValue ), getConfigValue(configValue) ); + } if( getConfigKey( configLine ).equals("skip") ) { + configValue = castToString( getConfigValue(configLine) ); + config_skip.add( configValue ); + } + + } + + bufferedReader.close(); + + } + + public String updateInheritanceForAllBoundaryClasses( String classes ) { + + String [] classList = classes.split(COMMA); + String listOfClasses = new String(); + + if( classes.trim().length() != 0 ) { + for ( String className : classList ) { + + if ( listOfClasses.trim().length() != 0 ) { + listOfClasses = new String( listOfClasses + ", " + className ); + } else { + listOfClasses = new String( className ); + } + + if( objects.get( objects.get( className.trim() ).get(EXTENDS) ) == null ) { + continue; // If there is nothing to extends in this class, continue the loop + } else { + + listOfClasses = new String( listOfClasses + ", " + + updateInheritanceForAllBoundaryClasses( castToString( objects.get( className.trim() ).get(EXTENDS) ) ) + ); + } + + } + return listOfClasses; + } else { + return new String( "" ); + } + + } + + /************************************************************************* + * + * Purpose: To convert an ArrayList of classes to a String separated by + * commas (,). + * + */ + public String convertSetToString( Set arrayList ) { + + String concatenatedStrings = new String(); + + for (String element : arrayList ) { + + if( concatenatedStrings.length() == 0 ) { + concatenatedStrings = new String( element.trim() ); + } else { + concatenatedStrings = new String( concatenatedStrings + ", " + element.trim() ); + } + } + + return concatenatedStrings; + + } + + + /************************************************************************* + * + * Purpose: To generate the classes for the SDK. + * + */ + public void writeClasses() throws Exception { + + for(String name: objects.keySet()){ + + if( !(config_skip.contains(name)) ) { + + // Write the start of class file + openClass( name ); + + // Clean the varible types for lookup in get Method return type + variableTypes = new HashMap(); + + // Check that there is nothing to extend + String inheritance = castToString( objectInformation.get(EXTENDS) ); + inheritance = updateInheritanceForAllBoundaryClasses( inheritance ); + // Write the Class' variables + writeVariables( name , name , null ); + + if( !isSpecializeEmpty( name ) || inheritance.length() != 0 ) { + + if( !(inheritance.contains(COMMA)) ) { + writeVariables( inheritance, name , (Map ) objectInformation.get(SPECIALIZE) ); + } else { + + String [] restOfClassCollection = inheritance.split(COMMA); + + for( String className : restOfClassCollection ) { + + String trimmedClassName = className.trim(); + writeVariables( trimmedClassName, name , (Map ) objectInformation.get(SPECIALIZE) ); + + } + } + } + + // Write the Class' constructor + writeConstructor( name ); + + // Write the Class' methods + writeMethods( name , name , null ); + + if( !isSpecializeEmpty( name ) || inheritance.length() != 0 ) { + + if( !(inheritance.contains(COMMA)) ) { + writeMethods( inheritance, name , (Map ) objectInformation.get(SPECIALIZE) ); + } else { + + String [] restOfClassCollection = inheritance.split(COMMA); + + for( String className : restOfClassCollection ) { + + String trimmedClassName = className.trim(); + + writeMethods( trimmedClassName, name , (Map ) objectInformation.get(SPECIALIZE) ); + + if ((Boolean) objects.get(trimmedClassName).get(ABSTRACT)) { + } + + } + } + } + + // To close the current class + closeClass( name ); + } + + } + + // Create the Any.java class file + writeAnyClass(); + + // Create the PrimitiveType.java class file + writePrimitiveTypeClass(); + + } + + + /************************************************************************* + * + * Purpose: To read the AUTHORS.TXT file to fill out the Authors' section. + * + */ + public void readAuthors() throws Exception { + + FileReader configFileDescriptor = new FileReader(new File(AUTHORS_FILE)); 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+ + // Write Authors section + for( String line : authors ) { + bufferedWriter.write( line ); + bufferedWriter.newLine(); + } + + // Write Package + bufferedWriter.newLine(); + bufferedWriter.write( SDK_PACKAGE ); + bufferedWriter.newLine(); + + // Write Any class + for( String line : Any_class ) { + bufferedWriter.write( line ); + bufferedWriter.newLine(); + } + + bufferedWriter.close(); + + } + + /************************************************************************* + * + * Purpose: To generate the PrimitiveType.java class. + * + */ + public void writePrimitiveTypeClass() throws Exception { + + String class_name = "PrimitiveType.java"; + + FileWriter fileWriter = new FileWriter( SDK_DIRECTORY + class_name ); + BufferedWriter bufferedWriter = new BufferedWriter(fileWriter); + + // PrimitiveType class code + String [] PrimitiveType_class = { + "", + "/*****************************************************************************************************", + "*", + "* Salad data types are based on Avro schema declarations. Refer to the", + "* [Avro schema declaration documentation](https://avro.apache.org/docs/current/spec.html#schemas) for", + "* detailed information.", + "* The types are: 1) null: no value,", + "* 2) boolean: a binary value,", + "* 3) int: 32-bit signed integer,", + "* 4) long: 64-bit signed integer,", + "* 5) float: single precision (32-bit) IEEE 754 floating-point number,", + "* 6) double: double precision (64-bit) IEEE 754 floating-point number, and", + "* 7) string: Unicode character sequence.", + "*", + "*/", + "public class PrimitiveType extends Object {", + "", + " Object value;", + "", + " public PrimitiveType( Object objectInstance ) {", + " value = objectInstance;", + " }", + "", + " /*****************************************************************************************************", + " *", + " * This method sets the value of PrimitiveType.", + " *", + " * @param objectInstance sets the value of PrimitiveType, and is a Boolean type.", + " *", + " */", + " public void set(Boolean objectInstance) {", + " value = objectInstance;", + " }", + "", + " /*****************************************************************************************************", + " *", + " * This method sets the value of PrimitiveType.", + " *", + " * @param objectInstance sets the value of PrimitiveType, and is a Integer type.", + " *", + " */", + " public void set(Integer objectInstance) {", + " value = objectInstance;", + " }", + "", + " /*****************************************************************************************************", + " *", + " * This method sets the value of PrimitiveType.", + " *", + " * @param objectInstance sets the value of PrimitiveType, and is a Long type.", + " *", + " */", + " public void set(Long objectInstance) {", + " value = objectInstance;", + " }", + "", + " /*****************************************************************************************************", + " *", + " * This method sets the value of PrimitiveType.", + " *", + " * @param objectInstance sets the value of PrimitiveType, and is a Float type.", + " *", + " */", + " public void set(Float objectInstance) {", + " value = objectInstance;", + " }", + "", + " /*****************************************************************************************************", + " *", + " * This method sets the value of PrimitiveType.", + " *", + " * @param objectInstance sets the value of PrimitiveType, and is a Double type.", + " *", + " */", + " public void set(Double objectInstance) {", + " value = objectInstance;", + " }", + "", + " /*****************************************************************************************************", + " *", + " * This method sets the value of PrimitiveType.", + " *", + " * @param objectInstance sets the value of PrimitiveType, and is a String type.", + " *", + " */", + " public void set(String objectInstance) {", + " value = objectInstance;", + " }", + "", + " /*****************************************************************************************************", + " *", + " * This method returns the value of PrimitiveType.", + " *", + " * @return This method will return the value of PrimitiveType, which is an Object type.", + " *", + " */", + " public Object get() {", + " return (Object) value;", + " }", + "", + "}", + "" + }; + + // Write Authors section + for( String line : authors ) { + bufferedWriter.write( line ); + bufferedWriter.newLine(); + } + + // Write Package + bufferedWriter.newLine(); + bufferedWriter.write( SDK_PACKAGE ); + bufferedWriter.newLine(); + + // Write PrimitiveType class + for( String line : PrimitiveType_class ) { + bufferedWriter.write( line ); + bufferedWriter.newLine(); + } + + bufferedWriter.close(); + } + + /************************************************************************* + * + * Purpose: To cast an Object to a String. + * + */ + public String castToString( Object object ) { + return (String) object; + } + + /************************************************************************* + * + * Purpose: To get the first class from a list of classes. + * + */ + public String getFirstClass( String text, String DELIMITER ){ + Integer indexOfDelimiter = text.indexOf(DELIMITER); + return text.substring(0, indexOfDelimiter).trim(); + } + + /************************************************************************* + * + * Purpose: To get the rest of the classes from a list of classes, + * after the first one. + * + */ + public String [] getRestOfClasses( String text, String DELIMITER ){ + Integer indexOfDelimiter = text.indexOf(DELIMITER); + return text.substring(indexOfDelimiter + 1).split(COMMA); + } + + /************************************************************************* + * + * Purpose: To get as a String the rest of the classes from a list of + * classes, after the first one. + * + */ + public String getRestOfClassesAsString( String text, String DELIMITER ){ + Integer indexOfDelimiter = text.indexOf(DELIMITER); + return text.substring(indexOfDelimiter + 1).trim(); + } + + + /************************************************************************* + * + * Purpose: To convert an ArrayList of classes to a String separated by + * commas (,). + * + */ + public String convertArrayListToString( ArrayList arrayList ) { + + String concatenatedStrings = new String(); + + for (String element : arrayList ) { + + if( concatenatedStrings.length() == 0 ) { + concatenatedStrings = new String( element.trim() ); + } else { + concatenatedStrings = new String( concatenatedStrings + ", " + element.trim() ); + } + } + + return concatenatedStrings; + + } + + /************************************************************************* + * + * Purpose: To convert a list of synmbols to a String separated by + * commas (,). + * + */ + public String printObjectSymbols( ArrayList symbolsList ) { + + String concatenatedSymbols = new String(); + + for (String symbol : symbolsList ) { + + if( concatenatedSymbols.length() == 0 ) { + concatenatedSymbols = new String(symbol); + } else { + concatenatedSymbols = new String(concatenatedSymbols + ", " + symbol); + } + } + + return concatenatedSymbols; + + } + + /************************************************************************* + * + * Purpose: To convert an enumarated list to a String separated by + * commas (,). + * + */ + public String printEnumObjectSymbols( ArrayList symbolsList ) { + + String concatenatedSymbols = new String(); + + for (String symbol : symbolsList ) { + + if( concatenatedSymbols.length() == 0 ) { + // This is because periods in Java indicate subclasses + concatenatedSymbols = new String( symbol.replace(".", "_")); + } else { + // This is because periods in Java indicate subclasses + concatenatedSymbols = new String(concatenatedSymbols + ", " + symbol.replace(".", "_") ); + } + } + + return concatenatedSymbols; + + } + + ArrayList getImplementedClasses( String text ) { + String [] textAsArray = text.split(COMMA); + ArrayList implementedClasses = new ArrayList(); + for( String className : textAsArray ) { + if( config_override.get(className.trim()) != null ) { + if( castToString(config_override.get( className.trim() )).equals(INTERFACE) ) { + implementedClasses.add( className.trim() ); + } + } else { + // Continue ... + } + } + return implementedClasses; + } + + String getExtendedClass( String text ) { + + String [] textAsArray = text.split(COMMA); + String extendedClass = new String(); + + for( String className : textAsArray ) { + print( className.trim() ); + if( config_override.get(className.trim()) != null ) { + // Continue ... + } else { + extendedClass = new String( className.trim() ); + } + } + return extendedClass; + } + + /************************************************************************* + * + * Purpose: To write out the start of the class file. + * + */ + public void openClass( String name ) throws Exception { + + objectInformation = objects.get(name); + + if ( castToString(objectInformation.get(TYPE)).contains(ENUM) ) { + + print( name ); + + FileWriter fileWriter = new FileWriter( SDK_DIRECTORY + name + ".java" ); + + BufferedWriter bufferedWriter = new BufferedWriter(fileWriter); + + for( String line : authors ) { + bufferedWriter.write( line ); + bufferedWriter.newLine(); + } + + bufferedWriter.newLine(); + + // Write Package + bufferedWriter.write( SDK_PACKAGE ); + bufferedWriter.newLine(); + bufferedWriter.newLine(); + + if( castToString(objectInformation.get(DOCUMENTATION)).length() != 0 ) { + + bufferedWriter.write( " /*****************************************************************************************************" ); + bufferedWriter.newLine(); + bufferedWriter.write( " *" ); + bufferedWriter.newLine(); + bufferedWriter.write( " * " + objectInformation.get(DOCUMENTATION) ); + bufferedWriter.newLine(); + bufferedWriter.write(" */"); + bufferedWriter.newLine(); + + } + + bufferedWriter.write( "public enum " + name + " {" ); + bufferedWriter.newLine(); + bufferedWriter.newLine(); + bufferedWriter.write(" " + printEnumObjectSymbols( ( ArrayList ) objectInformation.get(SYMBOLS))); + bufferedWriter.newLine(); + bufferedWriter.newLine(); + bufferedWriter.write( "}" ); + bufferedWriter.newLine(); + bufferedWriter.close(); + + } + + if ( castToString(objectInformation.get(TYPE)).contains(RECORD) ) { + + print( name ); + + FileWriter fileWriter = new FileWriter( SDK_DIRECTORY + name + ".java" ); + + BufferedWriter bufferedWriter = new BufferedWriter(fileWriter); + + for( String line : authors ) { + bufferedWriter.write( line ); + bufferedWriter.newLine(); + } + + bufferedWriter.newLine(); + + // Write Package + bufferedWriter.write( SDK_PACKAGE ); + bufferedWriter.newLine(); + bufferedWriter.newLine(); + + if( castToString(objectInformation.get(DOCUMENTATION)).length() != 0 ) { + + bufferedWriter.write( "/*****************************************************************************************************" ); + bufferedWriter.newLine(); + bufferedWriter.write( "*" ); + bufferedWriter.newLine(); + bufferedWriter.write( "* " + objectInformation.get(DOCUMENTATION) ); + bufferedWriter.newLine(); + bufferedWriter.write("*/"); + bufferedWriter.newLine(); + + } + + if ( castToString(objectInformation.get(EXTENDS)).length() != 0 && !((Boolean) objectInformation.get(ABSTRACT)) ) { + + String classInheritanceCollection = castToString(objectInformation.get(EXTENDS)); + String extendedClass = getExtendedClass( classInheritanceCollection ); + String implementedClasses = convertArrayListToString( getImplementedClasses( classInheritanceCollection )).trim(); + + if ( extendedClass.length() != 0 ) { + if( implementedClasses.length() != 0 ) { + bufferedWriter.write( PUBLIC_CLASS + name + " extends " + extendedClass + " implements " + implementedClasses + " {" ); + bufferedWriter.newLine(); + } else { + bufferedWriter.write( PUBLIC_CLASS + name + " extends " + extendedClass + " {" ); + bufferedWriter.newLine(); + } + } else { + if( implementedClasses.length() != 0 ) { + bufferedWriter.write( PUBLIC_CLASS + name + " implements " + implementedClasses + " {" ); + bufferedWriter.newLine(); + } else { + bufferedWriter.write( PUBLIC_CLASS + name + " {" ); + bufferedWriter.newLine(); + } + } + + } else { + if( config_override.get(name) != null ) { + if( castToString(config_override.get(name)).equals(INTERFACE) ) { + + String classInheritanceCollection = castToString(objectInformation.get(EXTENDS)); + String extendedClass = getExtendedClass( classInheritanceCollection ); + String implementedClasses = convertArrayListToString( getImplementedClasses( classInheritanceCollection )).trim(); + + if ( extendedClass.length() != 0 ) { + if( implementedClasses.length() != 0 ) { + bufferedWriter.write( PUBLIC_INTERFACE + name + " extends " + extendedClass + " implements " + implementedClasses + " {" ); + bufferedWriter.newLine(); + } else { + bufferedWriter.write( PUBLIC_INTERFACE + name + " extends " + extendedClass + " {" ); + bufferedWriter.newLine(); + } + } else { + if( implementedClasses.length() != 0 ) { + bufferedWriter.write( PUBLIC_INTERFACE + name + " extends " + implementedClasses + " {" ); + bufferedWriter.newLine(); + } else { + bufferedWriter.write( PUBLIC_INTERFACE + name + " {" ); + bufferedWriter.newLine(); + } + } + + } else { + // Continue ... + } + } else { + bufferedWriter.write( PUBLIC_CLASS + name + " {" ); + bufferedWriter.newLine(); + } + } + + bufferedWriter.close(); + } + + } + + /************************************************************************* + * + * Purpose: To write out the class' variables. + * + */ + public void writeVariables( String name, String filename, Map specialize ) throws Exception { + + if ( castToString(objectInformation.get(TYPE)).contains(RECORD) ) { + + // Since the class is recursive, this is in case of the need to extract the fields + // of an extended class/interface. + fields = (Map ) objects.get(name).get(FIELDS); + fieldsDocumentation = (Map ) objects.get(name).get(FIELDS_DOCUMENTATION); + + FileWriter fileWriter = new FileWriter( SDK_DIRECTORY + filename + ".java", true ); + + BufferedWriter bufferedWriter = new BufferedWriter(fileWriter); + + Boolean areThereAnyFields = false; + + // Each field might have one or more defined types + for(String field: fields.keySet()) { + + areThereAnyFields = true; + + if( getFieldElements( fields.get(field) ).length == 1 ) { + + bufferedWriter.newLine(); + + // Only element as the length is == 1 + String firstElementOfField = getFirstElementOfField( fields.get(field) ).trim(); + + if( specialize != null ) { + + if( specialize.containsKey( cleanArraySymbol( firstElementOfField ))) { + if( fieldsDocumentation.get( field.trim() ) != null ) { + + bufferedWriter.write( " /*****************************************************************************************************" ); + bufferedWriter.newLine(); + bufferedWriter.write( " *" ); + bufferedWriter.newLine(); + bufferedWriter.write( " * " + fieldsDocumentation.get( field.trim() ) ); + bufferedWriter.newLine(); + bufferedWriter.write(" */"); + bufferedWriter.newLine(); + + } + + bufferedWriter.write( " " + specializeTheType( reMapPrimitiveType( firstElementOfField ), specialize ) + " " + reMapFields( field.trim() ) + " = null;" ); + bufferedWriter.newLine(); + + //Don't remap to class_value or default_value, since the method is getclass or setclass + variableTypes.put( field.trim() , specializeTheType( reMapPrimitiveType( firstElementOfField ), specialize ) ); + + } else { + + if( fieldsDocumentation.get( field.trim() ) != null ) { + + bufferedWriter.write( " /*****************************************************************************************************" ); + bufferedWriter.newLine(); + bufferedWriter.write( " *" ); + bufferedWriter.newLine(); + bufferedWriter.write( " * " + fieldsDocumentation.get( field.trim() ) ); + bufferedWriter.newLine(); + bufferedWriter.write(" */"); + bufferedWriter.newLine(); + } + bufferedWriter.write( " " + reMapPrimitiveType( firstElementOfField ) + " " + reMapFields( field.trim() ) + " = null;" ); + bufferedWriter.newLine(); + variableTypes.put( field.trim() , reMapPrimitiveType( firstElementOfField ) ); + + } + + } else { + + if( fieldsDocumentation.get( field.trim() ) != null ) { + + bufferedWriter.write( " /*****************************************************************************************************" ); + bufferedWriter.newLine(); + bufferedWriter.write( " *" ); + bufferedWriter.newLine(); + bufferedWriter.write( " * " + fieldsDocumentation.get( field.trim() ) ); + bufferedWriter.newLine(); + bufferedWriter.write(" */"); + bufferedWriter.newLine(); + } + bufferedWriter.write( " " + reMapPrimitiveType( firstElementOfField ) + " " + reMapFields( field.trim() ) + " = null;" ); + bufferedWriter.newLine(); + + variableTypes.put( field.trim() , reMapPrimitiveType( firstElementOfField ) ); + + } + + } else { + + bufferedWriter.newLine(); + + if( fieldsDocumentation.get( field.trim() ) != null ) { + + bufferedWriter.write( " /*****************************************************************************************************" ); + bufferedWriter.newLine(); + bufferedWriter.write( " *" ); + bufferedWriter.newLine(); + bufferedWriter.write( " * " + fieldsDocumentation.get( field.trim() ) ); + bufferedWriter.newLine(); + bufferedWriter.write(" */"); + bufferedWriter.newLine(); + } + // This is okay since if the object is an array, it can be cast via (Object []) + bufferedWriter.write( " " + "Object" + " " + reMapFields( field.trim() ) + " = null;" ); + bufferedWriter.newLine(); + variableTypes.put( field.trim() , "Object" ); + + } + } + + if ( areThereAnyFields ) { + bufferedWriter.newLine(); + } + + bufferedWriter.close(); + + } + + } + + /************************************************************************* + * + * Purpose: To write out the class' constructor. + * + */ + public void writeConstructor( String name ) throws Exception { + + if ( castToString(objectInformation.get(TYPE)).contains(RECORD) ) { + + FileWriter fileWriter = new FileWriter( SDK_DIRECTORY + name + ".java", true ); + + BufferedWriter bufferedWriter = new BufferedWriter(fileWriter); + + if( config_override.get(name) != null ) { + if( castToString(config_override.get(name)).equals(INTERFACE) ) { + // Skip constructor construction for an interface + } + } else { + + if ( castToString(objectInformation.get(EXTENDS)).length() != 0 ) { + bufferedWriter.newLine(); + bufferedWriter.write( CONSTRUCTOR + name + "() { super(); }" ); + bufferedWriter.newLine(); + } else { + bufferedWriter.newLine(); + bufferedWriter.write( CONSTRUCTOR + name + "() { super(); }" ); + bufferedWriter.newLine(); + } + } + + bufferedWriter.close(); + + } + + } + + + /************************************************************************* + * + * Purpose: To get an array of the field elements. + * + */ + public String [] getFieldElements( String fieldElements ) { + return fieldElements.split( COMMA ); + } + + /************************************************************************* + * + * Purpose: To remap types to Java types. + * + */ + String reMapPrimitiveType( String primitiveType ) { + + String primitiveTypeTrimmed = primitiveType.trim(); + + if( primitiveTypeTrimmed.toLowerCase().equals("boolean") || + primitiveTypeTrimmed.toLowerCase().equals("boolean []") ) { + return primitiveTypeTrimmed.replace( "boolean", "Boolean"); + } else if( primitiveTypeTrimmed.toLowerCase().equals("int") || + primitiveTypeTrimmed.toLowerCase().equals("int []") ) { + return primitiveTypeTrimmed.replace( "int", "Integer"); + } else if( primitiveTypeTrimmed.toLowerCase().equals("long") || + primitiveTypeTrimmed.toLowerCase().equals("long []") ) { + return primitiveTypeTrimmed.replace( "long", "Long"); + } else if( primitiveTypeTrimmed.toLowerCase().equals("float") || + primitiveTypeTrimmed.toLowerCase().equals("float []") ) { + return primitiveTypeTrimmed.replace( "float", "Float"); + } else if( primitiveTypeTrimmed.toLowerCase().equals("double") || + primitiveTypeTrimmed.toLowerCase().equals("double []") ) { + return primitiveTypeTrimmed.replace( "double", "Double"); + } else if( primitiveTypeTrimmed.toLowerCase().equals("string") || + primitiveTypeTrimmed.toLowerCase().equals("string []") ) { + return primitiveTypeTrimmed.replace( "string", "String"); + } else if( primitiveTypeTrimmed.contains("{") || primitiveTypeTrimmed.contains("}") ) { + // The recursion is in case other symbols exist such as [] and _class + return reMapPrimitiveType( removeCurlyBrackets( getFirstElementOfField( primitiveTypeTrimmed ) ) ); + } else if( primitiveTypeTrimmed.toLowerCase().trim().equals("array_symbol") ) { + return primitiveTypeTrimmed.toLowerCase().trim().replace( "array_symbol", "Object []"); + } else if( primitiveTypeTrimmed.toLowerCase().trim().equals("enum_symbol") ) { + return primitiveTypeTrimmed.toLowerCase().trim().replace( "enum_symbol", "Enum"); + } else if( primitiveTypeTrimmed.toLowerCase().trim().equals("documentation_symbol") ) { + return primitiveTypeTrimmed.toLowerCase().trim().replace( "documentation_symbol", "Object"); + } else if( primitiveTypeTrimmed.toLowerCase().trim().equals("record_symbol") ) { + return primitiveTypeTrimmed.toLowerCase().trim().replace( "record_symbol", "Object"); + } else if( primitiveTypeTrimmed.toLowerCase().trim().equals("file_class") ) { + return primitiveTypeTrimmed.toLowerCase().trim().replace( "file_class", "File"); + } else if( primitiveTypeTrimmed.toLowerCase().trim().equals("directory_class") ) { + return primitiveTypeTrimmed.toLowerCase().trim().replace( "directory_class", "Directory"); + } + else { + return primitiveType.trim(); + } + + } + + /************************************************************************* + * + * Purpose: To fix variable names in order to avoid collisions with Java + * keywords. + * + */ + public String reMapFields( String field ) { + + if( field.equals("class") ) { + return new String( "class_value" ); + } else if( field.equals("default") ) { + return new String( "default_value" ); + } else if( field.equals("abstract") ) { + return new String( "abstract_value" ); + } else if( field.equals("extends") ) { + return new String( "extends_value" ); + } else if( field.equals("package") ) { + return new String( "package_value" ); + } else { + return field; + } + + } + + + /************************************************************************* + * + * Purpose: To get the first field from a list of fields. + * + */ + public String getFirstElementOfField( String text ) { + return getFieldElements( text )[0]; + } + + /************************************************************************* + * + * Purpose: To remove the curly brackets denoting enumerated type. + * + */ + public String removeCurlyBrackets( String text ){ + return text.replace( "{", "" ).replace( "}", "" ).trim(); + } + + + /************************************************************************* + * + * Purpose: To determine if there is a need to specialize types of the + * current class being processed. + * + */ + public Boolean isSpecializeEmpty( String name ) { + + Map specialize = (Map ) objectInformation.get(SPECIALIZE); + + if ( specialize.keySet().size() > 0 ) { + return false; + } else { + return true; + } + } + + /************************************************************************* + * + * Purpose: To remove the array symbols from the current type being + * processed. + * + */ + public String cleanArraySymbol( String text ) { + return text.replace("[", "").replace("]", "").trim(); + } + + /************************************************************************* + * + * Purpose: To specialize a particular type, by remapping to a new name. + * + */ + public String specializeTheType( String type , Map specialize ) { + + String specializeFrom = cleanArraySymbol( type ); + String specializeTo = specialize.get( specializeFrom ); + return type.replace( specializeFrom, specializeTo ); + + } + + /************************************************************************* + * + * Purpose: To read the AUTHORS.TXT file to fill out the Authors' section. + * + */ + String parseReturnType( String type ) { + if( type.contains("[") ) { + return new String( type.replace("[", "").replace("]", "").trim() + " array" ); + } if( type.contains("{") ) { + return new String( type.replace("{", "").replace("}", "").trim() + " enumeration" ); + } else { + return new String( type.trim() + " type"); + } + } + + /************************************************************************* + * + * Purpose: To read the AUTHORS.TXT file to fill out the Authors' section. + * + */ + public ArrayList populateJavaDoc( String typeOfMethod, String type, String variable, String actualParameterName ) throws Exception { + + ArrayList javaDoc = new ArrayList(); + + //authors.add(""); + javaDoc.add(" /*****************************************************************************************************"); + javaDoc.add(" *"); + if( typeOfMethod.contains("set") ) { + javaDoc.add(" * This method sets the value of " + variable + "." ); + javaDoc.add(" *"); + javaDoc.add(" * @param " + actualParameterName + " will update " + variable + ", which is a " + parseReturnType( type ) + "." ); + } else if ( typeOfMethod.contains("get") ) { + javaDoc.add(" * This method returns the value of " + variable + "." ); + javaDoc.add(" *"); + javaDoc.add(" * @return This method will return the value of " + variable + ", which is a " + parseReturnType( type ) + "." ); + } + + javaDoc.add(" *"); + javaDoc.add(" */"); + + return javaDoc; + + } + + /************************************************************************* + * + * Purpose: To write out the class' methods. + * + */ + public void writeMethods( String name, String filename, Map specialize ) throws Exception { + + if ( castToString(objectInformation.get(TYPE)).contains(RECORD) ) { + + // Since the class is recursive, this is in case of the need to extract the fields + // of an extended class/interface. + fields = (Map ) objects.get(name).get(FIELDS); + + FileWriter fileWriter = new FileWriter( SDK_DIRECTORY + filename + ".java", true ); + + BufferedWriter bufferedWriter = new BufferedWriter(fileWriter); + + for(String field: fields.keySet()) { + + for( String element : getFieldElements( fields.get(field) ) ) { +// System.out.println( filename + ": " + element ); + bufferedWriter.newLine(); + + // if there are things to specialize + if( specialize != null ) { + + if( specialize.containsKey( cleanArraySymbol( reMapPrimitiveType( element )) ) ) { + + // Write JavaDoc section + ArrayList javaDoc = populateJavaDoc( "set", reMapPrimitiveType( element ), reMapFields( field.trim() ), "value" ); + for( String line : javaDoc ) { + bufferedWriter.write( line ); + bufferedWriter.newLine(); + } + + if( config_override.get(filename) != null ) { + if( castToString(config_override.get(filename)).equals(INTERFACE) ) { + bufferedWriter.write( " public void set" + field.trim() + "( " + specializeTheType( reMapPrimitiveType( element ), specialize ) + " value " + ");" ); + } + } else { + bufferedWriter.write( " public void set" + field.trim() + "( " + specializeTheType( reMapPrimitiveType( element ), specialize ) + " value " + ") {" ); + } + + } else { // This type is not being specialized, but it needs to be written + + // Write JavaDoc section + ArrayList javaDoc = populateJavaDoc( "set", reMapPrimitiveType( element ), reMapFields( field.trim() ), "value" ); + for( String line : javaDoc ) { + bufferedWriter.write( line ); + bufferedWriter.newLine(); + } + + if( config_override.get(filename) != null ) { + if( castToString(config_override.get(filename)).equals(INTERFACE) ) { + bufferedWriter.write( " public void set" + field.trim() + "( " + reMapPrimitiveType( element ) + " value " + ");" ); + } + } else { + bufferedWriter.write( " public void set" + field.trim() + "( " + reMapPrimitiveType( element ) + " value " + ") {" ); + } + + } + } else { //Nothing to specialize + + // Write JavaDoc section + ArrayList javaDoc = populateJavaDoc( "set", reMapPrimitiveType( element ), reMapFields( field.trim() ), "value" ); + for( String line : javaDoc ) { + bufferedWriter.write( line ); + bufferedWriter.newLine(); + } + + if( config_override.get(filename) != null ) { + if( castToString(config_override.get(filename)).equals(INTERFACE) ) { + bufferedWriter.write( " public void set" + field.trim() + "( " + reMapPrimitiveType( element ) + " value " + ");" ); + } + } else { + bufferedWriter.write( " public void set" + field.trim() + "( " + reMapPrimitiveType( element ) + " value " + ") {" ); + } + + } + + + // Write the value to set, and if it's an interface skip it + if( config_override.get(filename) != null ) { + if( castToString(config_override.get(filename)).equals(INTERFACE) ) { + bufferedWriter.newLine(); // There is no implementation for an interface + //bufferedWriter.write( " public void set" + field.trim() + "( " + reMapPrimitiveType( element ) + " value " + ");" ); + } + } else { + bufferedWriter.newLine(); + bufferedWriter.write( " " + reMapFields( field.trim() ) + " = " + "value;" ); + bufferedWriter.newLine(); + bufferedWriter.write( " }"); + bufferedWriter.newLine(); + } + + //If there is a specialization but the name (implemenation) is abstract, then also write the original method + if( specialize != null ) { + if( specialize.containsKey( cleanArraySymbol( reMapPrimitiveType( element )) ) ) { + if( config_override.get( name ) != null ) { // meaning that it's an interface + + // Write JavaDoc section + ArrayList javaDoc = new ArrayList();//populateJavaDoc( "set", reMapPrimitiveType( element ), reMapFields( field.trim() ), "value" ); + javaDoc.add(" /*****************************************************************************************************"); + javaDoc.add(" *"); + javaDoc.add(" * This is a dummy method which has no functionality, and is required "); + javaDoc.add(" * for implementing an interface method that was previously specialized." ); + javaDoc.add(" *"); + javaDoc.add(" *"); + javaDoc.add(" */"); + //Add a spacer between methods + bufferedWriter.newLine(); + for( String line : javaDoc ) { + bufferedWriter.write( line ); + bufferedWriter.newLine(); + } + + bufferedWriter.write( " public void set" + field.trim() + "( " + reMapPrimitiveType( element ) + " value " + ") {" ); + bufferedWriter.newLine(); + bufferedWriter.newLine(); + bufferedWriter.write( " }"); + bufferedWriter.newLine(); + + } + } + } + + } // end of set by having going through all set possiblities + + // Beginning of get which only needs one implementation + + // Write JavaDoc section + ArrayList javaDoc = populateJavaDoc( "get", variableTypes.get( field.trim() ), reMapFields( field.trim() ), "" ); + // Add a spacer between the set and get method + bufferedWriter.newLine(); + for( String line : javaDoc ) { + bufferedWriter.write( line ); + bufferedWriter.newLine(); + } + + if( config_override.get(filename) != null ) { + if( castToString(config_override.get(filename)).equals(INTERFACE) ) { + bufferedWriter.write( " public " + variableTypes.get( field.trim() ) + " get" + field.trim() + "();" ); + } + } else { + bufferedWriter.write( " public " + variableTypes.get( field.trim() ) + " get" + field.trim() + "() {" ); + bufferedWriter.newLine(); + bufferedWriter.write( " return " + reMapFields( field.trim() ) + ";" ); + bufferedWriter.newLine(); + bufferedWriter.write( " }"); + bufferedWriter.newLine(); + } + + + } + + bufferedWriter.close(); + } + + } + + /************************************************************************* + * + * Purpose: To close the current class. + * + */ + public void closeClass( String name ) throws Exception { + + if ( castToString(objectInformation.get(TYPE)).contains(RECORD) ) { + + FileWriter fileWriter = new FileWriter( SDK_DIRECTORY + name + ".java", true ); + + BufferedWriter bufferedWriter = new BufferedWriter(fileWriter); + + bufferedWriter.newLine(); + + bufferedWriter.write( "}" ); + bufferedWriter.close(); + + } + + } + + /************************************************************************* + * + * Purpose: To retrieve the namespace value for a specific variable. + * + */ + public String getNamespaceFor( String element ) { + if ( config_namespace.get( element ) != null ) { + return config_namespace.get( element ); + } else { + return new String(""); + } + } + +} + diff --git a/sdk-and-javadoc-generation/CreateCWLJavaSDK.java b/sdk-and-javadoc-generation/CreateCWLJavaSDK.java new file mode 100755 index 00000000..318ef7ee --- /dev/null +++ b/sdk-and-javadoc-generation/CreateCWLJavaSDK.java @@ -0,0 +1,200 @@ + + +/************************************************************************* +* +* Authors: +* +* * Paul Grosu , Northeastern University +* +* Purpose: +* +* To parse Yaml file with YAMLParser and to generate a Java SDK. +* +* Requirements: +* +* * Java SDK +* * CommandLineTool.yml +* * Process.yml +* * Workflow.yml +* * metaschema.yml +* * cwl-sdk-config.txt +* * CreateCWLJavaSDK.java +* * YAMLParser.java +* * CWLSDKBuilder.java +* * Creating a directory called sdk, into which the +* CWL Java SDK will be generated +* +* Below is the command-line on how to compile and run the collection of +* programs: +* +* To compile and run: +* +* ./step1-generate_sdk.sh +* +* To compile: +* +* javac CreateCWLJavaSDK.java +* javac YAMLParser.java +* javac CWLSDKBuilder.java +* +* To run: +* +* java CreateCWLJavaSDK cwl-yaml-specs/CommandLineTool.yml cwl-yaml-specs/Process.yml cwl-yaml-specs/Workflow.yml cwl-yaml-specs/metaschema.yml +* +* +* Output of the program: +* +* The program will read Yaml files to gather the required data for +* generating the CWL Java SDK in the sdk folder. +* +* +*************************************************************************/ + +// ******************** Load the appropriate packages ******************** + +import java.util.*; +import java.io.*; + +public class CreateCWLJavaSDK { + + public static void main(String[] args) { + + // *************** Initialize the required variables *************** + + YAMLParser yamlParser; + CWLSDKBuilder sdkBuilder; + + Map objects = new HashMap(); + Map objectInformation = new HashMap(); + + /************************************************************************* + * + * To determine if there no YAML files provided for processing. + * + */ + try { + if( args[0].trim().length() == 0 ) { + print( "" ); + print( "Please run the program by including Yaml files as arguments." ); + System.exit(0); + } + } catch (Exception e) { + print( "" ); + print( "Please run the program by including Yaml files as arguments." ); + System.exit(0); + } + + /************************************************************************* + * + * Parse the YAML files and collect the relevant information for + * subsequent SDK creation. + * + */ + try { + + yamlParser = new YAMLParser(args); + + print(""); + print("Processing YAML file(s): " ); + print(""); + + for( String yamlFileName : args ) { + print( yamlFileName ); + } + + print(""); + + while( !yamlParser.reachedEOF ) { + + yamlParser.processNextObjectType(); + if ( yamlParser.reachedEOF ) { + break; + } else { + + yamlParser.getObjectName(); + yamlParser.getObjectType(); + yamlParser.getObjectDocumentation(); + yamlParser.getObjectAbstract(); + yamlParser.getObjectInheritance(); + yamlParser.getObjectRenamedFields(); + yamlParser.getObjectFields(); + yamlParser.getObjectSymbols(); + + if( yamlParser.objectName.trim().length() > 0 ) { + + objectInformation = new HashMap(); + + objectInformation.put( "name", yamlParser.objectName ); + objectInformation.put( "type", yamlParser.objectType ); + objectInformation.put( "documentation", yamlParser.objectDocumentation ); + objectInformation.put( "abstract", yamlParser.objectAbstract ); + objectInformation.put( "extends", yamlParser.objectExtends ); + objectInformation.put( "specialize", yamlParser.objectRenamedFields ); + objectInformation.put( "symbols", yamlParser.objectSymbolsList ); + objectInformation.put( "fields", yamlParser.objectFields ); + objectInformation.put( "fieldsDocumentation", yamlParser.objectFieldsDocumentation ); + + objects.put( yamlParser.objectName, objectInformation ); + + yamlParser.print( "Name: " + yamlParser.objectName ); + yamlParser.print( "Type: " + yamlParser.objectType ); + yamlParser.print( "Documentation: " + yamlParser.objectDocumentation ); + yamlParser.print( "Abstract: " + yamlParser.objectAbstract ); + yamlParser.print( "Inheritance: " + yamlParser.objectExtends ); + print( "Rename fields From/To: " ); + yamlParser.printObjectRenamedFields( yamlParser.objectRenamedFields ); + print( "Symbols: " ); + yamlParser.printObjectSymbols( yamlParser.objectSymbolsList ); + print( "Fields: " ); + yamlParser.printObjectFields( yamlParser.objectFields ); + print( "Fields Documentation: " ); + yamlParser.printObjectFieldsDocumentation( yamlParser.objectFieldsDocumentation ); + print("--------------------------"); + } + } + } + + print(""); + print("Fix fields to first extension if they abstract..." ); + print(""); + + /************************************************************************* + * + * Purpose: Update the types in fields which are abstract. + * Sometimes fields will point to types which are abstract, and + * the updateAbstractFields method will travel the dependency + * path to the first concrete class implemenation and replace + * the type with that of concrete class. + * + */ + objects = yamlParser.updateAbstractFields( objects ); + + print(""); + print("Finished processing YAML file(s)!" ); + print(""); + + + /************************************************************************* + * + * Build the SDK. + * + */ + sdkBuilder = new CWLSDKBuilder( objects ); + sdkBuilder.generateSDK(); + + } catch( Exception e ) { System.out.println("parser: " + e); } + + } + + /************************************************************************* + * + * Purpose: An alias method to print a String. + * + */ + public static void print( String text ) { + System.out.println( text ); + } + +} + + diff --git a/sdk-and-javadoc-generation/UML_Class_Diagram/UML_Diagram_of_CWLJava_Version_1_0.png b/sdk-and-javadoc-generation/UML_Class_Diagram/UML_Diagram_of_CWLJava_Version_1_0.png new file mode 100644 index 00000000..31b42a45 Binary files /dev/null and b/sdk-and-javadoc-generation/UML_Class_Diagram/UML_Diagram_of_CWLJava_Version_1_0.png differ diff --git a/sdk-and-javadoc-generation/YAMLParser.java b/sdk-and-javadoc-generation/YAMLParser.java new file mode 100755 index 00000000..429c0e9e --- /dev/null +++ b/sdk-and-javadoc-generation/YAMLParser.java @@ -0,0 +1,1459 @@ + + +/************************************************************************* +* +* Authors: +* +* * Paul Grosu , Northeastern University +* +* Purpose: +* +* To parse Yaml file with YAMLParser to gather the required data, +* for subsequently generating the CWL Java SDK through +* CWLSDKBuilder. +* +* Requirements: +* +* * Java SDK +* * CommandLineTool.yml +* * Process.yml +* * Workflow.yml +* * metaschema.yml +* * cwl-sdk-config.txt +* * CreateCWLJavaSDK.java +* * YAMLParser.java +* * CWLSDKBuilder.java +* * Creating a directory called sdk, into which the +* CWL Java SDK will be generated +* +* Below is the command-line on how to compile and run the collection of +* programs: +* +* To compile and run: +* +* ./step1-generate_sdk.sh +* +* To compile: +* +* javac CreateCWLJavaSDK.java +* javac YAMLParser.java +* javac CWLSDKBuilder.java +* +* To run: +* +* java CreateCWLJavaSDK cwl-yaml-specs/CommandLineTool.yml cwl-yaml-specs/Process.yml cwl-yaml-specs/Workflow.yml cwl-yaml-specs/metaschema.yml +* +* +* Output of the program: +* +* The program will read Yaml files to gather the required data for +* generating the CWL Java SDK in the sdk folder. +* +* +*************************************************************************/ + +// ******************** Load the appropriate packages ******************** + +import java.util.*; +import java.io.*; +import java.util.stream.Collectors; + +public class YAMLParser { + + // *************** Initialize the required variables *************** + + String [] YAML_FILENAME; + + String OBJECT_START = "- "; + String OBJECT_NAME = " name: "; + String OBJECT_TYPE = " type: "; + String OBJECT_DOCUMENTATION = " doc:"; + String OBJECT_DOCUMENTATION_MULTILINE = " doc: |"; + String OBJECT_SYMBOLS = " symbols:"; + String OBJECT_SPECIALIZE = " specialize:"; + String SPECIALIZE_FROM = " specializeFrom: "; + String SPECIALIZE_TO = " specializeTo: "; + String OBJECT_EXTENDS = " extends: "; + String OBJECT_ABSTRACT = " abstract: "; + Integer OBJECT_INDENT = 2; + + String FIELD_START = " - name: "; + String FIELDS_SECTION_START = " fields:"; + String FIELD_NAME = " - name:"; + String FIELD_DOCUMENTATION = "doc:"; + String FIELD_DOCUMENTATION_MULTILINE = "doc: |"; + String FIELD_TYPE = "type:"; + String FIELD_ITEMS = "items:"; + + String FIELD_SYMBOLS = "symbols:"; + String COLON = ":"; + String COMMA = ","; + String ARRAY = "array"; + String ENUM = "enum"; + String DASH = "-"; + String NULL_STRING = "null"; + String QUESTION_MARK = "?"; + + HashMap yamlFile; + public Integer length = 0; + public String currentLine = ""; + public Integer currentLineNumber = 0; + public ArrayList processedObjectsIndex = new ArrayList(); + Boolean reachedEOF = false; + + Integer objectStartLine = 0; + Integer currentFieldStartLine = 0; + + public String objectName = ""; + public String objectType = ""; + public String objectExtends = ""; + public Boolean objectAbstract = false; + public String objectDocumentation = new String(); + public Map objectRenamedFields = new HashMap(); + public ArrayList objectSymbolsList = new ArrayList(); + public Map objectFields = new HashMap(); + public Map objectFieldsDocumentation = new HashMap(); + + /************************************************************************* + * + * Purpose: Read the YAML file and store each line with the associated + * line-number in a HashMap for the proper + * creation of variables and methods during the SDK generation + * process. + * + */ + public YAMLParser( String [] yamlFileNames ) { + + yamlFile = new HashMap(); + + try { + String yamlLine; + Integer Counter = 0; + + for( String filename : yamlFileNames ) { + FileReader yamlFileDescriptor = new FileReader(new File(filename)); + BufferedReader bufferedReader = new BufferedReader(yamlFileDescriptor); + + while((yamlLine = bufferedReader.readLine()) != null) { + yamlFile.put(Counter, new String(yamlLine) ); + Counter = Counter + 1; + } + + bufferedReader.close(); + length = Counter; + } + } catch ( Exception e ) { print( "YAMLParser: " + e ); } + + } + + + /************************************************************************* + * + * Purpose: To retrieve a line of text that was stored in the + * HashMap representing the YAML file. + * + */ + public void readLine( Integer lineNumber ) throws Exception { + + if( lineNumber >= 0 && lineNumber < length ) { + currentLine = (String) yamlFile.get( lineNumber ); + } + + if( lineNumber >= length ) { + reachedEOF = true; + } + + } + + /************************************************************************* + * + * Purpose: To retrieve the next line of text that was stored in the + * HashMap representing the YAML file. + * + */ + public void readNextLine() throws Exception { + + currentLineNumber = currentLineNumber + 1; + readLine( currentLineNumber ); + + } + + /************************************************************************* + * + * Purpose: To retrieve the previous line of text that was stored in the + * HashMap representing the YAML file. + * + */ + public void readPreviousLine() throws Exception { + + currentLineNumber = currentLineNumber - 1; + readLine( currentLineNumber ); + + } + + /************************************************************************* + * + * Purpose: To reset the object data before reading the next object + * the YAML file, with which to populate the variables with. + * + */ + void resetObjectInformation() { + objectName = ""; + objectType = ""; + objectExtends = ""; + objectAbstract = false; + objectRenamedFields = new HashMap(); + } + + /************************************************************************* + * + * Purpose: To find and process the next object in the YAML file. + * + */ + public void processNextObjectType() throws Exception { + + resetObjectInformation(); + + while( currentLineNumber < length ) { + + readLine( currentLineNumber ); + + if( currentLine.startsWith(OBJECT_START) && + !processedObjectsIndex.contains(currentLineNumber) ) { + + objectStartLine = currentLineNumber; + processedObjectsIndex.add( objectStartLine ); + break; + + } else { + + currentLineNumber = currentLineNumber + 1; + + if( currentLineNumber >= length ) { + reachedEOF = true; + break; + } + + } + } + } + + /************************************************************************* + * + * Purpose: To print the current line being processed in the YAML file. + * + */ + public void printCurrentLine() { + print( currentLine ); + } + + /************************************************************************* + * + * Purpose: An alias method to print a String. + * + */ + public void print( String text ) { + System.out.println( text ); + } + + /************************************************************************* + * + * Purpose: To remove the object's label in a String, such as: + * (i.e. name:, type:, etc.) + * + */ + String removeLabel( String lineOfText ) { + + if( lineOfText.contains(COLON)) { + return new String( lineOfText.substring( lineOfText.indexOf(COLON) + 1).trim() ); + } else { + return lineOfText; + } + + } + + /************************************************************************* + * + * Purpose: To remove the object's question-mark (?) in a String, such as: + * (i.e. name:, type:, etc.) + * + */ + String removeQuestionMark( String lineOfText ) { + return new String( lineOfText.replace(QUESTION_MARK, "").trim() ); + } + + /************************************************************************* + * + * Purpose: Add a space to an array-defined type (i.e. string[]) + * + */ + String addSpacingToBrackets( String lineOfText ) { + return new String( lineOfText.replace("[", " [").trim() ); + } + + + + /************************************************************************* + * + * Purpose: To remove the namespace in a String, since it already is + * stored in the cwl-sdk-config.txt file. + * + */ + public String removeNamespace( String lineOfText ) { + + if( lineOfText.contains(COLON)) { + return new String( lineOfText.substring( lineOfText.indexOf(COLON) + 1).trim() ); + } else { + return lineOfText; + } + } + + /************************************************************************* + * + * Purpose: To move the current line being read back to the start of the + * current object being processed. + * + */ + void moveToStartOfObject() throws Exception { + reachedEOF = false; + currentLineNumber = objectStartLine; + readLine( currentLineNumber ); + } + + /************************************************************************* + * + * Purpose: To determine the name of the current object being processed. + * + */ + public void getObjectName() throws Exception { + + moveToStartOfObject(); + + if( currentLine.contains( OBJECT_NAME ) && + currentLine.startsWith(OBJECT_START) ) { + + objectName = removeLabel( currentLine ); + + } else { + + readNextLine(); + + while( !currentLine.contains( OBJECT_NAME ) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + readNextLine(); + } + + // Found the name line + if( currentLine.contains( OBJECT_NAME ) && + (currentLine.indexOf( OBJECT_NAME.trim() ) == OBJECT_INDENT) && + !currentLine.startsWith(OBJECT_START) ) { + + objectName = removeLabel( currentLine ); + + } + } + } + + /************************************************************************* + * + * Purpose: To determine the type of the current object being processed. + * + */ + public void getObjectType() throws Exception { + + moveToStartOfObject(); + + if( currentLine.contains( OBJECT_TYPE ) && + currentLine.startsWith(OBJECT_START) ) { + + objectType = removeLabel( currentLine ); + + } else { + + readNextLine(); + + while( !currentLine.contains( OBJECT_TYPE ) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + readNextLine(); + } + + if( currentLine.contains( OBJECT_TYPE ) && + (currentLine.indexOf( OBJECT_TYPE.trim() ) == OBJECT_INDENT) && + !currentLine.startsWith(OBJECT_START) ) { + + objectType = removeLabel( currentLine ); + + } + } + } + + /************************************************************************* + * + * Purpose: To get a String representation of the symbols list. + * + */ + public String printObjectSymbols( ArrayList symbolsList ) { + + String concatenatedSymbols = new String(); + + for (String symbol : symbolsList ) { + + print( symbol ); + + if( concatenatedSymbols.length() == 0 ) { + concatenatedSymbols = new String(symbol); + } else { + concatenatedSymbols = new String(concatenatedSymbols + ", " + symbol); + } + } + + return concatenatedSymbols; + + } + + + /************************************************************************* + * + * Purpose: To determine the symbols of the current object being + * processed. + * + */ + public void getObjectSymbols() throws Exception { + + moveToStartOfObject(); + objectSymbolsList = new ArrayList(); + + if( currentLine.contains( OBJECT_SYMBOLS ) && + currentLine.startsWith(OBJECT_START) ) { + + // Continue, since found the symbols start line. + + } else { + + readNextLine(); + + while( !currentLine.contains( OBJECT_SYMBOLS ) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + readNextLine(); + } + } + + // Found the symbols line + if( currentLine.contains( OBJECT_SYMBOLS ) && + (currentLine.indexOf( OBJECT_SYMBOLS.trim() ) == OBJECT_INDENT) ) { + + Integer symbolsIndentation = -1; + + // Determine where the indentation of symbols is, for later checking if still + // within the Symbols definition + if ( currentLine.contains( OBJECT_SYMBOLS ) ) { + symbolsIndentation = currentLine.indexOf( OBJECT_SYMBOLS.trim() ); + } + + Boolean isWithinSymbols = true; + + // Reached the end of the current Symbols section + while( isWithinSymbols && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + + // Continue to the next line + readNextLine(); + + if( currentLine.contains(DASH) ) { + objectSymbolsList.add( removeNamespace( removeDash(currentLine) ) ); + } + + // Has moved beyond the Symbols section + if( currentLine.trim().length() == 0 ) { + isWithinSymbols = false; + } else if( (currentLine.substring( symbolsIndentation, symbolsIndentation + 1 ).trim().length() > 0) ) { + isWithinSymbols = false; + } + + // Completed the symbols section + if( !isWithinSymbols && + !currentLine.contains(FIELD_NAME) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + break; + } + } + } + } + + /************************************************************************* + * + * Purpose: To print the objects that the current object being processed + * extends. + * + */ + public void printObjectRenamedFields( Map map ) { + + for(String key: map.keySet()){ + + print(key + " -> " + map.get(key)); + + } + + } + + /************************************************************************* + * + * Purpose: To determine the objects that the current object being + * processed extends. + * + */ + public void getObjectRenamedFields() throws Exception { + + moveToStartOfObject(); + + if( currentLine.contains( OBJECT_SPECIALIZE ) && + currentLine.startsWith(OBJECT_START) ) { + + // Continue, since found the specialize start line. + + } else { + readNextLine(); + while( !currentLine.contains( OBJECT_SPECIALIZE ) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + readNextLine(); + } + } + + // Found a current line + if( currentLine.contains( OBJECT_SPECIALIZE ) && + (currentLine.indexOf( OBJECT_SPECIALIZE.trim() ) == OBJECT_INDENT) ) { + + Integer specializeIndentation = -1; + + // Determine where the indentation of this type definition is, for later checking if still + // within the Specialize definition + if ( currentLine.contains( OBJECT_SPECIALIZE ) ) { + specializeIndentation = currentLine.indexOf( OBJECT_SPECIALIZE.trim() ); + } + + Boolean isWithinSpecialize = true; + String renameFrom, renameTo; + + // Reached the end of the current Specialize section + while( isWithinSpecialize && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + + // Continue to the next line + readNextLine(); + + if( currentLine.contains(SPECIALIZE_FROM) ) { + + // Get the specializeFrom + renameFrom = cleanUpReference( removeLabel( currentLine ) ); + + if( renameFrom.contains(COLON) ) { + renameFrom = removeNamespace( renameFrom ) ; + } + + readNextLine(); + + // Get the specializeTo + renameTo = cleanUpReference( removeLabel( currentLine ) ); + + if( renameTo.contains(COLON) ) { + renameTo = removeNamespace( renameTo ) ; + } + + objectRenamedFields.put( renameFrom, renameTo ); + + } + + // Has moved beyond the Specialize section + if( currentLine.trim().length() == 0 ) { + isWithinSpecialize = false; + } else if( (currentLine.substring( specializeIndentation, specializeIndentation + 1 ).trim().length() > 0) ) { + isWithinSpecialize = false; + } + + // Completed the type definition section of this field + if( !isWithinSpecialize && + !currentLine.contains(FIELD_NAME) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + break; + } + + } + + } + + } + + + + + /************************************************************************* + * + * Purpose: Retreive the current description/documentation of this + * object. + * + */ + public void getObjectDocumentation() throws Exception { + + moveToStartOfObject(); + objectDocumentation = ""; + + if( currentLine.contains( OBJECT_DOCUMENTATION ) && + currentLine.startsWith(OBJECT_START) ) { + + // Continue, since found the specialize start line. + + } else { + readNextLine(); + while( !currentLine.contains( OBJECT_DOCUMENTATION ) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + readNextLine(); + } + } + + + // Found a current line + if( currentLine.contains( OBJECT_DOCUMENTATION ) && + (currentLine.indexOf( OBJECT_DOCUMENTATION.trim() ) == OBJECT_INDENT) ) { + + // Check if current documentation is not multiline + // The second check is for CWLType where it is a multiline list + if( !currentLine.contains( OBJECT_DOCUMENTATION_MULTILINE ) ) { + // For CWLType where it's a multiline list + if ( currentLine.replace( OBJECT_DOCUMENTATION, "" ).trim().length() != 0 ) { + objectDocumentation = new String( replaceAngleBrackets( removeDoubleQuotes( removeLabel(currentLine ) ) ) ); + objectDocumentation = new String( makeAmpersandLiteralForJavaDoc(objectDocumentation) ); + return; + } + } else { + // Continue ... + } + + Integer documentationIndentation = -1; + + // Determine where the indentation of this type definition is, for later checking if still + // within the Documentation definition + if ( currentLine.contains( OBJECT_DOCUMENTATION ) ) { + documentationIndentation = currentLine.indexOf( OBJECT_DOCUMENTATION.trim() ); + } + + Boolean isWithinDocumentation = true; + + // Reached the end of the current Specialize section + while( isWithinDocumentation && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + + // Continue to the next line + readNextLine(); + + // Has moved beyond the Documentation section + if( currentLine.trim().length() == 0 ) { + isWithinDocumentation = false; + } else if( (currentLine.substring( documentationIndentation, documentationIndentation + 1 ).trim().length() > 0) ) { + isWithinDocumentation = false; + } + + // Completed the type definition section of this field + if( !isWithinDocumentation && + !currentLine.contains(FIELD_NAME) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + break; + } + + // Get the specializeFrom + objectDocumentation = new String( objectDocumentation + " " + replaceAngleBrackets( removeDoubleQuotes( currentLine ) ) ); + objectDocumentation = new String( makeAmpersandLiteralForJavaDoc(objectDocumentation) ); + + } + + } + + } + + /************************************************************************* + * + * Purpose: To get information if this object is abstract. + * + */ + public void getObjectAbstract() throws Exception { + + moveToStartOfObject(); + + if( currentLine.contains( OBJECT_ABSTRACT ) && + currentLine.startsWith(OBJECT_START) ) { + + // Continue, since found the abstract line. + + } else { + + readNextLine(); + + while( !currentLine.contains( OBJECT_ABSTRACT ) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + readNextLine(); + } + } + + // Found the extends line + if( currentLine.contains( OBJECT_ABSTRACT ) && + (currentLine.indexOf( OBJECT_ABSTRACT.trim() ) == OBJECT_INDENT) ) { + + String abstractLine = removeBrackets( removeNamespace( cleanUpReference( removeLabel( currentLine ) ) ) ); + if (abstractLine.equals("true") ) { + objectAbstract = true; + } else { + objectAbstract = false; + } + + } + } + + + /************************************************************************* + * + * Purpose: To remove the links (# sign) and array marking ([]) in a + * String, in order to only list the element(s), which might be + * separated by the comma (,) delimiter. + * + */ + String removeBrackets( String reference ) { + return new String( reference.replace("[", "").replace("]", "") ); + } + + /************************************************************************* + * + * Purpose: To remove the links (# sign) and array marking ([]) in a + * String, in order to only list the element(s), which might be + * separated by the comma (,) delimiter. + * + */ + String removeCurlyBrackets( String reference ) { + return new String( reference.replace("{", "").replace("}", "") ); + } + + + /************************************************************************* + * + * Purpose: To get information regarding what objects are being inherited + * by this object. + * + */ + public void getObjectInheritance() throws Exception { + + moveToStartOfObject(); + + if( currentLine.contains( OBJECT_EXTENDS ) && + currentLine.startsWith(OBJECT_START) ) { + + // Continue, since found the extends line. + + } else { + + readNextLine(); + + while( !currentLine.contains( OBJECT_EXTENDS ) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + readNextLine(); + } + } + + // Found the extends line + if( currentLine.contains( OBJECT_EXTENDS ) && + (currentLine.indexOf( OBJECT_EXTENDS.trim() ) == OBJECT_INDENT) ) { + + objectExtends = removeBrackets( removeNamespace( cleanUpReference( removeLabel( currentLine ) ) ) ); + + } + } + + /************************************************************************* + * + * Purpose: To remove the links (# sign) and double-quote marking ("") in + * a String, in order to only list the element(s), which might be + * be separated by the comma (,) delimiter. + * + */ + String cleanUpReference( String reference ) { + return new String( reference.replace("\"", "").replace("#", "") ); + } + + /************************************************************************* + * + * Purpose: To remove double-quotation marks ("") from document lines. + * + */ + String removeDoubleQuotes( String reference ) { + return new String( reference.replace("\"", "").trim() ); + } + + /************************************************************************* + * + * Purpose: To replace angle brackets <> from document lines, with + * parantheses (), as they interfere with JavaDoc formatting. + * + */ + String replaceAngleBrackets( String reference ) { + return new String( reference.replace("<", "(").replace(">", ")").trim() ); + } + + /************************************************************************* + * + * Purpose: To replace `&` from document lines, with `{@literal &}`, + * as they interfere with JavaDoc formatting. + * + */ + String makeAmpersandLiteralForJavaDoc( String reference ) { + return new String( reference.replace("`&`", "`{@literal &}`").trim() ); + } + + /************************************************************************* + * + * Purpose: To determine the end of the "fields" section as has been + * reached in the current object being processed extends. + * + */ + Boolean reachedEndOfFieldsSection() { + if( currentLine.trim().length() == 0 ) { + + return false; + + } else if ( currentLine.substring( OBJECT_INDENT, OBJECT_INDENT + 1 ).trim().length() == 0 ) { + + return false; + + } else { + + return true; + + } + } + + /************************************************************************* + * + * Purpose: To move the current line being read back to the start of the + * "field" section of the current object being processed. + * + */ + void moveToStartOfField() throws Exception { + currentLineNumber = currentFieldStartLine; + readLine( currentLineNumber ); + } + + + /************************************************************************* + * + * Purpose: To print the fields and their types. + * + */ + public void printObjectFields( Map map ) { + + for(String key: map.keySet()){ + + print(key +" -> "+ map.get(key)); + + } + + } + + /************************************************************************* + * + * Purpose: To print the fields and their documentation. + * + */ + public void printObjectFieldsDocumentation( Map map ) { + + for(String key: map.keySet()){ + + print( "Field name: " + key +" -doc-> "+ map.get(key)); + + } + + } + + /************************************************************************* + * + * Purpose: To initiate the processing of all fields for an object. It + * will loop until it reaches the end of the object's fields. + * + */ + public void getObjectFields() throws Exception { + + moveToStartOfObject(); + currentFieldStartLine = -1; + objectFields = new HashMap(); + objectFieldsDocumentation = new HashMap(); + + if( currentLine.contains( FIELDS_SECTION_START ) && + currentLine.startsWith(OBJECT_START) ) { + + // Continue... + + } else { + readNextLine(); + while( !currentLine.contains( FIELDS_SECTION_START ) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + readNextLine(); + } + } + + // Found a current line + if( currentLine.contains( FIELDS_SECTION_START ) && + (currentLine.indexOf( FIELDS_SECTION_START.trim() ) == OBJECT_INDENT) ) { + + // Skip the first line since it's never defined + readNextLine(); + + while( !reachedEndOfFieldsSection() && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + + if( processNextField() ) { + + // Keep looking for the next field + + } else { + break; + } + + } + + } + } + + + /************************************************************************* + * + * Purpose: Process the next field section. If it is the last field then + * return false denoting there are no more fields in this object + * to process, otherwise return true. + * + */ + Boolean processNextField() throws Exception { + + // Note: Next version add an indent-check as well + if ( currentLine.contains(FIELD_START) ) { + + currentFieldStartLine = currentLineNumber; + + } else { + + while ( !currentLine.contains(FIELD_START) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + readNextLine(); + + } + + if( currentLine.contains(FIELD_START) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + currentFieldStartLine = currentLineNumber; + } + } + + // Process the first line in fields section + if( currentFieldStartLine != -1 && + !currentLine.startsWith(OBJECT_START) ) { + + String fieldName = cleanUpReference(removeLabel( getFieldName() )); + String fieldTypes = getFieldType(); + String fieldDocumentation = getFieldDocumentation(); + + if( fieldName.length() != 0 && fieldTypes.length() != 0 ) { + objectFields.put( fieldName, fieldTypes ); + if ( fieldDocumentation.length() != 0 ) { + objectFieldsDocumentation.put( fieldName, fieldDocumentation ); + } + } + + // Move forward (advance to not stay in a loop) + //readNextLine(); //not needed because documentation performs it already + + return true; + + } else { + + return false; + + } + + } + + /************************************************************************* + * + * Purpose: Determine the name of the current field being processed. + * + */ + String getFieldName() throws Exception { + + moveToStartOfField(); + + while( !currentLine.contains(FIELD_NAME) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + readNextLine(); + } + + if( currentLine.contains(FIELD_NAME) ) { + return new String( currentLine ); + } else { + return new String(""); + } + + } + + Boolean isFieldDocumentationMultiline( String text ) throws Exception { + + if( + text.contains( FIELD_DOCUMENTATION_MULTILINE ) || + text.replace( FIELD_DOCUMENTATION, "" ).trim().length() == 0 + ) { + // Continue to the next line + readNextLine(); + return true; + } else { + return false; + } + + } + + /************************************************************************* + * + * Purpose: To get the documentation of a field for the object + * being processed. + * + */ + String getFieldDocumentation() throws Exception { + + moveToStartOfField(); + + // Move from start of field + if( currentLine.contains(FIELD_START) ) { + readNextLine(); + } + + + // Get to start of type section + while( !currentLine.contains(FIELD_DOCUMENTATION) && + !currentLine.contains(FIELD_START) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + + readNextLine(); + + // If found next field stop! + if( currentLine.contains(FIELD_START) ) { + break; + } + + if( currentLine.contains(FIELD_DOCUMENTATION) && + !currentLine.contains(FIELD_START) && + !currentLine.startsWith(OBJECT_START) && !reachedEOF ) { + break; + } + } + + // If found next field stop! + if( currentLine.contains(FIELD_START) ) { + return new String(""); + } + + if( !currentLine.startsWith(OBJECT_START) ) { + + Integer documentIndentation = -1; + + // Determine where the indentation of this type definition is, for later checking if still + // within the Type definition + if ( currentLine.contains( FIELD_DOCUMENTATION ) ) { + documentIndentation = currentLine.indexOf( FIELD_DOCUMENTATION ); + } + + Boolean isWithinDocumentation = true; + Boolean isDocumentationMultiLine = isFieldDocumentationMultiline( currentLine ); + + String fieldDocumentation = new String(); + + // Reached the end of the current field's type + while( isWithinDocumentation && + !currentLine.contains(FIELD_NAME) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + + // Process multiple lines if the check does pass (false) + if( !isDocumentationMultiLine ) { + fieldDocumentation = new String( fieldDocumentation + replaceAngleBrackets(removeDoubleQuotes(removeLabel( currentLine)) )); + fieldDocumentation = new String( makeAmpersandLiteralForJavaDoc(fieldDocumentation) ); + break; + } else { + fieldDocumentation = new String( fieldDocumentation + " " + replaceAngleBrackets( removeDoubleQuotes( currentLine ) ) ); + fieldDocumentation = new String( makeAmpersandLiteralForJavaDoc(fieldDocumentation) ); + } + + readNextLine(); + + // Has moved beyond the Type definition of the field + if( currentLine.trim().length() != 0 ) { + if( (currentLine.substring( documentIndentation, documentIndentation + 1 ).trim().length() > 0) ) { + isWithinDocumentation = false; + } + } + + // Completed the type definition section of this field + if( !isWithinDocumentation && + !currentLine.contains(FIELD_NAME) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + break; + } + } + + //return processArrayListTypes(typeDefinitions); + return fieldDocumentation; + + } else { + return new String( "" ); + } + + } + + /************************************************************************* + * + * Purpose: Get the list of types in the field being processed as an array. + * This is the case if they are listed only on one line. + * + */ + String [] cleanUpOneLineTypes( String lineOfText ) { + String cleanedUpLine = new String( lineOfText.replace("\"", "").replace("#", "").replace("[", "").replace("]", "") ); + return cleanedUpLine.split(COMMA); + } + + /************************************************************************* + * + * Purpose: Determine if the current type in the field being processed is + * multi-line. + * + */ + Boolean checkIfTypeIsMultiLine( String lineOfText ) { + return ( removeLabel( lineOfText ).length() == 0); + } + + String getFieldType() throws Exception { + + moveToStartOfField(); + + // Get to start of type section + while( !currentLine.contains(FIELD_TYPE) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + + readNextLine(); + + if( currentLine.contains(FIELD_TYPE) && !currentLine.startsWith(OBJECT_START) && !reachedEOF ) { + break; + } + } + + if( !currentLine.startsWith(OBJECT_START) ) { + + Integer typeIndentation = -1; + + // Determine where the indentation of this type definition is, for later checking if still + // within the Type definition + if ( currentLine.contains( FIELD_TYPE ) ) { + typeIndentation = currentLine.indexOf( FIELD_TYPE ); + } + + Boolean isWithinType = true; + Boolean isTypeMultiLine = checkIfTypeIsMultiLine( currentLine ); + ArrayList typeDefinitions = new ArrayList(); + + // Reached the end of the current field's type + while( isWithinType && + !currentLine.contains(FIELD_NAME) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + + // Process multiple lines if the check does pass (false) + if( !isTypeMultiLine ) { + for( String typeElement : cleanUpOneLineTypes( removeLabel(currentLine) ) ) { + typeDefinitions.add( typeElement.trim() ); + } + break; + } else { + + if( currentLine.contains(COMMA) ) { + + for( String typeElement : cleanUpOneLineTypes( removeLabel(currentLine) ) ) { + typeDefinitions.add( typeElement.trim() ); + } + } else { + + typeDefinitions.add( currentLine.trim() ); + } + } + + readNextLine(); + + // Has moved beyond the Type definition of the field + if( currentLine.trim().length() != 0 ) { + if( (currentLine.substring( typeIndentation, typeIndentation + 1 ).trim().length() > 0) ) { + isWithinType = false; + } + } + + // Completed the type definition section of this field + if( !isWithinType && + !currentLine.contains(FIELD_NAME) && + !currentLine.startsWith(OBJECT_START) && + !reachedEOF ) { + break; + } + } + + return processArrayListTypes(typeDefinitions); + + } else { + return new String( "" ); + } + + } + + /************************************************************************* + * + * Purpose: Remove the dash (-) in a String. + * + */ + String removeDash( String lineOfText ) { + String cleanedUpLine = new String( lineOfText.replace(DASH, "").trim() ); + return cleanedUpLine; + } + + + /************************************************************************* + * + * Purpose: Process and annotate the field types in the current object, + * and return them as one String, with the types being + * comma-separated. This is for the proper creation of variables + * and methods during the SDK generation process. + * + */ + String processArrayListTypes( ArrayList typesList ) { + + String processedString = new String(); + Boolean isArray = false; + Boolean isSymbol = false; + Boolean isEnum = false; + + for (String type : typesList ) { + + //System.out.println("TYPE =--------------------------> " + type); + if( type.contains(FIELD_SYMBOLS) ) { + isSymbol = true; + continue; + } + + // On the next loop to see if symbol section is complete + if ( isSymbol && !(type.contains(FIELD_NAME) || type.contains(FIELD_TYPE)) ) { + continue; + } else { + isSymbol = false; + } + + if( type.contains(FIELD_TYPE) && + type.contains(ARRAY) ) { + isArray = true; + continue; + } + + if( type.contains(FIELD_TYPE) && + type.contains(ENUM) ) { + isEnum = true; + continue; + } + + if ( type.contains(FIELD_ITEMS) ) { + + // Continue... + + type = removeDash( type.replace( FIELD_ITEMS, "" ) ); + } + + if( type.trim().length() != 0 && !type.contains(NULL_STRING)) { + + if( isArray ) { + if( processedString.trim().length() != 0 ) { + processedString = new String(processedString + ", " + + removeDash(cleanUpReference(removeLabel(type))) + " [] "); + } else { + processedString = new String( + removeDash(cleanUpReference(removeLabel(type))) + " [] "); + } + } else if( isEnum ){ + if( processedString.trim().length() != 0 ) { + processedString = new String(processedString + ", " + "{}" + + removeDash(cleanUpReference(removeLabel(type))) ); + } else { + processedString = new String("{}" + + removeDash(cleanUpReference(removeLabel(type))) ); + } + } else { + + // Remove question mark, and might need to remove them above as well + // Ref: https://github.com/common-workflow-language/cwljava/issues/20 + // Ref: http://www.commonwl.org/v1.0/CommandLineTool.html#Document_preprocessing + + if( processedString.trim().length() != 0 ) { + processedString = new String(processedString + ", " + + removeDash(cleanUpReference(removeLabel(removeQuestionMark(type))))); + + // Ensure there is a spacing in between the type and the brackets (i.e. string[]) and an array + processedString = new String( addSpacingToBrackets(processedString) ); + //System.out.println( "BRACKETS -------------> " + processedString); + + } else { + processedString = new String( + removeDash(cleanUpReference(removeLabel(removeQuestionMark(type))))); + + // Ensure there is a spacing in between the type and the brackets (i.e. string[]) and an array + processedString = new String( addSpacingToBrackets(processedString) ); + //System.out.println( "BRACKETS -------------> " + processedString); + + } + } + } + + } + return processedString; + } + + /************************************************************************* + * + * Purpose: Update the types in fields which are abstract. + * Sometimes fields will point to types which are abstract, and + * this method will travel the dependency path to the first + * concrete class implemenation and replace the type with that + * of concrete class. + * + */ + public Map updateAbstractFields(Map objects) { + + String objectName; + Map objectInformation; + Map extendsInformation = new HashMap(); + Set extendedFieldTypes = new HashSet(); + + String FIELDS = "fields"; + String ABSTRACT = "abstract"; + String EXTENDS = "extends"; + Map fields; + String [] fieldTypes; + String fieldElement; + String updatedFieldType; + + + // Build the list of class which extend classes + for(String nameOfObject: objects.keySet()) { + String extendsClasses = (String) objects.get(nameOfObject).get(EXTENDS); + String [] extendedClassList = ((String) objects.get(nameOfObject).get(EXTENDS)).split(COMMA); + for( String className : extendedClassList ) { + extendsInformation.put( nameOfObject.trim(), className.trim() ); + } + } + + for( String nameOfObject: objects.keySet() ) { + print(nameOfObject); + objectInformation = objects.get(nameOfObject); + fields = (Map ) objects.get(nameOfObject).get(FIELDS); + + if( fields.keySet().size() > 0 ) { + for( String fieldName : fields.keySet() ) { + + //Get the types for the specific fieldName + fieldTypes = fields.get( fieldName ).split(COMMA); + extendedFieldTypes = new HashSet(); + + // Process all the types for that fieldName + for( String fieldType : fieldTypes ) { + + fieldElement = removeCurlyBrackets( removeBrackets(fieldType) ).trim(); + + //i.e. string, etc. + if( objects.get(fieldElement) != null ) { + + // Check if it is abstract + if ( (Boolean) objects.get(fieldElement).get(ABSTRACT) ) { + for( String className : extendsInformation.keySet() ) { + + // See if it extends an abstract object + if( extendsInformation.get(className).equals(fieldElement) ) { + updatedFieldType = new String( fieldType ); + print( className + " => " + fieldElement + " to " + updatedFieldType); + updatedFieldType = updatedFieldType.replace( fieldElement, className ); + extendedFieldTypes.add( updatedFieldType ); + } + } + } else { + //extendedFieldTypes.add( fieldElement ); + extendedFieldTypes.add( fieldType ); + } + + } else { //for string, etc. + extendedFieldTypes.add( fieldType ); + } + + } + + Map updatedObjectInformation = new HashMap(); + + updatedObjectInformation = objects.get( nameOfObject ); + fields = (Map ) objects.get(nameOfObject).get(FIELDS); + fields.put( fieldName, convertSetToString( extendedFieldTypes ) ); + + updatedObjectInformation.put( FIELDS, fields ); + objects.put( nameOfObject, updatedObjectInformation ); + + } + } // otherwise nothing is changed + } + + return objects; + } + + /************************************************************************* + * + * Purpose: To convert an ArrayList of classes to a String separated by + * commas (,). + * + */ + public String convertSetToString( Set arrayList ) { + + String concatenatedStrings = new String(); + + for (String element : arrayList ) { + + if( concatenatedStrings.length() == 0 ) { + concatenatedStrings = new String( element.trim() ); + } else { + concatenatedStrings = new String( concatenatedStrings + ", " + element.trim() ); + } + } + + return concatenatedStrings; + + } + + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/cwl-sdk-config.txt b/sdk-and-javadoc-generation/cwl-sdk-config.txt new file mode 100755 index 00000000..123572ac --- /dev/null +++ b/sdk-and-javadoc-generation/cwl-sdk-config.txt @@ -0,0 +1,74 @@ +override : Sink : interface +override : NamedType : interface +override : DocType : interface +override : SchemaDefinedType : interface +override : SchemaBase : interface +override : Parameter : interface +override : InputBinding : interface +override : OutputBinding : interface +override : InputSchema : interface +override : OutputSchema : interface +override : ProcessRequirement : interface +override : Process : interface +skip : PrimitiveType +skip : "Any" +namespace : _id : sld +namespace : specializeFrom : sld +namespace : specializeTo : sld +namespace : doc : sld +namespace : docParent : sld +namespace : docAfter : sld +namespace : jsonldPredicate : sld +namespace : type : sld +namespace : jsonldPredicate : sld +namespace : record : sld +namespace : fields : sld +namespace : extends : sld +namespace : enum : sld +namespace : symbols : sld +namespace : array : sld +namespace : items : sld +namespace : documentation : sld +namespace : null : sld +namespace : boolean : xsd +namespace : int : xsd +namespace : long : xsd +namespace : float : xsd +namespace : double : xsd +namespace : string : xsd +namespace : RecordSchema : sld +namespace : EnumSchema : sld +namespace : ArraySchema : sld +namespace : PrimitiveType : sld +namespace : File : cwl +namespace : Directory : cwl +namespace : secondaryFiles : cwl +namespace : format : cwl +namespace : default : cwl +namespace : ExpressionPlaceholder : cwl +namespace : inputBinding : cwl +namespace : outputBinding : cwl +namespace : inputs : cwl +namespace : outputs : cwl +namespace : requirements : cwl +namespace : hints : cwl +namespace : cwlVersion : cwl +namespace : baseCommand : cwl +namespace : arguments : cwl +namespace : source : cwl +namespace : steps : cwl +namespace : scatter : cwl +namespace : scatterMethod : cwl +namespace : creator : dct +namespace : comment : rdfs +namespace : label : rdfs +namespace : name : foaf +namespace : mbox : foaf +namespace : cwl : https://w3id.org/cwl/cwl# +namespace : sld : https://w3id.org/cwl/salad# +namespace : avro : https://w3id.org/cwl/avro# +namespace : dct : http://purl.org/dc/terms/ +namespace : rdf : http://www.w3.org/1999/02/22-rdf-syntax-ns# +namespace : rdfs : http://www.w3.org/2000/01/rdf-schema# +namespace : foaf : http://xmlns.com/foaf/0.1/ +namespace : xsd : http://www.w3.org/2001/XMLSchema# diff --git a/sdk-and-javadoc-generation/cwl-yaml-specs/CommandLineTool.yml b/sdk-and-javadoc-generation/cwl-yaml-specs/CommandLineTool.yml new file mode 100644 index 00000000..3e85541c --- /dev/null +++ b/sdk-and-javadoc-generation/cwl-yaml-specs/CommandLineTool.yml @@ -0,0 +1,895 @@ +$base: "https://w3id.org/cwl/cwl#" + +$namespaces: + cwl: "https://w3id.org/cwl/cwl#" + +$graph: + +- name: CommandLineToolDoc + type: documentation + doc: + - | + # Common Workflow Language (CWL) Command Line Tool Description, v1.0 + + This version: + * https://w3id.org/cwl/v1.0/ + + Current version: + * https://w3id.org/cwl/ + - "\n\n" + - {$include: contrib.md} + - "\n\n" + - | + # Abstract + + A Command Line Tool is a non-interactive executable program that reads + some input, performs a computation, and terminates after producing some + output. Command line programs are a flexible unit of code sharing and + reuse, unfortunately the syntax and input/output semantics among command + line programs is extremely heterogeneous. A common layer for describing + the syntax and semantics of programs can reduce this incidental + complexity by providing a consistent way to connect programs together. + This specification defines the Common Workflow Language (CWL) Command + Line Tool Description, a vendor-neutral standard for describing the + syntax and input/output semantics of command line programs. + + - {$include: intro.md} + + - | + ## Introduction to v1.0 + + This specification represents the first full release from the CWL group. + Since draft-3, version 1.0 introduces the following changes and additions: + + * The [Directory](#Directory) type. + * Syntax simplifcations: denoted by the `map<>` syntax. Example: inputs + contains a list of items, each with an id. Now one can specify + a mapping of that identifier to the corresponding + `CommandInputParamater`. + ``` + inputs: + - id: one + type: string + doc: First input parameter + - id: two + type: int + doc: Second input parameter + ``` + can be + ``` + inputs: + one: + type: string + doc: First input parameter + two: + type: int + doc: Second input parameter + ``` + * [InitialWorkDirRequirement](#InitialWorkDirRequirement): list of + files and subdirectories to be present in the output directory prior + to execution. + * Shortcuts for specifying the standard [output](#stdout) and/or + [error](#stderr) streams as a (streamable) File output. + * [SoftwareRequirement](#SoftwareRequirement) for describing software + dependencies of a tool. + * The common `description` field has been renamed to `doc`. + + ## Errata + + Post v1.0 release changes to the spec. + + * 13 July 2016: Mark `baseCommand` as optional and update descriptive text. + + ## Purpose + + Standalone programs are a flexible and interoperable form of code reuse. + Unlike monolithic applications, applications and analysis workflows which + are composed of multiple separate programs can be written in multiple + languages and execute concurrently on multiple hosts. However, POSIX + does not dictate computer-readable grammar or semantics for program input + and output, resulting in extremely heterogeneous command line grammar and + input/output semantics among program. This is a particular problem in + distributed computing (multi-node compute clusters) and virtualized + environments (such as Docker containers) where it is often necessary to + provision resources such as input files before executing the program. + + Often this gap is filled by hard coding program invocation and + implicitly assuming requirements will be met, or abstracting program + invocation with wrapper scripts or descriptor documents. Unfortunately, + where these approaches are application or platform specific it creates a + significant barrier to reproducibility and portability, as methods + developed for one platform must be manually ported to be used on new + platforms. Similarly it creates redundant work, as wrappers for popular + tools must be rewritten for each application or platform in use. + + The Common Workflow Language Command Line Tool Description is designed to + provide a common standard description of grammar and semantics for + invoking programs used in data-intensive fields such as Bioinformatics, + Chemistry, Physics, Astronomy, and Statistics. This specification + defines a precise data and execution model for Command Line Tools that + can be implemented on a variety of computing platforms, ranging from a + single workstation to cluster, grid, cloud, and high performance + computing platforms. + + - {$include: concepts.md} + - {$include: invocation.md} + + +- type: record + name: EnvironmentDef + doc: | + Define an environment variable that will be set in the runtime environment + by the workflow platform when executing the command line tool. May be the + result of executing an expression, such as getting a parameter from input. + fields: + - name: envName + type: string + doc: The environment variable name + - name: envValue + type: [string, Expression] + doc: The environment variable value + +- type: record + name: CommandLineBinding + extends: InputBinding + doc: | + + When listed under `inputBinding` in the input schema, the term + "value" refers to the the corresponding value in the input object. For + binding objects listed in `CommandLineTool.arguments`, the term "value" + refers to the effective value after evaluating `valueFrom`. + + The binding behavior when building the command line depends on the data + type of the value. If there is a mismatch between the type described by + the input schema and the effective value, such as resulting from an + expression evaluation, an implementation must use the data type of the + effective value. + + - **string**: Add `prefix` and the string to the command line. + + - **number**: Add `prefix` and decimal representation to command line. + + - **boolean**: If true, add `prefix` to the command line. If false, add + nothing. + + - **File**: Add `prefix` and the value of + [`File.path`](#File) to the command line. + + - **array**: If `itemSeparator` is specified, add `prefix` and the join + the array into a single string with `itemSeparator` separating the + items. Otherwise first add `prefix`, then recursively process + individual elements. + + - **object**: Add `prefix` only, and recursively add object fields for + which `inputBinding` is specified. + + - **null**: Add nothing. + + fields: + - name: position + type: int? + doc: "The sorting key. Default position is 0." + - name: prefix + type: string? + doc: "Command line prefix to add before the value." + - name: separate + type: boolean? + doc: | + If true (default), then the prefix and value must be added as separate + command line arguments; if false, prefix and value must be concatenated + into a single command line argument. + - name: itemSeparator + type: string? + doc: | + Join the array elements into a single string with the elements + separated by by `itemSeparator`. + - name: valueFrom + type: + - "null" + - string + - Expression + jsonldPredicate: "cwl:valueFrom" + doc: | + If `valueFrom` is a constant string value, use this as the value and + apply the binding rules above. + + If `valueFrom` is an expression, evaluate the expression to yield the + actual value to use to build the command line and apply the binding + rules above. If the inputBinding is associated with an input + parameter, the value of `self` in the expression will be the value of the + input parameter. + + When a binding is part of the `CommandLineTool.arguments` field, + the `valueFrom` field is required. + - name: shellQuote + type: boolean? + doc: | + If `ShellCommandRequirement` is in the requirements for the current command, + this controls whether the value is quoted on the command line (default is true). + Use `shellQuote: false` to inject metacharacters for operations such as pipes. + +- type: record + name: CommandOutputBinding + extends: OutputBinding + doc: | + Describes how to generate an output parameter based on the files produced + by a CommandLineTool. + + The output parameter is generated by applying these operations in + the following order: + + - glob + - loadContents + - outputEval + fields: + - name: glob + type: + - "null" + - string + - Expression + - type: array + items: string + doc: | + Find files relative to the output directory, using POSIX glob(3) + pathname matching. If an array is provided, find files that match any + pattern in the array. If an expression is provided, the expression must + return a string or an array of strings, which will then be evaluated as + one or more glob patterns. Must only match and return files which + actually exist. + - name: loadContents + type: + - "null" + - boolean + jsonldPredicate: "cwl:loadContents" + doc: | + For each file matched in `glob`, read up to + the first 64 KiB of text from the file and place it in the `contents` + field of the file object for manipulation by `outputEval`. + - name: outputEval + type: + - "null" + - string + - Expression + doc: | + Evaluate an expression to generate the output value. If `glob` was + specified, the value of `self` must be an array containing file objects + that were matched. If no files were matched, `self` must be a zero + length array; if a single file was matched, the value of `self` is an + array of a single element. Additionally, if `loadContents` is `true`, + the File objects must include up to the first 64 KiB of file contents + in the `contents` field. + + +- name: CommandInputRecordField + type: record + extends: InputRecordField + specialize: + - specializeFrom: InputRecordSchema + specializeTo: CommandInputRecordSchema + - specializeFrom: InputEnumSchema + specializeTo: CommandInputEnumSchema + - specializeFrom: InputArraySchema + specializeTo: CommandInputArraySchema + - specializeFrom: InputBinding + specializeTo: CommandLineBinding + + +- name: CommandInputRecordSchema + type: record + extends: InputRecordSchema + specialize: + - specializeFrom: InputRecordField + specializeTo: CommandInputRecordField + + +- name: CommandInputEnumSchema + type: record + extends: InputEnumSchema + specialize: + - specializeFrom: InputBinding + specializeTo: CommandLineBinding + + +- name: CommandInputArraySchema + type: record + extends: InputArraySchema + specialize: + - specializeFrom: InputRecordSchema + specializeTo: CommandInputRecordSchema + - specializeFrom: InputEnumSchema + specializeTo: CommandInputEnumSchema + - specializeFrom: InputArraySchema + specializeTo: CommandInputArraySchema + - specializeFrom: InputBinding + specializeTo: CommandLineBinding + + +- name: CommandOutputRecordField + type: record + extends: OutputRecordField + specialize: + - specializeFrom: OutputRecordSchema + specializeTo: CommandOutputRecordSchema + - specializeFrom: OutputEnumSchema + specializeTo: CommandOutputEnumSchema + - specializeFrom: OutputArraySchema + specializeTo: CommandOutputArraySchema + - specializeFrom: OutputBinding + specializeTo: CommandOutputBinding + + +- name: CommandOutputRecordSchema + type: record + extends: OutputRecordSchema + specialize: + - specializeFrom: OutputRecordField + specializeTo: CommandOutputRecordField + + +- name: CommandOutputEnumSchema + type: record + extends: OutputEnumSchema + specialize: + - specializeFrom: OutputRecordSchema + specializeTo: CommandOutputRecordSchema + - specializeFrom: OutputEnumSchema + specializeTo: CommandOutputEnumSchema + - specializeFrom: OutputArraySchema + specializeTo: CommandOutputArraySchema + - specializeFrom: OutputBinding + specializeTo: CommandOutputBinding + + +- name: CommandOutputArraySchema + type: record + extends: OutputArraySchema + specialize: + - specializeFrom: OutputRecordSchema + specializeTo: CommandOutputRecordSchema + - specializeFrom: OutputEnumSchema + specializeTo: CommandOutputEnumSchema + - specializeFrom: OutputArraySchema + specializeTo: CommandOutputArraySchema + - specializeFrom: OutputBinding + specializeTo: CommandOutputBinding + + +- type: record + name: CommandInputParameter + extends: InputParameter + doc: An input parameter for a CommandLineTool. + specialize: + - specializeFrom: InputRecordSchema + specializeTo: CommandInputRecordSchema + - specializeFrom: InputEnumSchema + specializeTo: CommandInputEnumSchema + - specializeFrom: InputArraySchema + specializeTo: CommandInputArraySchema + - specializeFrom: InputBinding + specializeTo: CommandLineBinding + +- type: record + name: CommandOutputParameter + extends: OutputParameter + doc: An output parameter for a CommandLineTool. + specialize: + - specializeFrom: OutputBinding + specializeTo: CommandOutputBinding + fields: + - name: type + type: + - "null" + - CWLType + - stdout + - stderr + - CommandOutputRecordSchema + - CommandOutputEnumSchema + - CommandOutputArraySchema + - string + - type: array + items: + - CWLType + - CommandOutputRecordSchema + - CommandOutputEnumSchema + - CommandOutputArraySchema + - string + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True + doc: | + Specify valid types of data that may be assigned to this parameter. + +- name: stdout + type: enum + symbols: [ "cwl:stdout" ] + docParent: "#CommandOutputParameter" + doc: | + Only valid as a `type` for a `CommandLineTool` output with no + `outputBinding` set. + + The following + ``` + outputs: + an_output_name: + type: stdout + + stdout: a_stdout_file + ``` + is equivalent to + ``` + outputs: + an_output_name: + type: File + streamable: true + outputBinding: + glob: a_stdout_file + + stdout: a_stdout_file + ``` + + If there is no `stdout` name provided, a random filename will be created. + For example, the following + ``` + outputs: + an_output_name: + type: stdout + ``` + is equivalent to + ``` + outputs: + an_output_name: + type: File + streamable: true + outputBinding: + glob: random_stdout_filenameABCDEFG + + stdout: random_stdout_filenameABCDEFG + ``` + + +- name: stderr + type: enum + symbols: [ "cwl:stderr" ] + docParent: "#CommandOutputParameter" + doc: | + Only valid as a `type` for a `CommandLineTool` output with no + `outputBinding` set. + + The following + ``` + outputs: + an_output_name: + type: stderr + + stderr: a_stderr_file + ``` + is equivalent to + ``` + outputs: + an_output_name: + type: File + streamable: true + outputBinding: + glob: a_stderr_file + + stderr: a_stderr_file + ``` + + If there is no `stderr` name provided, a random filename will be created. + For example, the following + ``` + outputs: + an_output_name: + type: stderr + ``` + is equivalent to + ``` + outputs: + an_output_name: + type: File + streamable: true + outputBinding: + glob: random_stderr_filenameABCDEFG + + stderr: random_stderr_filenameABCDEFG + ``` + + +- type: record + name: CommandLineTool + extends: Process + documentRoot: true + specialize: + - specializeFrom: InputParameter + specializeTo: CommandInputParameter + - specializeFrom: OutputParameter + specializeTo: CommandOutputParameter + doc: | + This defines the schema of the CWL Command Line Tool Description document. + + fields: + - name: class + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + type: string + - name: baseCommand + doc: | + Specifies the program to execute. If an array, the first element of + the array is the command to execute, and subsequent elements are + mandatory command line arguments. The elements in `baseCommand` must + appear before any command line bindings from `inputBinding` or + `arguments`. + + If `baseCommand` is not provided or is an empty array, the first + element of the command line produced after processing `inputBinding` or + `arguments` must be used as the program to execute. + + If the program includes a path separator character it must + be an absolute path, otherwise it is an error. If the program does not + include a path separator, search the `$PATH` variable in the runtime + environment of the workflow runner find the absolute path of the + executable. + type: + - string? + - string[]? + jsonldPredicate: + "_id": "cwl:baseCommand" + "_container": "@list" + - name: arguments + doc: | + Command line bindings which are not directly associated with input parameters. + type: + - "null" + - type: array + items: [string, Expression, CommandLineBinding] + jsonldPredicate: + "_id": "cwl:arguments" + "_container": "@list" + - name: stdin + type: ["null", string, Expression] + doc: | + A path to a file whose contents must be piped into the command's + standard input stream. + - name: stderr + type: ["null", string, Expression] + jsonldPredicate: "https://w3id.org/cwl/cwl#stderr" + doc: | + Capture the command's standard error stream to a file written to + the designated output directory. + + If `stderr` is a string, it specifies the file name to use. + + If `stderr` is an expression, the expression is evaluated and must + return a string with the file name to use to capture stderr. If the + return value is not a string, or the resulting path contains illegal + characters (such as the path separator `/`) it is an error. + - name: stdout + type: ["null", string, Expression] + jsonldPredicate: "https://w3id.org/cwl/cwl#stdout" + doc: | + Capture the command's standard output stream to a file written to + the designated output directory. + + If `stdout` is a string, it specifies the file name to use. + + If `stdout` is an expression, the expression is evaluated and must + return a string with the file name to use to capture stdout. If the + return value is not a string, or the resulting path contains illegal + characters (such as the path separator `/`) it is an error. + - name: successCodes + type: int[]? + doc: | + Exit codes that indicate the process completed successfully. + + - name: temporaryFailCodes + type: int[]? + doc: | + Exit codes that indicate the process failed due to a possibly + temporary condition, where executing the process with the same + runtime environment and inputs may produce different results. + + - name: permanentFailCodes + type: int[]? + doc: + Exit codes that indicate the process failed due to a permanent logic + error, where executing the process with the same runtime environment and + same inputs is expected to always fail. + + +- type: record + name: DockerRequirement + extends: ProcessRequirement + doc: | + Indicates that a workflow component should be run in a + [Docker](http://docker.com) container, and specifies how to fetch or build + the image. + + If a CommandLineTool lists `DockerRequirement` under + `hints` (or `requirements`), it may (or must) be run in the specified Docker + container. + + The platform must first acquire or install the correct Docker image as + specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`. + + The platform must execute the tool in the container using `docker run` with + the appropriate Docker image and tool command line. + + The workflow platform may provide input files and the designated output + directory through the use of volume bind mounts. The platform may rewrite + file paths in the input object to correspond to the Docker bind mounted + locations. + + When running a tool contained in Docker, the workflow platform must not + assume anything about the contents of the Docker container, such as the + presence or absence of specific software, except to assume that the + generated command line represents a valid command within the runtime + environment of the container. + + ## Interaction with other requirements + + If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a + DockerRequirement, the environment variables must be provided to Docker + using `--env` or `--env-file` and interact with the container's preexisting + environment as defined by Docker. + + fields: + - name: class + type: string + doc: "Always 'DockerRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + - name: dockerPull + type: string? + doc: "Specify a Docker image to retrieve using `docker pull`." + - name: dockerLoad + type: string? + doc: "Specify a HTTP URL from which to download a Docker image using `docker load`." + - name: dockerFile + type: string? + doc: "Supply the contents of a Dockerfile which will be built using `docker build`." + - name: dockerImport + type: string? + doc: "Provide HTTP URL to download and gunzip a Docker images using `docker import." + - name: dockerImageId + type: string? + doc: | + The image id that will be used for `docker run`. May be a + human-readable image name or the image identifier hash. May be skipped + if `dockerPull` is specified, in which case the `dockerPull` image id + must be used. + - name: dockerOutputDirectory + type: string? + doc: | + Set the designated output directory to a specific location inside the + Docker container. + + +- type: record + name: SoftwareRequirement + extends: ProcessRequirement + doc: | + A list of software packages that should be configured in the environment of + the defined process. + fields: + - name: class + type: string + doc: "Always 'SoftwareRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + - name: packages + type: SoftwarePackage[] + doc: "The list of software to be configured." + jsonldPredicate: + mapSubject: package + mapPredicate: specs + +- name: SoftwarePackage + type: record + fields: + - name: package + type: string + doc: "The common name of the software to be configured." + jsonldPredicate: "@id" + - name: version + type: string[]? + doc: "The (optional) version of the software to configured." + - name: specs + type: string[]? + doc: | + Must be one or more IRIs identifying resources for installing or + enabling the software. Implementations may provide resolvers which map + well-known software spec IRIs to some configuration action. + + For example, an IRI `https://packages.debian.org/jessie/bowtie` could + be resolved with `apt-get install bowtie`. An IRI + `https://anaconda.org/bioconda/bowtie` could be resolved with `conda + install -c bioconda bowtie`. + + Tools may also provide IRIs to index entries such as + [RRID](http://www.identifiers.org/rrid/), such as + `http://identifiers.org/rrid/RRID:SCR_005476` + + +- name: Dirent + type: record + doc: | + Define a file or subdirectory that must be placed in the designated output + directory prior to executing the command line tool. May be the result of + executing an expression, such as building a configuration file from a + template. + fields: + - name: entryname + type: ["null", string, Expression] + jsonldPredicate: + _id: cwl:entryname + doc: | + The name of the file or subdirectory to create in the output directory. + If `entry` is a File or Directory, this overrides `basename`. Optional. + - name: entry + type: [string, Expression] + jsonldPredicate: + _id: cwl:entry + doc: | + If the value is a string literal or an expression which evaluates to a + string, a new file must be created with the string as the file contents. + + If the value is an expression that evaluates to a `File` object, this + indicates the referenced file should be added to the designated output + directory prior to executing the tool. + + If the value is an expression that evaluates to a `Dirent` object, this + indicates that the File or Directory in `entry` should be added to the + designated output directory with the name in `entryname`. + + If `writable` is false, the file may be made available using a bind + mount or file system link to avoid unnecessary copying of the input + file. + - name: writable + type: boolean? + doc: | + If true, the file or directory must be writable by the tool. Changes + to the file or directory must be isolated and not visible by any other + CommandLineTool process. This may be implemented by making a copy of + the original file or directory. Default false (files and directories + read-only by default). + + +- name: InitialWorkDirRequirement + type: record + extends: ProcessRequirement + doc: + Define a list of files and subdirectories that must be created by the + workflow platform in the designated output directory prior to executing the + command line tool. + fields: + - name: class + type: string + doc: InitialWorkDirRequirement + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + - name: listing + type: + - type: array + items: [File, Directory, Dirent, string, Expression] + - string + - Expression + jsonldPredicate: + _id: "cwl:listing" + doc: | + The list of files or subdirectories that must be placed in the + designated output directory prior to executing the command line tool. + + May be an expression. If so, the expression return value must validate + as `{type: array, items: [File, Directory]}`. + + +- name: EnvVarRequirement + type: record + extends: ProcessRequirement + doc: | + Define a list of environment variables which will be set in the + execution environment of the tool. See `EnvironmentDef` for details. + fields: + - name: class + type: string + doc: "Always 'EnvVarRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + - name: envDef + type: EnvironmentDef[] + doc: The list of environment variables. + jsonldPredicate: + mapSubject: envName + mapPredicate: envValue + + +- type: record + name: ShellCommandRequirement + extends: ProcessRequirement + doc: | + Modify the behavior of CommandLineTool to generate a single string + containing a shell command line. Each item in the argument list must be + joined into a string separated by single spaces and quoted to prevent + intepretation by the shell, unless `CommandLineBinding` for that argument + contains `shellQuote: false`. If `shellQuote: false` is specified, the + argument is joined into the command string without quoting, which allows + the use of shell metacharacters such as `|` for pipes. + fields: + - name: class + type: string + doc: "Always 'ShellCommandRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + + +- type: record + name: ResourceRequirement + extends: ProcessRequirement + doc: | + Specify basic hardware resource requirements. + + "min" is the minimum amount of a resource that must be reserved to schedule + a job. If "min" cannot be satisfied, the job should not be run. + + "max" is the maximum amount of a resource that the job shall be permitted + to use. If a node has sufficient resources, multiple jobs may be scheduled + on a single node provided each job's "max" resource requirements are + met. If a job attempts to exceed its "max" resource allocation, an + implementation may deny additional resources, which may result in job + failure. + + If "min" is specified but "max" is not, then "max" == "min" + If "max" is specified by "min" is not, then "min" == "max". + + It is an error if max < min. + + It is an error if the value of any of these fields is negative. + + If neither "min" nor "max" is specified for a resource, an implementation may provide a default. + + fields: + - name: class + type: string + doc: "Always 'ResourceRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + - name: coresMin + type: ["null", long, string, Expression] + doc: Minimum reserved number of CPU cores + + - name: coresMax + type: ["null", int, string, Expression] + doc: Maximum reserved number of CPU cores + + - name: ramMin + type: ["null", long, string, Expression] + doc: Minimum reserved RAM in mebibytes (2**20) + + - name: ramMax + type: ["null", long, string, Expression] + doc: Maximum reserved RAM in mebibytes (2**20) + + - name: tmpdirMin + type: ["null", long, string, Expression] + doc: Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) + + - name: tmpdirMax + type: ["null", long, string, Expression] + doc: Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) + + - name: outdirMin + type: ["null", long, string, Expression] + doc: Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) + + - name: outdirMax + type: ["null", long, string, Expression] + doc: Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) diff --git a/sdk-and-javadoc-generation/cwl-yaml-specs/Process.yml b/sdk-and-javadoc-generation/cwl-yaml-specs/Process.yml new file mode 100644 index 00000000..37b20387 --- /dev/null +++ b/sdk-and-javadoc-generation/cwl-yaml-specs/Process.yml @@ -0,0 +1,743 @@ +$base: "https://w3id.org/cwl/cwl#" + +$namespaces: + cwl: "https://w3id.org/cwl/cwl#" + sld: "https://w3id.org/cwl/salad#" + +$graph: + +- name: "Common Workflow Language, v1.0" + type: documentation + doc: {$include: concepts.md} + +- $import: "salad/schema_salad/metaschema/metaschema_base.yml" + +- name: BaseTypesDoc + type: documentation + doc: | + ## Base types + docChild: + - "#CWLType" + - "#Process" + +- type: enum + name: CWLVersion + doc: "Version symbols for published CWL document versions." + symbols: + - cwl:draft-2 + - cwl:draft-3.dev1 + - cwl:draft-3.dev2 + - cwl:draft-3.dev3 + - cwl:draft-3.dev4 + - cwl:draft-3.dev5 + - cwl:draft-3 + - cwl:draft-4.dev1 + - cwl:draft-4.dev2 + - cwl:draft-4.dev3 + - cwl:v1.0.dev4 + - cwl:v1.0 + +- name: CWLType + type: enum + extends: "sld:PrimitiveType" + symbols: + - cwl:File + - cwl:Directory + doc: + - "Extends primitive types with the concept of a file and directory as a builtin type." + - "File: A File object" + - "Directory: A Directory object" + +- name: File + type: record + docParent: "#CWLType" + doc: | + Represents a file (or group of files if `secondaryFiles` is specified) that + must be accessible by tools using standard POSIX file system call API such as + open(2) and read(2). + fields: + - name: class + type: + type: enum + name: File_class + symbols: + - cwl:File + jsonldPredicate: + _id: "@type" + _type: "@vocab" + doc: Must be `File` to indicate this object describes a file. + - name: location + type: string? + doc: | + An IRI that identifies the file resource. This may be a relative + reference, in which case it must be resolved using the base IRI of the + document. The location may refer to a local or remote resource; the + implementation must use the IRI to retrieve file content. If an + implementation is unable to retrieve the file content stored at a + remote resource (due to unsupported protocol, access denied, or other + issue) it must signal an error. + + If the `location` field is not provided, the `contents` field must be + provided. The implementation must assign a unique identifier for + the `location` field. + + If the `path` field is provided but the `location` field is not, an + implementation may assign the value of the `path` field to `location`, + then follow the rules above. + jsonldPredicate: + _id: "@id" + _type: "@id" + - name: path + type: string? + doc: | + The local host path where the File is available when a CommandLineTool is + executed. This field must be set by the implementation. The final + path component must match the value of `basename`. This field + must not be used in any other context. The command line tool being + executed must be able to to access the file at `path` using the POSIX + `open(2)` syscall. + + As a special case, if the `path` field is provided but the `location` + field is not, an implementation may assign the value of the `path` + field to `location`, and remove the `path` field. + + If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) + (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, + ``, ``, and ``) or characters + [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) + for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) + then implementations may terminate the process with a + `permanentFailure`. + jsonldPredicate: + "_id": "cwl:path" + "_type": "@id" + - name: basename + type: string? + doc: | + The base name of the file, that is, the name of the file without any + leading directory path. The base name must not contain a slash `/`. + + If not provided, the implementation must set this field based on the + `location` field by taking the final path component after parsing + `location` as an IRI. If `basename` is provided, it is not required to + match the value from `location`. + + When this file is made available to a CommandLineTool, it must be named + with `basename`, i.e. the final component of the `path` field must match + `basename`. + jsonldPredicate: "cwl:basename" + - name: dirname + type: string? + doc: | + The name of the directory containing file, that is, the path leading up + to the final slash in the path such that `dirname + '/' + basename == + path`. + + The implementation must set this field based on the value of `path` + prior to evaluating parameter references or expressions in a + CommandLineTool document. This field must not be used in any other + context. + - name: nameroot + type: string? + doc: | + The basename root such that `nameroot + nameext == basename`, and + `nameext` is empty or begins with a period and contains at most one + period. For the purposess of path splitting leading periods on the + basename are ignored; a basename of `.cshrc` will have a nameroot of + `.cshrc`. + + The implementation must set this field automatically based on the value + of `basename` prior to evaluating parameter references or expressions. + - name: nameext + type: string? + doc: | + The basename extension such that `nameroot + nameext == basename`, and + `nameext` is empty or begins with a period and contains at most one + period. Leading periods on the basename are ignored; a basename of + `.cshrc` will have an empty `nameext`. + + The implementation must set this field automatically based on the value + of `basename` prior to evaluating parameter references or expressions. + - name: checksum + type: string? + doc: | + Optional hash code for validating file integrity. Currently must be in the form + "sha1$ + hexadecimal string" using the SHA-1 algorithm. + - name: size + type: long? + doc: Optional file size + - name: "secondaryFiles" + type: + - "null" + - type: array + items: [File, Directory] + jsonldPredicate: "cwl:secondaryFiles" + doc: | + A list of additional files that are associated with the primary file + and must be transferred alongside the primary file. Examples include + indexes of the primary file, or external references which must be + included when loading primary document. A file object listed in + `secondaryFiles` may itself include `secondaryFiles` for which the same + rules apply. + - name: format + type: string? + jsonldPredicate: + _id: cwl:format + _type: "@id" + identity: true + doc: | + The format of the file: this must be an IRI of a concept node that + represents the file format, preferrably defined within an ontology. + If no ontology is available, file formats may be tested by exact match. + + Reasoning about format compatability must be done by checking that an + input file format is the same, `owl:equivalentClass` or + `rdfs:subClassOf` the format required by the input parameter. + `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if + ` owl:equivalentClass ` and ` owl:subclassOf ` then infer + ` owl:subclassOf `. + + File format ontologies may be provided in the "$schema" metadata at the + root of the document. If no ontologies are specified in `$schema`, the + runtime may perform exact file format matches. + - name: contents + type: string? + doc: | + File contents literal. Maximum of 64 KiB. + + If neither `location` nor `path` is provided, `contents` must be + non-null. The implementation must assign a unique identifier for the + `location` field. When the file is staged as input to CommandLineTool, + the value of `contents` must be written to a file. + + If `loadContents` of `inputBinding` or `outputBinding` is true and + `location` is valid, the implementation must read up to the first 64 + KiB of text from the file and place it in the "contents" field. + + +- name: Directory + type: record + docAfter: "#File" + doc: | + Represents a directory to present to a command line tool. + fields: + - name: class + type: + type: enum + name: Directory_class + symbols: + - cwl:Directory + jsonldPredicate: + _id: "@type" + _type: "@vocab" + doc: Must be `Directory` to indicate this object describes a Directory. + - name: location + type: string? + doc: | + An IRI that identifies the directory resource. This may be a relative + reference, in which case it must be resolved using the base IRI of the + document. The location may refer to a local or remote resource. If + the `listing` field is not set, the implementation must use the + location IRI to retrieve directory listing. If an implementation is + unable to retrieve the directory listing stored at a remote resource (due to + unsupported protocol, access denied, or other issue) it must signal an + error. + + If the `location` field is not provided, the `listing` field must be + provided. The implementation must assign a unique identifier for + the `location` field. + + If the `path` field is provided but the `location` field is not, an + implementation may assign the value of the `path` field to `location`, + then follow the rules above. + jsonldPredicate: + _id: "@id" + _type: "@id" + - name: path + type: string? + doc: | + The local path where the Directory is made available prior to executing a + CommandLineTool. This must be set by the implementation. This field + must not be used in any other context. The command line tool being + executed must be able to to access the directory at `path` using the POSIX + `opendir(2)` syscall. + + If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) + (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, + ``, ``, and ``) or characters + [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) + for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) + then implementations may terminate the process with a + `permanentFailure`. + jsonldPredicate: + _id: "cwl:path" + _type: "@id" + - name: basename + type: string? + doc: | + The base name of the directory, that is, the name of the file without any + leading directory path. The base name must not contain a slash `/`. + + If not provided, the implementation must set this field based on the + `location` field by taking the final path component after parsing + `location` as an IRI. If `basename` is provided, it is not required to + match the value from `location`. + + When this file is made available to a CommandLineTool, it must be named + with `basename`, i.e. the final component of the `path` field must match + `basename`. + jsonldPredicate: "cwl:basename" + - name: listing + type: + - "null" + - type: array + items: [File, Directory] + doc: | + List of files or subdirectories contained in this directory. The name + of each file or subdirectory is determined by the `basename` field of + each `File` or `Directory` object. It is an error if a `File` shares a + `basename` with any other entry in `listing`. If two or more + `Directory` object share the same `basename`, this must be treated as + equivalent to a single subdirectory with the listings recursively + merged. + jsonldPredicate: + _id: "cwl:listing" + +- name: SchemaBase + type: record + abstract: true + fields: + - name: label + type: + - "null" + - string + jsonldPredicate: "rdfs:label" + doc: "A short, human-readable label of this object." + + +- name: Parameter + type: record + extends: SchemaBase + abstract: true + doc: | + Define an input or output parameter to a process. + + fields: + - name: secondaryFiles + type: + - "null" + - string + - Expression + - type: array + items: [string, Expression] + jsonldPredicate: "cwl:secondaryFiles" + doc: | + Only valid when `type: File` or is an array of `items: File`. + + Describes files that must be included alongside the primary file(s). + + If the value is an expression, the value of `self` in the expression + must be the primary input or output File to which this binding applies. + + If the value is a string, it specifies that the following pattern + should be applied to the primary file: + + 1. If string begins with one or more caret `^` characters, for each + caret, remove the last file extension from the path (the last + period `.` and all following characters). If there are no file + extensions, the path is unchanged. + 2. Append the remainder of the string to the end of the file path. + + - name: format + type: + - "null" + - string + - type: array + items: string + - Expression + jsonldPredicate: + _id: cwl:format + _type: "@id" + identity: true + doc: | + Only valid when `type: File` or is an array of `items: File`. + + For input parameters, this must be one or more IRIs of concept nodes + that represents file formats which are allowed as input to this + parameter, preferrably defined within an ontology. If no ontology is + available, file formats may be tested by exact match. + + For output parameters, this is the file format that will be assigned to + the output parameter. + + - name: streamable + type: boolean? + doc: | + Only valid when `type: File` or is an array of `items: File`. + + A value of `true` indicates that the file is read or written + sequentially without seeking. An implementation may use this flag to + indicate whether it is valid to stream file contents using a named + pipe. Default: `false`. + + - name: doc + type: + - string? + - string[]? + doc: "A documentation string for this type, or an array of strings which should be concatenated." + jsonldPredicate: "rdfs:comment" + + +- type: enum + name: Expression + doc: | + 'Expression' is not a real type. It indicates that a field must allow + runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement) + is declared and supported by the platform, the field must also allow + Javascript expressions. + symbols: + - cwl:ExpressionPlaceholder + + +- name: InputBinding + type: record + abstract: true + fields: + - name: loadContents + type: + - "null" + - boolean + jsonldPredicate: "cwl:loadContents" + doc: | + Only valid when `type: File` or is an array of `items: File`. + + Read up to the first 64 KiB of text from the file and place it in the + "contents" field of the file object for use by expressions. + + +- name: OutputBinding + type: record + abstract: true + + +- name: InputSchema + extends: SchemaBase + type: record + abstract: true + + +- name: OutputSchema + extends: SchemaBase + type: record + abstract: true + + +- name: InputRecordField + type: record + extends: "sld:RecordField" + specialize: + - specializeFrom: "sld:RecordSchema" + specializeTo: InputRecordSchema + - specializeFrom: "sld:EnumSchema" + specializeTo: InputEnumSchema + - specializeFrom: "sld:ArraySchema" + specializeTo: InputArraySchema + - specializeFrom: "sld:PrimitiveType" + specializeTo: CWLType + fields: + - name: inputBinding + type: InputBinding? + jsonldPredicate: "cwl:inputBinding" + - name: label + type: string? + jsonldPredicate: "rdfs:label" + doc: "A short, human-readable label of this process object." + + +- name: InputRecordSchema + type: record + extends: ["sld:RecordSchema", InputSchema] + specialize: + - specializeFrom: "sld:RecordField" + specializeTo: InputRecordField + + +- name: InputEnumSchema + type: record + extends: ["sld:EnumSchema", InputSchema] + fields: + - name: inputBinding + type: InputBinding? + jsonldPredicate: "cwl:inputBinding" + + +- name: InputArraySchema + type: record + extends: ["sld:ArraySchema", InputSchema] + specialize: + - specializeFrom: "sld:RecordSchema" + specializeTo: InputRecordSchema + - specializeFrom: "sld:EnumSchema" + specializeTo: InputEnumSchema + - specializeFrom: "sld:ArraySchema" + specializeTo: InputArraySchema + - specializeFrom: "sld:PrimitiveType" + specializeTo: CWLType + fields: + - name: inputBinding + type: InputBinding? + jsonldPredicate: "cwl:inputBinding" + + +- name: OutputRecordField + type: record + extends: "sld:RecordField" + specialize: + - specializeFrom: "sld:RecordSchema" + specializeTo: OutputRecordSchema + - specializeFrom: "sld:EnumSchema" + specializeTo: OutputEnumSchema + - specializeFrom: "sld:ArraySchema" + specializeTo: OutputArraySchema + - specializeFrom: "sld:PrimitiveType" + specializeTo: CWLType + fields: + - name: outputBinding + type: OutputBinding? + jsonldPredicate: "cwl:outputBinding" + + +- name: OutputRecordSchema + type: record + extends: ["sld:RecordSchema", "#OutputSchema"] + docParent: "#OutputParameter" + specialize: + - specializeFrom: "sld:RecordField" + specializeTo: OutputRecordField + + +- name: OutputEnumSchema + type: record + extends: ["sld:EnumSchema", OutputSchema] + docParent: "#OutputParameter" + fields: + - name: outputBinding + type: OutputBinding? + jsonldPredicate: "cwl:outputBinding" + +- name: OutputArraySchema + type: record + extends: ["sld:ArraySchema", OutputSchema] + docParent: "#OutputParameter" + specialize: + - specializeFrom: "sld:RecordSchema" + specializeTo: OutputRecordSchema + - specializeFrom: "sld:EnumSchema" + specializeTo: OutputEnumSchema + - specializeFrom: "sld:ArraySchema" + specializeTo: OutputArraySchema + - specializeFrom: "sld:PrimitiveType" + specializeTo: CWLType + fields: + - name: outputBinding + type: OutputBinding? + jsonldPredicate: "cwl:outputBinding" + + +- name: InputParameter + type: record + extends: Parameter + fields: + - name: id + type: string + jsonldPredicate: "@id" + doc: "The unique identifier for this parameter object." + + - name: inputBinding + type: InputBinding? + jsonldPredicate: "cwl:inputBinding" + doc: | + Describes how to handle the inputs of a process and convert them + into a concrete form for execution, such as command line parameters. + + - name: default + type: Any? + jsonldPredicate: "cwl:default" + doc: | + The default value for this parameter if not provided in the input + object. + + - name: type + type: + - "null" + - CWLType + - InputRecordSchema + - InputEnumSchema + - InputArraySchema + - string + - type: array + items: + - CWLType + - InputRecordSchema + - InputEnumSchema + - InputArraySchema + - string + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True + doc: | + Specify valid types of data that may be assigned to this parameter. + +- name: OutputParameter + type: record + extends: Parameter + fields: + - name: id + type: string + jsonldPredicate: "@id" + doc: "The unique identifier for this parameter object." + - name: outputBinding + type: OutputBinding? + jsonldPredicate: "cwl:outputBinding" + doc: | + Describes how to handle the outputs of a process. + + +- type: record + name: ProcessRequirement + abstract: true + doc: | + A process requirement declares a prerequisite that may or must be fulfilled + before executing a process. See [`Process.hints`](#process) and + [`Process.requirements`](#process). + + Process requirements are the primary mechanism for specifying extensions to + the CWL core specification. + + +- type: record + name: Process + abstract: true + doc: | + + The base executable type in CWL is the `Process` object defined by the + document. Note that the `Process` object is abstract and cannot be + directly executed. + + fields: + - name: id + type: string? + jsonldPredicate: "@id" + doc: "The unique identifier for this process object." + - name: inputs + type: + type: array + items: InputParameter + jsonldPredicate: + _id: "cwl:inputs" + mapSubject: id + mapPredicate: type + doc: | + Defines the input parameters of the process. The process is ready to + run when all required input parameters are associated with concrete + values. Input parameters include a schema for each parameter which is + used to validate the input object. It may also be used to build a user + interface for constructing the input object. + - name: outputs + type: + type: array + items: OutputParameter + jsonldPredicate: + _id: "cwl:outputs" + mapSubject: id + mapPredicate: type + doc: | + Defines the parameters representing the output of the process. May be + used to generate and/or validate the output object. + - name: requirements + type: ProcessRequirement[]? + jsonldPredicate: + _id: "cwl:requirements" + mapSubject: class + doc: | + Declares requirements that apply to either the runtime environment or the + workflow engine that must be met in order to execute this process. If + an implementation cannot satisfy all requirements, or a requirement is + listed which is not recognized by the implementation, it is a fatal + error and the implementation must not attempt to run the process, + unless overridden at user option. + - name: hints + type: Any[]? + doc: | + Declares hints applying to either the runtime environment or the + workflow engine that may be helpful in executing this process. It is + not an error if an implementation cannot satisfy all hints, however + the implementation may report a warning. + jsonldPredicate: + _id: cwl:hints + noLinkCheck: true + mapSubject: class + - name: label + type: string? + jsonldPredicate: "rdfs:label" + doc: "A short, human-readable label of this process object." + - name: doc + type: string? + jsonldPredicate: "rdfs:comment" + doc: "A long, human-readable description of this process object." + - name: cwlVersion + type: CWLVersion? + doc: | + CWL document version. Always required at the document root. Not + required for a Process embedded inside another Process. + jsonldPredicate: + "_id": "cwl:cwlVersion" + "_type": "@vocab" + +- name: InlineJavascriptRequirement + type: record + extends: ProcessRequirement + doc: | + Indicates that the workflow platform must support inline Javascript expressions. + If this requirement is not present, the workflow platform must not perform expression + interpolatation. + fields: + - name: class + type: string + doc: "Always 'InlineJavascriptRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + - name: expressionLib + type: string[]? + doc: | + Additional code fragments that will also be inserted + before executing the expression code. Allows for function definitions that may + be called from CWL expressions. + + +- name: SchemaDefRequirement + type: record + extends: ProcessRequirement + doc: | + This field consists of an array of type definitions which must be used when + interpreting the `inputs` and `outputs` fields. When a `type` field + contain a IRI, the implementation must check if the type is defined in + `schemaDefs` and use that definition. If the type is not found in + `schemaDefs`, it is an error. The entries in `schemaDefs` must be + processed in the order listed such that later schema definitions may refer + to earlier schema definitions. + fields: + - name: class + type: string + doc: "Always 'SchemaDefRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + - name: types + type: + type: array + items: InputSchema + doc: The list of type definitions. diff --git a/sdk-and-javadoc-generation/cwl-yaml-specs/Workflow.yml b/sdk-and-javadoc-generation/cwl-yaml-specs/Workflow.yml new file mode 100644 index 00000000..2809e58a --- /dev/null +++ b/sdk-and-javadoc-generation/cwl-yaml-specs/Workflow.yml @@ -0,0 +1,582 @@ +$base: "https://w3id.org/cwl/cwl#" + +$namespaces: + cwl: "https://w3id.org/cwl/cwl#" + +$graph: + +- name: "WorkflowDoc" + type: documentation + doc: + - | + # Common Workflow Language (CWL) Workflow Description, v1.0 + + This version: + * https://w3id.org/cwl/v1.0/ + + Current version: + * https://w3id.org/cwl/ + - "\n\n" + - {$include: contrib.md} + - "\n\n" + - | + # Abstract + + One way to define a workflow is: an analysis task represented by a + directed graph describing a sequence of operations that transform an + input data set to output. This specification defines the Common Workflow + Language (CWL) Workflow description, a vendor-neutral standard for + representing workflows intended to be portable across a variety of + computing platforms. + + - {$include: intro.md} + + - | + + ## Introduction to v1.0 + + This specification represents the first full release from the CWL group. + Since draft-3, this draft introduces the following changes and additions: + + * The `inputs` and `outputs` fields have been renamed `in` and `out`. + * Syntax simplifcations: denoted by the `map<>` syntax. Example: `in` + contains a list of items, each with an id. Now one can specify + a mapping of that identifier to the corresponding + `InputParameter`. + ``` + in: + - id: one + type: string + doc: First input parameter + - id: two + type: int + doc: Second input parameter + ``` + can be + ``` + in: + one: + type: string + doc: First input parameter + two: + type: int + doc: Second input parameter + ``` + * The common field 'description` has been renamed to `doc`. + + ## Purpose + + The Common Workflow Language Command Line Tool Description express + workflows for data-intensive science, such as Bioinformatics, Chemistry, + Physics, and Astronomy. This specification is intended to define a data + and execution model for Workflows that can be implemented on top of a + variety of computing platforms, ranging from an individual workstation to + cluster, grid, cloud, and high performance computing systems. + + - {$include: concepts.md} + +- name: ExpressionToolOutputParameter + type: record + extends: OutputParameter + fields: + - name: type + type: + - "null" + - "#CWLType" + - "#OutputRecordSchema" + - "#OutputEnumSchema" + - "#OutputArraySchema" + - string + - type: array + items: + - "#CWLType" + - "#OutputRecordSchema" + - "#OutputEnumSchema" + - "#OutputArraySchema" + - string + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True + doc: | + Specify valid types of data that may be assigned to this parameter. + +- type: record + name: ExpressionTool + extends: Process + specialize: + - specializeFrom: "#OutputParameter" + specializeTo: "#ExpressionToolOutputParameter" + documentRoot: true + doc: | + Execute an expression as a Workflow step. + fields: + - name: "class" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + type: string + - name: expression + type: [string, Expression] + doc: | + The expression to execute. The expression must return a JSON object which + matches the output parameters of the ExpressionTool. + +- name: LinkMergeMethod + type: enum + docParent: "#WorkflowStepInput" + doc: The input link merge method, described in [WorkflowStepInput](#WorkflowStepInput). + symbols: + - merge_nested + - merge_flattened + + +- name: WorkflowOutputParameter + type: record + extends: OutputParameter + docParent: "#Workflow" + doc: | + Describe an output parameter of a workflow. The parameter must be + connected to one or more parameters defined in the workflow that will + provide the value of the output parameter. + fields: + - name: outputSource + doc: | + Specifies one or more workflow parameters that supply the value of to + the output parameter. + jsonldPredicate: + "_id": "cwl:outputSource" + "_type": "@id" + refScope: 0 + type: + - string? + - string[]? + - name: linkMerge + type: ["null", "#LinkMergeMethod"] + jsonldPredicate: "cwl:linkMerge" + doc: | + The method to use to merge multiple sources into a single array. + If not specified, the default method is "merge_nested". + - name: type + type: + - "null" + - "#CWLType" + - "#OutputRecordSchema" + - "#OutputEnumSchema" + - "#OutputArraySchema" + - string + - type: array + items: + - "#CWLType" + - "#OutputRecordSchema" + - "#OutputEnumSchema" + - "#OutputArraySchema" + - string + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True + doc: | + Specify valid types of data that may be assigned to this parameter. + + +- name: Sink + type: record + abstract: true + fields: + - name: source + doc: | + Specifies one or more workflow parameters that will provide input to + the underlying step parameter. + jsonldPredicate: + "_id": "cwl:source" + "_type": "@id" + refScope: 2 + type: + - string? + - string[]? + - name: linkMerge + type: LinkMergeMethod? + jsonldPredicate: "cwl:linkMerge" + doc: | + The method to use to merge multiple inbound links into a single array. + If not specified, the default method is "merge_nested". + + +- type: record + name: WorkflowStepInput + extends: Sink + docParent: "#WorkflowStep" + doc: | + The input of a workflow step connects an upstream parameter (from the + workflow inputs, or the outputs of other workflows steps) with the input + parameters of the underlying step. + + ## Input object + + A WorkflowStepInput object must contain an `id` field in the form + `#fieldname` or `#stepname.fieldname`. When the `id` field contains a + period `.` the field name consists of the characters following the final + period. This defines a field of the workflow step input object with the + value of the `source` parameter(s). + + ## Merging + + To merge multiple inbound data links, + [MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified + in the workflow or workflow step requirements. + + If the sink parameter is an array, or named in a [workflow + scatter](#WorkflowStep) operation, there may be multiple inbound data links + listed in the `source` field. The values from the input links are merged + depending on the method specified in the `linkMerge` field. If not + specified, the default method is "merge_nested". + + * **merge_nested** + + The input must be an array consisting of exactly one entry for each + input link. If "merge_nested" is specified with a single link, the value + from the link must be wrapped in a single-item list. + + * **merge_flattened** + + 1. The source and sink parameters must be compatible types, or the source + type must be compatible with single element from the "items" type of + the destination array parameter. + 2. Source parameters which are arrays are concatenated. + Source parameters which are single element types are appended as + single elements. + + fields: + - name: id + type: string + jsonldPredicate: "@id" + doc: "A unique identifier for this workflow input parameter." + - name: default + type: ["null", Any] + doc: | + The default value for this parameter if there is no `source` + field. + jsonldPredicate: "cwl:default" + - name: valueFrom + type: + - "null" + - "string" + - "#Expression" + jsonldPredicate: "cwl:valueFrom" + doc: | + To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must + be specified in the workflow or workflow step requirements. + + If `valueFrom` is a constant string value, use this as the value for + this input parameter. + + If `valueFrom` is a parameter reference or expression, it must be + evaluated to yield the actual value to be assiged to the input field. + + The `self` value of in the parameter reference or expression must be + the value of the parameter(s) specified in the `source` field, or + null if there is no `source` field. + + The value of `inputs` in the parameter reference or expression must be + the input object to the workflow step after assigning the `source` + values and then scattering. The order of evaluating `valueFrom` among + step input parameters is undefined and the result of evaluating + `valueFrom` on a parameter must not be visible to evaluation of + `valueFrom` on other parameters. + + +- type: record + name: WorkflowStepOutput + docParent: "#WorkflowStep" + doc: | + Associate an output parameter of the underlying process with a workflow + parameter. The workflow parameter (given in the `id` field) be may be used + as a `source` to connect with input parameters of other workflow steps, or + with an output parameter of the process. + fields: + - name: id + type: string + jsonldPredicate: "@id" + doc: | + A unique identifier for this workflow output parameter. This is the + identifier to use in the `source` field of `WorkflowStepInput` to + connect the output value to downstream parameters. + + +- name: ScatterMethod + type: enum + docParent: "#WorkflowStep" + doc: The scatter method, as described in [workflow step scatter](#WorkflowStep). + symbols: + - dotproduct + - nested_crossproduct + - flat_crossproduct + + +- name: WorkflowStep + type: record + docParent: "#Workflow" + doc: | + A workflow step is an executable element of a workflow. It specifies the + underlying process implementation (such as `CommandLineTool` or another + `Workflow`) in the `run` field and connects the input and output parameters + of the underlying process to workflow parameters. + + # Scatter/gather + + To use scatter/gather, + [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified + in the workflow or workflow step requirements. + + A "scatter" operation specifies that the associated workflow step or + subworkflow should execute separately over a list of input elements. Each + job making up a scatter operation is independent and may be executed + concurrently. + + The `scatter` field specifies one or more input parameters which will be + scattered. An input parameter may be listed more than once. The declared + type of each input parameter is implicitly wrapped in an array for each + time it appears in the `scatter` field. As a result, upstream parameters + which are connected to scattered parameters may be arrays. + + All output parameter types are also implicitly wrapped in arrays. Each job + in the scatter results in an entry in the output array. + + If `scatter` declares more than one input parameter, `scatterMethod` + describes how to decompose the input into a discrete set of jobs. + + * **dotproduct** specifies that each of the input arrays are aligned and one + element taken from each array to construct each job. It is an error + if all input arrays are not the same length. + + * **nested_crossproduct** specifies the Cartesian product of the inputs, + producing a job for every combination of the scattered inputs. The + output must be nested arrays for each level of scattering, in the + order that the input arrays are listed in the `scatter` field. + + * **flat_crossproduct** specifies the Cartesian product of the inputs, + producing a job for every combination of the scattered inputs. The + output arrays must be flattened to a single level, but otherwise listed in the + order that the input arrays are listed in the `scatter` field. + + # Subworkflows + + To specify a nested workflow as part of a workflow step, + [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be + specified in the workflow or workflow step requirements. + + fields: + - name: id + type: string + jsonldPredicate: "@id" + doc: "The unique identifier for this workflow step." + - name: in + type: WorkflowStepInput[] + jsonldPredicate: + _id: "cwl:in" + mapSubject: id + mapPredicate: source + doc: | + Defines the input parameters of the workflow step. The process is ready to + run when all required input parameters are associated with concrete + values. Input parameters include a schema for each parameter which is + used to validate the input object. It may also be used build a user + interface for constructing the input object. + - name: out + type: + - type: array + items: [string, WorkflowStepOutput] + jsonldPredicate: + _id: "cwl:out" + _type: "@id" + identity: true + doc: | + Defines the parameters representing the output of the process. May be + used to generate and/or validate the output object. + - name: requirements + type: ProcessRequirement[]? + jsonldPredicate: + _id: "cwl:requirements" + mapSubject: class + doc: | + Declares requirements that apply to either the runtime environment or the + workflow engine that must be met in order to execute this workflow step. If + an implementation cannot satisfy all requirements, or a requirement is + listed which is not recognized by the implementation, it is a fatal + error and the implementation must not attempt to run the process, + unless overridden at user option. + - name: hints + type: Any[]? + jsonldPredicate: + _id: "cwl:hints" + noLinkCheck: true + mapSubject: class + doc: | + Declares hints applying to either the runtime environment or the + workflow engine that may be helpful in executing this workflow step. It is + not an error if an implementation cannot satisfy all hints, however + the implementation may report a warning. + - name: label + type: string? + jsonldPredicate: "rdfs:label" + doc: "A short, human-readable label of this process object." + - name: doc + type: string? + jsonldPredicate: "rdfs:comment" + doc: "A long, human-readable description of this process object." + - name: run + type: [string, Process] + jsonldPredicate: + "_id": "cwl:run" + "_type": "@id" + doc: | + Specifies the process to run. + - name: scatter + type: + - string? + - string[]? + jsonldPredicate: + "_id": "cwl:scatter" + "_type": "@id" + "_container": "@list" + refScope: 0 + - name: scatterMethod + doc: | + Required if `scatter` is an array of more than one element. + type: ScatterMethod? + jsonldPredicate: + "_id": "cwl:scatterMethod" + "_type": "@vocab" + + +- name: Workflow + type: record + extends: "#Process" + documentRoot: true + specialize: + - specializeFrom: "#OutputParameter" + specializeTo: "#WorkflowOutputParameter" + doc: | + A workflow describes a set of **steps** and the **dependencies** between + those steps. When a step produces output that will be consumed by a + second step, the first step is a dependency of the second step. + + When there is a dependency, the workflow engine must execute the preceeding + step and wait for it to successfully produce output before executing the + dependent step. If two steps are defined in the workflow graph that + are not directly or indirectly dependent, these steps are **independent**, + and may execute in any order or execute concurrently. A workflow is + complete when all steps have been executed. + + Dependencies between parameters are expressed using the `source` field on + [workflow step input parameters](#WorkflowStepInput) and [workflow output + parameters](#WorkflowOutputParameter). + + The `source` field expresses the dependency of one parameter on another + such that when a value is associated with the parameter specified by + `source`, that value is propagated to the destination parameter. When all + data links inbound to a given step are fufilled, the step is ready to + execute. + + ## Workflow success and failure + + A completed step must result in one of `success`, `temporaryFailure` or + `permanentFailure` states. An implementation may choose to retry a step + execution which resulted in `temporaryFailure`. An implementation may + choose to either continue running other steps of a workflow, or terminate + immediately upon `permanentFailure`. + + * If any step of a workflow execution results in `permanentFailure`, then + the workflow status is `permanentFailure`. + + * If one or more steps result in `temporaryFailure` and all other steps + complete `success` or are not executed, then the workflow status is + `temporaryFailure`. + + * If all workflow steps are executed and complete with `success`, then the + workflow status is `success`. + + # Extensions + + [ScatterFeatureRequirement](#ScatterFeatureRequirement) and + [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are + available as standard [extensions](#Extensions_and_Metadata) to core + workflow semantics. + + fields: + - name: "class" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + type: string + - name: steps + doc: | + The individual steps that make up the workflow. Each step is executed when all of its + input data links are fufilled. An implementation may choose to execute + the steps in a different order than listed and/or execute steps + concurrently, provided that dependencies between steps are met. + type: + - type: array + items: "#WorkflowStep" + jsonldPredicate: + mapSubject: id + + +- type: record + name: SubworkflowFeatureRequirement + extends: ProcessRequirement + doc: | + Indicates that the workflow platform must support nested workflows in + the `run` field of [WorkflowStep](#WorkflowStep). + fields: + - name: "class" + type: "string" + doc: "Always 'SubworkflowFeatureRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + +- name: ScatterFeatureRequirement + type: record + extends: ProcessRequirement + doc: | + Indicates that the workflow platform must support the `scatter` and + `scatterMethod` fields of [WorkflowStep](#WorkflowStep). + fields: + - name: "class" + type: "string" + doc: "Always 'ScatterFeatureRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + +- name: MultipleInputFeatureRequirement + type: record + extends: ProcessRequirement + doc: | + Indicates that the workflow platform must support multiple inbound data links + listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput). + fields: + - name: "class" + type: "string" + doc: "Always 'MultipleInputFeatureRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + +- type: record + name: StepInputExpressionRequirement + extends: ProcessRequirement + doc: | + Indicate that the workflow platform must support the `valueFrom` field + of [WorkflowStepInput](#WorkflowStepInput). + fields: + - name: "class" + type: "string" + doc: "Always 'StepInputExpressionRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" diff --git a/sdk-and-javadoc-generation/cwl-yaml-specs/metaschema.yml b/sdk-and-javadoc-generation/cwl-yaml-specs/metaschema.yml new file mode 100644 index 00000000..d5472e96 --- /dev/null +++ b/sdk-and-javadoc-generation/cwl-yaml-specs/metaschema.yml @@ -0,0 +1,317 @@ +$base: "https://w3id.org/cwl/salad#" + +$namespaces: + sld: "https://w3id.org/cwl/salad#" + dct: "http://purl.org/dc/terms/" + rdf: "http://www.w3.org/1999/02/22-rdf-syntax-ns#" + rdfs: "http://www.w3.org/2000/01/rdf-schema#" + xsd: "http://www.w3.org/2001/XMLSchema#" + +$graph: + +- name: "Semantic_Annotations_for_Linked_Avro_Data" + type: documentation + doc: + - $include: salad.md + - $import: field_name.yml + - $import: ident_res.yml + - $import: link_res.yml + - $import: vocab_res.yml + - $include: import_include.md + +- name: "Link_Validation" + type: documentation + doc: | + # Link validation + + Once a document has been preprocessed, an implementation may validate + links. The link validation traversal may visit fields which the schema + designates as link fields and check that each URI references an existing + object in the current document, an imported document, file system, or + network resource. Failure to validate links may be a fatal error. Link + validation behavior for individual fields may be modified by `identity` and + `noLinkCheck` in the `jsonldPredicate` section of the field schema. + + +- name: "Schema_validation" + type: documentation + doc: "" + + +# - name: "JSON_LD_Context" +# type: documentation +# doc: | +# # Generating JSON-LD Context + +# How to generate the json-ld context... + + +- $import: metaschema_base.yml + +- name: JsonldPredicate + type: record + doc: | + Attached to a record field to define how the parent record field is handled for + URI resolution and JSON-LD context generation. + fields: + - name: _id + type: string? + jsonldPredicate: + _id: sld:_id + _type: "@id" + identity: true + doc: | + The predicate URI that this field corresponds to. + Corresponds to JSON-LD `@id` directive. + - name: _type + type: string? + doc: | + The context type hint, corresponds to JSON-LD `@type` directive. + + * If the value of this field is `@id` and `identity` is false or + unspecified, the parent field must be resolved using the link + resolution rules. If `identity` is true, the parent field must be + resolved using the identifier expansion rules. + + * If the value of this field is `@vocab`, the parent field must be + resolved using the vocabulary resolution rules. + + - name: _container + type: string? + doc: | + Structure hint, corresponds to JSON-LD `@container` directive. + - name: identity + type: boolean? + doc: | + If true and `_type` is `@id` this indicates that the parent field must + be resolved according to identity resolution rules instead of link + resolution rules. In addition, the field value is considered an + assertion that the linked value exists; absence of an object in the loaded document + with the URI is not an error. + - name: noLinkCheck + type: boolean? + doc: | + If true, this indicates that link validation traversal must stop at + this field. This field (it is is a URI) or any fields under it (if it + is an object or array) are not subject to link checking. + - name: mapSubject + type: string? + doc: | + If the value of the field is a JSON object, it must be transformed + into an array of JSON objects, where each key-value pair from the + source JSON object is a list item, the list items must be JSON objects, + and the key is assigned to the field specified by `mapSubject`. + - name: mapPredicate + type: string? + doc: | + Only applies if `mapSubject` is also provided. If the value of the + field is a JSON object, it is transformed as described in `mapSubject`, + with the addition that when the value of a map item is not an object, + the item is transformed to a JSON object with the key assigned to the + field specified by `mapSubject` and the value assigned to the field + specified by `mapPredicate`. + - name: refScope + type: int? + doc: | + If the field contains a relative reference, it must be resolved by + searching for valid document references in each successive parent scope + in the document fragment. For example, a reference of `foo` in the + context `#foo/bar/baz` will first check for the existence of + `#foo/bar/baz/foo`, followed by `#foo/bar/foo`, then `#foo/foo` and + then finally `#foo`. The first valid URI in the search order shall be + used as the fully resolved value of the identifier. The value of the + refScope field is the specified number of levels from the containing + identifer scope before starting the search, so if `refScope: 2` then + "baz" and "bar" must be stripped to get the base `#foo` and search + `#foo/foo` and the `#foo`. The last scope searched must be the top + level scope before determining if the identifier cannot be resolved. + - name: typeDSL + type: boolean? + doc: | + Field must be expanded based on the the Schema Salad type DSL. + + +- name: SpecializeDef + type: record + fields: + - name: specializeFrom + type: string + doc: "The data type to be replaced" + jsonldPredicate: + _id: "sld:specializeFrom" + _type: "@id" + refScope: 1 + + - name: specializeTo + type: string + doc: "The new data type to replace with" + jsonldPredicate: + _id: "sld:specializeTo" + _type: "@id" + refScope: 1 + + +- name: NamedType + type: record + abstract: true + fields: + - name: name + type: string + jsonldPredicate: "@id" + doc: "The identifier for this type" + + +- name: DocType + type: record + abstract: true + fields: + - name: doc + type: + - string? + - string[]? + doc: "A documentation string for this type, or an array of strings which should be concatenated." + jsonldPredicate: "rdfs:comment" + + - name: docParent + type: string? + doc: | + Hint to indicate that during documentation generation, documentation + for this type should appear in a subsection under `docParent`. + jsonldPredicate: + _id: "sld:docParent" + _type: "@id" + + - name: docChild + type: + - string? + - string[]? + doc: | + Hint to indicate that during documentation generation, documentation + for `docChild` should appear in a subsection under this type. + jsonldPredicate: + _id: "sld:docChild" + _type: "@id" + + - name: docAfter + type: string? + doc: | + Hint to indicate that during documentation generation, documentation + for this type should appear after the `docAfter` section at the same + level. + jsonldPredicate: + _id: "sld:docAfter" + _type: "@id" + + +- name: SchemaDefinedType + type: record + extends: DocType + doc: | + Abstract base for schema-defined types. + abstract: true + fields: + - name: jsonldPredicate + type: + - string? + - JsonldPredicate? + doc: | + Annotate this type with linked data context. + jsonldPredicate: sld:jsonldPredicate + + - name: documentRoot + type: boolean? + doc: | + If true, indicates that the type is a valid at the document root. At + least one type in a schema must be tagged with `documentRoot: true`. + + +- name: SaladRecordField + type: record + extends: RecordField + doc: "A field of a record." + fields: + - name: jsonldPredicate + type: + - string? + - JsonldPredicate? + doc: | + Annotate this type with linked data context. + jsonldPredicate: "sld:jsonldPredicate" + + +- name: SaladRecordSchema + type: record + extends: [NamedType, RecordSchema, SchemaDefinedType] + documentRoot: true + specialize: + RecordField: SaladRecordField + fields: + - name: abstract + type: boolean? + doc: | + If true, this record is abstract and may be used as a base for other + records, but is not valid on its own. + + - name: extends + type: + - string? + - string[]? + jsonldPredicate: + _id: "sld:extends" + _type: "@id" + refScope: 1 + doc: | + Indicates that this record inherits fields from one or more base records. + + - name: specialize + type: + - SpecializeDef[]? + doc: | + Only applies if `extends` is declared. Apply type specialization using the + base record as a template. For each field inherited from the base + record, replace any instance of the type `specializeFrom` with + `specializeTo`. + jsonldPredicate: + _id: "sld:specialize" + mapSubject: specializeFrom + mapPredicate: specializeTo + +- name: SaladEnumSchema + type: record + extends: [EnumSchema, SchemaDefinedType] + documentRoot: true + doc: | + Define an enumerated type. + fields: + - name: extends + type: + - string? + - string[]? + jsonldPredicate: + _id: "sld:extends" + _type: "@id" + refScope: 1 + doc: | + Indicates that this enum inherits symbols from a base enum. + + +- name: Documentation + type: record + extends: [NamedType, DocType] + documentRoot: true + doc: | + A documentation section. This type exists to facilitate self-documenting + schemas but has no role in formal validation. + fields: + - name: type + doc: "Must be `documentation`" + type: + name: Documentation_symbol + type: enum + symbols: + - "sld:documentation" + jsonldPredicate: + _id: "sld:type" + _type: "@vocab" + typeDSL: true + refScope: 2 diff --git a/sdk-and-javadoc-generation/cwl-yaml-specs/metaschema_base.yml b/sdk-and-javadoc-generation/cwl-yaml-specs/metaschema_base.yml new file mode 100644 index 00000000..73511d14 --- /dev/null +++ b/sdk-and-javadoc-generation/cwl-yaml-specs/metaschema_base.yml @@ -0,0 +1,164 @@ +$base: "https://w3id.org/cwl/salad#" + +$namespaces: + sld: "https://w3id.org/cwl/salad#" + dct: "http://purl.org/dc/terms/" + rdf: "http://www.w3.org/1999/02/22-rdf-syntax-ns#" + rdfs: "http://www.w3.org/2000/01/rdf-schema#" + xsd: "http://www.w3.org/2001/XMLSchema#" + +$graph: +- name: PrimitiveType + type: enum + symbols: + - "sld:null" + - "xsd:boolean" + - "xsd:int" + - "xsd:long" + - "xsd:float" + - "xsd:double" + - "xsd:string" + doc: + - | + Salad data types are based on Avro schema declarations. Refer to the + [Avro schema declaration documentation](https://avro.apache.org/docs/current/spec.html#schemas) for + detailed information. + - "null: no value" + - "boolean: a binary value" + - "int: 32-bit signed integer" + - "long: 64-bit signed integer" + - "float: single precision (32-bit) IEEE 754 floating-point number" + - "double: double precision (64-bit) IEEE 754 floating-point number" + - "string: Unicode character sequence" + + +- name: Any + type: enum + symbols: ["#Any"] + doc: | + The **Any** type validates for any non-null value. + + +- name: RecordField + type: record + doc: A field of a record. + fields: + - name: name + type: string + jsonldPredicate: "@id" + doc: | + The name of the field + + - name: doc + type: string? + doc: | + A documentation string for this field + jsonldPredicate: "rdfs:comment" + + - name: type + type: + - PrimitiveType + - RecordSchema + - EnumSchema + - ArraySchema + - string + - type: array + items: + - PrimitiveType + - RecordSchema + - EnumSchema + - ArraySchema + - string + jsonldPredicate: + _id: sld:type + _type: "@vocab" + typeDSL: true + refScope: 2 + doc: | + The field type + + +- name: RecordSchema + type: record + fields: + type: + doc: "Must be `record`" + type: + name: Record_symbol + type: enum + symbols: + - "sld:record" + jsonldPredicate: + _id: "sld:type" + _type: "@vocab" + typeDSL: true + refScope: 2 + fields: + type: RecordField[]? + jsonldPredicate: + _id: sld:fields + mapSubject: name + mapPredicate: type + doc: "Defines the fields of the record." + + +- name: EnumSchema + type: record + doc: | + Define an enumerated type. + fields: + type: + doc: "Must be `enum`" + type: + name: Enum_symbol + type: enum + symbols: + - "sld:enum" + jsonldPredicate: + _id: "sld:type" + _type: "@vocab" + typeDSL: true + refScope: 2 + symbols: + type: string[] + jsonldPredicate: + _id: "sld:symbols" + _type: "@id" + identity: true + doc: "Defines the set of valid symbols." + + +- name: ArraySchema + type: record + fields: + type: + doc: "Must be `array`" + type: + name: Array_symbol + type: enum + symbols: + - "sld:array" + jsonldPredicate: + _id: "sld:type" + _type: "@vocab" + typeDSL: true + refScope: 2 + items: + type: + - PrimitiveType + - RecordSchema + - EnumSchema + - ArraySchema + - string + - type: array + items: + - PrimitiveType + - RecordSchema + - EnumSchema + - ArraySchema + - string + jsonldPredicate: + _id: "sld:items" + _type: "@vocab" + refScope: 2 + doc: "Defines the type of the array elements." diff --git a/sdk-and-javadoc-generation/examples/CWLJavaCodeGeneratorDemo.java b/sdk-and-javadoc-generation/examples/CWLJavaCodeGeneratorDemo.java new file mode 100644 index 00000000..c84438b5 --- /dev/null +++ b/sdk-and-javadoc-generation/examples/CWLJavaCodeGeneratorDemo.java @@ -0,0 +1,48 @@ + +// Compile: ./compile-demo.sh wc-tool.cwl wc-job.json +// +// Run: ./run-demo.sh wc-tool.cwl wc-job.json + +import java.util.*; +import org.commonwl.lang.*; +import org.commonwl.util.*; + +public class CWLJavaCodeGeneratorDemo { + + public static void main( String [] args ) throws Exception { + + CWLJavaCodeGenerator cwlJCG = new CWLJavaCodeGenerator( args[0] ); + cwlJCG.processFile(); + /* + //CWLReader tool = new CWLReader("wc-tool.cwl"); + CWLReader tool = new CWLReader( args[0] ); + tool.processFile(); + CommandLineTool CommandLineTool_Instance = tool.getCommandLineToolInstance(); + + //JSONReader job = new JSONReader("wc-job.json"); + JSONReader job = new JSONReader( args[1] ); + job.processFile(); + + // Execute the job + SystemCommandExecution engine = new SystemCommandExecution(); + + // Initialize a new command to execute + engine.newExecutionCommand(); + + // Prepare the command to execute + engine.extendExecutionCommand( CommandLineTool_Instance.getbaseCommand() ); + String stdinPath = (String) CommandLineTool_Instance.getstdin(); + stdinPath = stdinPath.replace( "inputs.", "" ); + engine.extendExecutionCommand( job.getValue( stdinPath ) ); + + // Execute the command + engine.executeCommand(); + + // Return the result + System.out.println( engine.getStandardOutput() ); + + */ + + } + +} diff --git a/sdk-and-javadoc-generation/examples/CommandLineToolDemo.java b/sdk-and-javadoc-generation/examples/CommandLineToolDemo.java new file mode 100644 index 00000000..3ae77132 --- /dev/null +++ b/sdk-and-javadoc-generation/examples/CommandLineToolDemo.java @@ -0,0 +1,43 @@ + +// Compile: ./compile-demo.sh wc-tool.cwl wc-job.json +// +// Run: ./run-demo.sh wc-tool.cwl wc-job.json + +import java.util.*; +import org.commonwl.lang.*; +import org.commonwl.util.*; + +public class CommandLineToolDemo { + + public static void main( String [] args ) throws Exception { + + //CWLReader tool = new CWLReader("wc-tool.cwl"); + CWLReader tool = new CWLReader( args[0] ); + tool.processFile(); + CommandLineTool CommandLineTool_Instance = tool.getCommandLineToolInstance(); + + //JSONReader job = new JSONReader("wc-job.json"); + JSONReader job = new JSONReader( args[1] ); + job.processFile(); + + // Execute the job + SystemCommandExecution engine = new SystemCommandExecution(); + + // Initialize a new command to execute + engine.newExecutionCommand(); + + // Prepare the command to execute + engine.extendExecutionCommand( CommandLineTool_Instance.getbaseCommand() ); + String stdinPath = (String) CommandLineTool_Instance.getstdin(); + stdinPath = stdinPath.replace( "inputs.", "" ); + engine.extendExecutionCommand( job.getValue( stdinPath ) ); + + // Execute the command + engine.executeCommand(); + + // Return the result + System.out.println( engine.getStandardOutput() ); + + } + +} diff --git a/sdk-and-javadoc-generation/examples/compile-demo.sh b/sdk-and-javadoc-generation/examples/compile-demo.sh new file mode 100755 index 00000000..7d6db4f4 --- /dev/null +++ b/sdk-and-javadoc-generation/examples/compile-demo.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +javac -cp ../lib/cwl.jar:../lib/json-simple-1.1.1.jar:../lib/snakeyaml-1.16.jar:. CommandLineToolDemo.java + diff --git a/sdk-and-javadoc-generation/examples/compile_and_run-CWLJavaCodeGeneratorDemo.sh b/sdk-and-javadoc-generation/examples/compile_and_run-CWLJavaCodeGeneratorDemo.sh new file mode 100755 index 00000000..4dba679d --- /dev/null +++ b/sdk-and-javadoc-generation/examples/compile_and_run-CWLJavaCodeGeneratorDemo.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +javac -cp ../lib/cwl.jar:../lib/json-simple-1.1.1.jar:../lib/snakeyaml-1.16.jar:. CWLJavaCodeGeneratorDemo.java +java -cp ../lib/cwl.jar:../lib/json-simple-1.1.1.jar:../lib/snakeyaml-1.16.jar:. CWLJavaCodeGeneratorDemo $1 diff --git a/sdk-and-javadoc-generation/examples/run-demo.sh b/sdk-and-javadoc-generation/examples/run-demo.sh new file mode 100755 index 00000000..3eccb7ff --- /dev/null +++ b/sdk-and-javadoc-generation/examples/run-demo.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +java -cp ../lib/cwl.jar:../lib/json-simple-1.1.1.jar:../lib/snakeyaml-1.16.jar:. CommandLineToolDemo $1 $2 \ No newline at end of file diff --git a/sdk-and-javadoc-generation/examples/sdk-example-for-presentation.txt b/sdk-and-javadoc-generation/examples/sdk-example-for-presentation.txt new file mode 100644 index 00000000..743703e7 --- /dev/null +++ b/sdk-and-javadoc-generation/examples/sdk-example-for-presentation.txt @@ -0,0 +1,67 @@ + +import java.util.*; + +public class sdktest { + + public static void main( String [] args ) throws Exception { + + CWLReader cwlr = new CWLReader("wc-tool.cwl"); + cwlr.processFile(); + CommandLineTool CommandLineTool_Instance = cwlr.getCommandLineToolInstance(); + // CommandLineTool clt = new CommandLineTool(); + + // CommandInputParameter [] cip = new CommandInputParameter[1]; + // cip[0] = new CommandInputParameter(); + // cip[0].setid("file1"); + // cip[0].settype("File"); + + // CommandOutputParameter [] cop = new CommandOutputParameter[1]; + // cop[0] = new CommandOutputParameter(); + // cop[0].setid("output"); + // cop[0].settype("File"); + + // CommandOutputBinding cob = new CommandOutputBinding(); + // cob.setglob( new String( "output" ) ); + + // cop[0].setoutputBinding( cob ); + + + // clt.setinputs( cip ); + // clt.setoutputs( cop ); + + // clt.setbaseCommand( "wc" ); + + // clt.setstdin( "inputs.file1.path" ); + // clt.setstdout( "output" ); + + // Ref: wc-job.json + // Map json = new HashMap(); + // json.put("file1.class", "File"); + // json.put("file1.path" , "whale.txt"); + + JSONReader jr = new JSONReader("wc-job.json"); + jr.processFile(); + + //write engine file + + // Expected: wc file1.class.path > output + //process( clt, json ); + + // org.commonwl.lang.*; + + //Process p = Runtime.getRuntime().exec("ps -ef"); + //SystemCommandExecution sce = new SystemCommandExecution("ls -l"); + SystemCommandExecution sce = new SystemCommandExecution(); + sce.newExecutionCommand(); + //sce.extendExecutionCommand( clt.getbaseCommand() ); + sce.extendExecutionCommand( CommandLineTool_Instance.\ ); + String stdinPath = (String) CommandLineTool_Instance.getstdin(); + stdinPath = stdinPath.replace( "inputs.", "" ); + sce.extendExecutionCommand( jr.getValue( stdinPath ) ); + //sce.extendExecutionCommand( json.get( "file1.path" ) ); + sce.executeCommand(); + System.out.println( sce.getStandardOutput() ); + + } + +} diff --git a/sdk-and-javadoc-generation/examples/wc-job.json b/sdk-and-javadoc-generation/examples/wc-job.json new file mode 100644 index 00000000..32ffc842 --- /dev/null +++ b/sdk-and-javadoc-generation/examples/wc-job.json @@ -0,0 +1,6 @@ +{ + "file1": { + "class": "File", + "path": "whale.txt" + } +} diff --git a/sdk-and-javadoc-generation/examples/wc-tool.cwl b/sdk-and-javadoc-generation/examples/wc-tool.cwl new file mode 100644 index 00000000..6e26b988 --- /dev/null +++ b/sdk-and-javadoc-generation/examples/wc-tool.cwl @@ -0,0 +1,15 @@ +#!/usr/bin/env cwl-runner + +class: CommandLineTool +cwlVersion: cwl:draft-3 + +inputs: + - { id: file1, type: File } + +"outputs": + - { id: output, type: File, outputBinding: { glob: output } } + +baseCommand: [wc] + +stdin: $(inputs.file1.path) +stdout: output diff --git a/sdk-and-javadoc-generation/examples/wc-tool.java b/sdk-and-javadoc-generation/examples/wc-tool.java new file mode 100644 index 00000000..b912ceb2 --- /dev/null +++ b/sdk-and-javadoc-generation/examples/wc-tool.java @@ -0,0 +1,33 @@ +import org.commonwl.lang.*; +import org.commonwl.util.*; + + public class wc-tool() { + + public wc-tool() { } + + public Object build() { + + CommandLineTool CWL = new CWL(); + + CommandInputParameter [] inputs = new CommandInputParameter[1]; + inputs[0] = new CommandInputParameter(); + inputs[0].setid( "file1" ); + inputs[0].settype( "File" ); + CWL.setinputs( inputs ); + + CommandOutputParameter [] outputs = new CommandOutputParameter[1]; + outputs[0] = new CommandInputParameter(); + outputs[0].setid( "output" ); + outputs[0].settype( "File" ); + CWL.setoutputs( outputs ); + + CWL.setbaseCommand( "[wc]" ); + + CWL.setstdin( "$(inputs.file1.path)" ); + + CWL.setstdout( "output" ); + + return CWL; + } + +} diff --git a/sdk-and-javadoc-generation/examples/wc_tool.java b/sdk-and-javadoc-generation/examples/wc_tool.java new file mode 100644 index 00000000..c09f267d --- /dev/null +++ b/sdk-and-javadoc-generation/examples/wc_tool.java @@ -0,0 +1,33 @@ +import org.commonwl.lang.*; +import org.commonwl.util.*; + + public class wc_tool { + + public wc_tool() { } + + public Object build() { + + CommandLineTool CWL = new CommandLineTool(); + + CommandInputParameter [] inputs = new CommandInputParameter[1]; + inputs[0] = new CommandInputParameter(); + inputs[0].setid( "file1" ); + inputs[0].settype( "File" ); + CWL.setinputs( inputs ); + + CommandOutputParameter [] outputs = new CommandOutputParameter[1]; + outputs[0] = new CommandOutputParameter(); + outputs[0].setid( "output" ); + outputs[0].settype( "File" ); + CWL.setoutputs( outputs ); + + CWL.setbaseCommand( "[wc]" ); + + CWL.setstdin( "$(inputs.file1.path)" ); + + CWL.setstdout( "output" ); + + return CWL; + } + +} diff --git a/sdk-and-javadoc-generation/examples/whale.txt b/sdk-and-javadoc-generation/examples/whale.txt new file mode 100644 index 00000000..425d1ed0 --- /dev/null +++ b/sdk-and-javadoc-generation/examples/whale.txt @@ -0,0 +1,16 @@ +Call me Ishmael. Some years ago--never mind how long precisely--having +little or no money in my purse, and nothing particular to interest me on +shore, I thought I would sail about a little and see the watery part of +the world. It is a way I have of driving off the spleen and regulating +the circulation. Whenever I find myself growing grim about the mouth; +whenever it is a damp, drizzly November in my soul; whenever I find +myself involuntarily pausing before coffin warehouses, and bringing up +the rear of every funeral I meet; and especially whenever my hypos get +such an upper hand of me, that it requires a strong moral principle to +prevent me from deliberately stepping into the street, and methodically +knocking people's hats off--then, I account it high time to get to sea +as soon as I can. This is my substitute for pistol and ball. With a +philosophical flourish Cato throws himself upon his sword; I quietly +take to the ship. There is nothing surprising in this. If they but knew +it, almost all men in their degree, some time or other, cherish very +nearly the same feelings towards the ocean with me. diff --git a/sdk-and-javadoc-generation/javadoc/allclasses-frame.html b/sdk-and-javadoc-generation/javadoc/allclasses-frame.html new file mode 100644 index 00000000..b5d22f3f --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/allclasses-frame.html @@ -0,0 +1,100 @@ + + + + + +All Classes + + + + + +

All Classes

+
+ +
+ + diff --git a/sdk-and-javadoc-generation/javadoc/allclasses-noframe.html b/sdk-and-javadoc-generation/javadoc/allclasses-noframe.html new file mode 100644 index 00000000..f9619059 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/allclasses-noframe.html @@ -0,0 +1,100 @@ + + + + + +All Classes + + + + + +

All Classes

+
+ +
+ + diff --git a/sdk-and-javadoc-generation/javadoc/constant-values.html b/sdk-and-javadoc-generation/javadoc/constant-values.html new file mode 100644 index 00000000..7d45407c --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/constant-values.html @@ -0,0 +1,122 @@ + + + + + +Constant Field Values + + + + + + + + +
+ + +
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+ + + + +
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+

Constant Field Values

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Contents

+
+ +
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+ + + diff --git a/sdk-and-javadoc-generation/javadoc/deprecated-list.html b/sdk-and-javadoc-generation/javadoc/deprecated-list.html new file mode 100644 index 00000000..9f3542fc --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/deprecated-list.html @@ -0,0 +1,122 @@ + + + + + +Deprecated List + + + + + + + + +
+ + +
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+

Deprecated API

+

Contents

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+ + + diff --git a/sdk-and-javadoc-generation/javadoc/help-doc.html b/sdk-and-javadoc-generation/javadoc/help-doc.html new file mode 100644 index 00000000..18202e4f --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/help-doc.html @@ -0,0 +1,223 @@ + + + + + +API Help + + + + + + + + +
+ + +
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+ +
+

How This API Document Is Organized

+
This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows.
+
+
+
    +
  • +

    Overview

    +

    The Overview page is the front page of this API document and provides a list of all packages with a summary for each. This page can also contain an overall description of the set of packages.

    +
    • +
  • +

    Package

    +

    Each package has a page that contains a list of its classes and interfaces, with a summary for each. This page can contain six categories:

    +
      +
    • Interfaces (italic)
      • +
    • Classes
      • +
    • Enums
      • +
    • Exceptions
      • +
    • Errors
      • +
    • Annotation Types
      • +
    +
    • +
  • +

    Class/Interface

    +

    Each class, interface, nested class and nested interface has its own separate page. Each of these pages has three sections consisting of a class/interface description, summary tables, and detailed member descriptions:

    +
      +
    • Class inheritance diagram
      • +
    • Direct Subclasses
      • +
    • All Known Subinterfaces
      • +
    • All Known Implementing Classes
      • +
    • Class/interface declaration
      • +
    • Class/interface description
      • +
    +
      +
    • Nested Class Summary
      • +
    • Field Summary
      • +
    • Constructor Summary
      • +
    • Method Summary
      • +
    +
      +
    • Field Detail
      • +
    • Constructor Detail
      • +
    • Method Detail
      • +
    +

    Each summary entry contains the first sentence from the detailed description for that item. The summary entries are alphabetical, while the detailed descriptions are in the order they appear in the source code. This preserves the logical groupings established by the programmer.

    +
    • +
  • +

    Annotation Type

    +

    Each annotation type has its own separate page with the following sections:

    +
      +
    • Annotation Type declaration
      • +
    • Annotation Type description
      • +
    • Required Element Summary
      • +
    • Optional Element Summary
      • +
    • Element Detail
      • +
    +
    • +
  • +

    Enum

    +

    Each enum has its own separate page with the following sections:

    +
      +
    • Enum declaration
      • +
    • Enum description
      • +
    • Enum Constant Summary
      • +
    • Enum Constant Detail
      • +
    +
    • +
  • +

    Tree (Class Hierarchy)

    +

    There is a Class Hierarchy page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. The classes are organized by inheritance structure starting with java.lang.Object. The interfaces do not inherit from java.lang.Object.

    +
      +
    • When viewing the Overview page, clicking on "Tree" displays the hierarchy for all packages.
      • +
    • When viewing a particular package, class or interface page, clicking "Tree" displays the hierarchy for only that package.
      • +
    +
    • +
  • +

    Deprecated API

    +

    The Deprecated API page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.

    +
    • +
  • +

    Index

    +

    The Index contains an alphabetic list of all classes, interfaces, constructors, methods, and fields.

    +
    • +
  • +

    Prev/Next

    +

    These links take you to the next or previous class, interface, package, or related page.

    +
    • +
  • +

    Frames/No Frames

    +

    These links show and hide the HTML frames. All pages are available with or without frames.

    +
    • +
  • +

    All Classes

    +

    The All Classes link shows all classes and interfaces except non-static nested types.

    +
    • +
  • +

    Serialized Form

    +

    Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.

    +
    • +
  • +

    Constant Field Values

    +

    The Constant Field Values page lists the static final fields and their values.

    +
    • +
+This help file applies to API documentation generated using the standard doclet.
+ +
+ + +
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+ + + diff --git a/sdk-and-javadoc-generation/javadoc/index-all.html b/sdk-and-javadoc-generation/javadoc/index-all.html new file mode 100644 index 00000000..a52272c5 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/index-all.html @@ -0,0 +1,5242 @@ + + + + + +Index + + + + + + + + +
+ + +
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+ +
A B C D E F G H I J L M N O P R S T V W _  + + +

A

+
+
abstract_value - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
If true, this record is abstract and may be used as a base for other records, but is not valid on its own.
+
+
addIndentedNewline(String) - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
This method adds a newline character to a string of text.
+
+
addNewline(String) - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
This method adds a newline character to a string of text.
+
+
Any - Class in org.commonwl.lang
+
+
The Any type validates for any non-null value.
+
+
Any(Object) - Constructor for class org.commonwl.lang.Any
+
 
+
arguments - Variable in class org.commonwl.lang.CommandLineTool
+
+
Command line bindings which are not directly associated with input parameters.
+
+
ArraySchema - Class in org.commonwl.lang
+
 
+
ArraySchema() - Constructor for class org.commonwl.lang.ArraySchema
+
 
+
+ + + +

B

+
+
baseCommand - Variable in class org.commonwl.lang.CommandLineTool
+
+
Specifies the program to execute.
+
+
basename - Variable in class org.commonwl.lang.Directory
+
+
The base name of the directory, that is, the name of the file without any leading directory path.
+
+
basename - Variable in class org.commonwl.lang.File
+
+
The base name of the file, that is, the name of the file without any leading directory path.
+
+
+ + + +

C

+
+
checksum - Variable in class org.commonwl.lang.File
+
+
Optional hash code for validating file integrity.
+
+
class_value - Variable in class org.commonwl.lang.CommandLineTool
+
 
+
class_value - Variable in class org.commonwl.lang.Directory
+
+
Must be `Directory` to indicate this object describes a Directory.
+
+
class_value - Variable in class org.commonwl.lang.DockerRequirement
+
+
Always 'DockerRequirement'
+
+
class_value - Variable in class org.commonwl.lang.EnvVarRequirement
+
+
Always 'EnvVarRequirement'
+
+
class_value - Variable in class org.commonwl.lang.ExpressionTool
+
 
+
class_value - Variable in class org.commonwl.lang.File
+
+
Must be `File` to indicate this object describes a file.
+
+
class_value - Variable in class org.commonwl.lang.InitialWorkDirRequirement
+
+
InitialWorkDirRequirement
+
+
class_value - Variable in class org.commonwl.lang.InlineJavascriptRequirement
+
+
Always 'InlineJavascriptRequirement'
+
+
class_value - Variable in class org.commonwl.lang.MultipleInputFeatureRequirement
+
+
Always 'MultipleInputFeatureRequirement'
+
+
class_value - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Always 'ResourceRequirement'
+
+
class_value - Variable in class org.commonwl.lang.ScatterFeatureRequirement
+
+
Always 'ScatterFeatureRequirement'
+
+
class_value - Variable in class org.commonwl.lang.SchemaDefRequirement
+
+
Always 'SchemaDefRequirement'
+
+
class_value - Variable in class org.commonwl.lang.ShellCommandRequirement
+
+
Always 'ShellCommandRequirement'
+
+
class_value - Variable in class org.commonwl.lang.SoftwareRequirement
+
+
Always 'SoftwareRequirement'
+
+
class_value - Variable in class org.commonwl.lang.StepInputExpressionRequirement
+
+
Always 'StepInputExpressionRequirement'
+
+
class_value - Variable in class org.commonwl.lang.SubworkflowFeatureRequirement
+
+
Always 'SubworkflowFeatureRequirement'
+
+
class_value - Variable in class org.commonwl.lang.Workflow
+
 
+
cleanStandardInput(String) - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
Purpose: To remove the paranthesis "()" and dollar sign ($) + standard input.
+
+
cleanStandardInput(String) - Method in class org.commonwl.util.CWLReader
+
+
Purpose: To remove the paranthesis "()" and dollar sign ($) + standard input.
+
+
cleanupClassName(String) - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method removes the "class" string from the class name, produced by the getClass() method.
+
+
COMMAND_LINE_TOOL - Variable in class org.commonwl.util.CWLReader
+
+
The CommandLineTool used for storing class in the CWL file.
+
+
CommandInputArraySchema - Class in org.commonwl.lang
+
 
+
CommandInputArraySchema() - Constructor for class org.commonwl.lang.CommandInputArraySchema
+
 
+
CommandInputEnumSchema - Class in org.commonwl.lang
+
 
+
CommandInputEnumSchema() - Constructor for class org.commonwl.lang.CommandInputEnumSchema
+
 
+
CommandInputParameter - Class in org.commonwl.lang
+
+
An input parameter for a CommandLineTool.
+
+
CommandInputParameter() - Constructor for class org.commonwl.lang.CommandInputParameter
+
 
+
CommandInputRecordField - Class in org.commonwl.lang
+
 
+
CommandInputRecordField() - Constructor for class org.commonwl.lang.CommandInputRecordField
+
 
+
CommandInputRecordSchema - Class in org.commonwl.lang
+
 
+
CommandInputRecordSchema() - Constructor for class org.commonwl.lang.CommandInputRecordSchema
+
 
+
CommandLineBinding - Class in org.commonwl.lang
+
 
+
CommandLineBinding() - Constructor for class org.commonwl.lang.CommandLineBinding
+
 
+
CommandLineTool - Class in org.commonwl.lang
+
+
This defines the schema of the CWL Command Line Tool Description document.
+
+
CommandLineTool() - Constructor for class org.commonwl.lang.CommandLineTool
+
 
+
CommandOutputArraySchema - Class in org.commonwl.lang
+
 
+
CommandOutputArraySchema() - Constructor for class org.commonwl.lang.CommandOutputArraySchema
+
 
+
CommandOutputBinding - Class in org.commonwl.lang
+
+
Describes how to generate an output parameter based on the files produced by a CommandLineTool.
+
+
CommandOutputBinding() - Constructor for class org.commonwl.lang.CommandOutputBinding
+
 
+
CommandOutputEnumSchema - Class in org.commonwl.lang
+
 
+
CommandOutputEnumSchema() - Constructor for class org.commonwl.lang.CommandOutputEnumSchema
+
 
+
CommandOutputParameter - Class in org.commonwl.lang
+
+
An output parameter for a CommandLineTool.
+
+
CommandOutputParameter() - Constructor for class org.commonwl.lang.CommandOutputParameter
+
 
+
CommandOutputRecordField - Class in org.commonwl.lang
+
 
+
CommandOutputRecordField() - Constructor for class org.commonwl.lang.CommandOutputRecordField
+
 
+
CommandOutputRecordSchema - Class in org.commonwl.lang
+
 
+
CommandOutputRecordSchema() - Constructor for class org.commonwl.lang.CommandOutputRecordSchema
+
 
+
contents - Variable in class org.commonwl.lang.File
+
+
File contents literal.
+
+
coresMax - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Maximum reserved number of CPU cores
+
+
coresMin - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Minimum reserved number of CPU cores
+
+
CWL_FILE - Variable in class org.commonwl.util.CWLJavaCodeGenerator
+
+
The String used for storing CWL filename.
+
+
CWL_FILE - Variable in class org.commonwl.util.CWLReader
+
+
The String used for storing CWL filename.
+
+
CWL_JAVA_CLASS_NAME - Variable in class org.commonwl.util.CWLJavaCodeGenerator
+
+
The String used for storing CWL Java code-generated class name.
+
+
CWL_JAVA_FILE - Variable in class org.commonwl.util.CWLJavaCodeGenerator
+
+
The String used for storing CWL Java code-generated filename.
+
+
CWL_OBJECT - Variable in class org.commonwl.util.CWLJavaCodeGenerator
+
+
The String used for storing CWL Java code-generated filename.
+
+
CWLJavaCodeGenerator - Class in org.commonwl.util
+
 
+
CWLJavaCodeGenerator(String) - Constructor for class org.commonwl.util.CWLJavaCodeGenerator
+
+
The CommandOutputParameter used for storing outputs in the CWL file.
+
+
CWLReader - Class in org.commonwl.util
+
 
+
CWLReader(String) - Constructor for class org.commonwl.util.CWLReader
+
 
+
CWLType - Enum in org.commonwl.lang
+
+
- Extends primitive types with the concept of a file and directory as a builtin type.
+
+
CWLType() - Constructor for enum org.commonwl.lang.CWLType
+
 
+
cwlVersion - Variable in class org.commonwl.lang.CommandLineTool
+
+
CWL document version.
+
+
CWLVersion - Enum in org.commonwl.lang
+
+
Version symbols for published CWL document versions.
+
+
CWLVersion() - Constructor for enum org.commonwl.lang.CWLVersion
+
 
+
cwlVersion - Variable in class org.commonwl.lang.ExpressionTool
+
+
CWL document version.
+
+
cwlVersion - Static variable in interface org.commonwl.lang.Process
+
+
CWL document version.
+
+
cwlVersion - Variable in class org.commonwl.lang.Workflow
+
+
CWL document version.
+
+
+ + + +

D

+
+
default_value - Variable in class org.commonwl.lang.CommandInputParameter
+
+
The default value for this parameter if not provided in the input object.
+
+
default_value - Variable in class org.commonwl.lang.InputParameter
+
+
The default value for this parameter if not provided in the input object.
+
+
default_value - Variable in class org.commonwl.lang.WorkflowStepInput
+
+
The default value for this parameter if there is no `source` field.
+
+
Directory - Class in org.commonwl.lang
+
+
Represents a directory to present to a command line tool.
+
+
Directory() - Constructor for class org.commonwl.lang.Directory
+
 
+
Dirent - Class in org.commonwl.lang
+
+
Define a file or subdirectory that must be placed in the designated output directory prior to executing the command line tool.
+
+
Dirent() - Constructor for class org.commonwl.lang.Dirent
+
 
+
dirname - Variable in class org.commonwl.lang.File
+
+
The name of the directory containing file, that is, the path leading up to the final slash in the path such that `dirname + '/' + basename == path`.
+
+
doc - Variable in class org.commonwl.lang.CommandInputParameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.CommandInputRecordField
+
+
A documentation string for this field
+
+
doc - Variable in class org.commonwl.lang.CommandLineTool
+
+
A long, human-readable description of this process object.
+
+
doc - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.CommandOutputRecordField
+
+
A documentation string for this field
+
+
doc - Static variable in interface org.commonwl.lang.DocType
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.Documentation
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.ExpressionTool
+
+
A long, human-readable description of this process object.
+
+
doc - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.InputParameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.InputRecordField
+
+
A documentation string for this field
+
+
doc - Variable in class org.commonwl.lang.OutputParameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.OutputRecordField
+
+
A documentation string for this field
+
+
doc - Static variable in interface org.commonwl.lang.Parameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Static variable in interface org.commonwl.lang.Process
+
+
A long, human-readable description of this process object.
+
+
doc - Variable in class org.commonwl.lang.RecordField
+
+
A documentation string for this field
+
+
doc - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.SaladRecordField
+
+
A documentation string for this field
+
+
doc - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Static variable in interface org.commonwl.lang.SchemaDefinedType
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.Workflow
+
+
A long, human-readable description of this process object.
+
+
doc - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
A documentation string for this type, or an array of strings which should be concatenated.
+
+
doc - Variable in class org.commonwl.lang.WorkflowStep
+
+
A long, human-readable description of this process object.
+
+
docAfter - Static variable in interface org.commonwl.lang.DocType
+
+
Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
+
+
docAfter - Variable in class org.commonwl.lang.Documentation
+
+
Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
+
+
docAfter - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
+
+
docAfter - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
+
+
docAfter - Static variable in interface org.commonwl.lang.SchemaDefinedType
+
+
Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
+
+
docChild - Static variable in interface org.commonwl.lang.DocType
+
+
Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
+
+
docChild - Variable in class org.commonwl.lang.Documentation
+
+
Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
+
+
docChild - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
+
+
docChild - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
+
+
docChild - Static variable in interface org.commonwl.lang.SchemaDefinedType
+
+
Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
+
+
dockerFile - Variable in class org.commonwl.lang.DockerRequirement
+
+
Supply the contents of a Dockerfile which will be built using `docker build`.
+
+
dockerImageId - Variable in class org.commonwl.lang.DockerRequirement
+
+
The image id that will be used for `docker run`.
+
+
dockerImport - Variable in class org.commonwl.lang.DockerRequirement
+
+
Provide HTTP URL to download and gunzip a Docker images using `docker import.
+
+
dockerLoad - Variable in class org.commonwl.lang.DockerRequirement
+
+
Specify a HTTP URL from which to download a Docker image using `docker load`.
+
+
dockerOutputDirectory - Variable in class org.commonwl.lang.DockerRequirement
+
+
Set the designated output directory to a specific location inside the Docker container.
+
+
dockerPull - Variable in class org.commonwl.lang.DockerRequirement
+
+
Specify a Docker image to retrieve using `docker pull`.
+
+
DockerRequirement - Class in org.commonwl.lang
+
+
Indicates that a workflow component should be run in a [Docker](http://docker.com) container, and specifies how to fetch or build the image.
+
+
DockerRequirement() - Constructor for class org.commonwl.lang.DockerRequirement
+
 
+
docParent - Static variable in interface org.commonwl.lang.DocType
+
+
Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
+
+
docParent - Variable in class org.commonwl.lang.Documentation
+
+
Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
+
+
docParent - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
+
+
docParent - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
+
+
docParent - Static variable in interface org.commonwl.lang.SchemaDefinedType
+
+
Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
+
+
DocType - Interface in org.commonwl.lang
+
 
+
Documentation - Class in org.commonwl.lang
+
+
A documentation section.
+
+
Documentation() - Constructor for class org.commonwl.lang.Documentation
+
 
+
documentRoot - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
If true, indicates that the type is a valid at the document root.
+
+
documentRoot - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
If true, indicates that the type is a valid at the document root.
+
+
documentRoot - Static variable in interface org.commonwl.lang.SchemaDefinedType
+
+
If true, indicates that the type is a valid at the document root.
+
+
+ + + +

E

+
+
entry - Variable in class org.commonwl.lang.Dirent
+
+
If the value is a string literal or an expression which evaluates to a string, a new file must be created with the string as the file contents.
+
+
entryname - Variable in class org.commonwl.lang.Dirent
+
+
The name of the file or subdirectory to create in the output directory.
+
+
EnumSchema - Class in org.commonwl.lang
+
+
Define an enumerated type.
+
+
EnumSchema() - Constructor for class org.commonwl.lang.EnumSchema
+
 
+
envDef - Variable in class org.commonwl.lang.EnvVarRequirement
+
+
The list of environment variables.
+
+
EnvironmentDef - Class in org.commonwl.lang
+
+
Define an environment variable that will be set in the runtime environment by the workflow platform when executing the command line tool.
+
+
EnvironmentDef() - Constructor for class org.commonwl.lang.EnvironmentDef
+
 
+
envName - Variable in class org.commonwl.lang.EnvironmentDef
+
+
The environment variable name
+
+
envValue - Variable in class org.commonwl.lang.EnvironmentDef
+
+
The environment variable value
+
+
EnvVarRequirement - Class in org.commonwl.lang
+
+
Define a list of environment variables which will be set in the execution environment of the tool.
+
+
EnvVarRequirement() - Constructor for class org.commonwl.lang.EnvVarRequirement
+
 
+
executeCommand() - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method executes the command and returns a String array of the standard input, + standard output, and standard error.
+
+
Expression - Enum in org.commonwl.lang
+
+
'Expression' is not a real type.
+
+
Expression() - Constructor for enum org.commonwl.lang.Expression
+
 
+
expression - Variable in class org.commonwl.lang.ExpressionTool
+
+
The expression to execute.
+
+
expressionLib - Variable in class org.commonwl.lang.InlineJavascriptRequirement
+
+
Additional code fragments that will also be inserted before executing the expression code.
+
+
ExpressionTool - Class in org.commonwl.lang
+
+
Execute an expression as a Workflow step.
+
+
ExpressionTool() - Constructor for class org.commonwl.lang.ExpressionTool
+
 
+
ExpressionToolOutputParameter - Class in org.commonwl.lang
+
 
+
ExpressionToolOutputParameter() - Constructor for class org.commonwl.lang.ExpressionToolOutputParameter
+
 
+
extendExecutionCommand(Object) - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method is a helper method to process any object being requested to be run, such as + the ones returned by getbaseCommand() which are actually a String type.
+
+
extendExecutionCommand(String) - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method is a method to process a String command being requested to be run.
+
+
extends_value - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
Indicates that this enum inherits symbols from a base enum.
+
+
extends_value - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
Indicates that this record inherits fields from one or more base records.
+
+
+ + + +

F

+
+
File - Class in org.commonwl.lang
+
+
Represents a file (or group of files if `secondaryFiles` is specified) that must be accessible by tools using standard POSIX file system call API such as open(2) and read(2).
+
+
File() - Constructor for class org.commonwl.lang.File
+
 
+
format - Variable in class org.commonwl.lang.CommandInputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
format - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
format - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
format - Variable in class org.commonwl.lang.File
+
+
The format of the file: this must be an IRI of a concept node that represents the file format, preferrably defined within an ontology.
+
+
format - Variable in class org.commonwl.lang.InputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
format - Variable in class org.commonwl.lang.OutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
format - Static variable in interface org.commonwl.lang.Parameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
format - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
+ + + +

G

+
+
get() - Method in class org.commonwl.lang.Any
+
+
This method returns the value of Any.
+
+
get() - Method in class org.commonwl.lang.PrimitiveType
+
+
This method returns the value of PrimitiveType.
+
+
get_container() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of _container.
+
+
get_id() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of _id.
+
+
get_type() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of _type.
+
+
getabstract() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of abstract_value.
+
+
getarguments() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of arguments.
+
+
getbaseCommand() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of baseCommand.
+
+
getbasename() - Method in class org.commonwl.lang.Directory
+
+
This method returns the value of basename.
+
+
getbasename() - Method in class org.commonwl.lang.File
+
+
This method returns the value of basename.
+
+
getchecksum() - Method in class org.commonwl.lang.File
+
+
This method returns the value of checksum.
+
+
getclass() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.Directory
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.EnvVarRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.File
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.InlineJavascriptRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.MultipleInputFeatureRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.ScatterFeatureRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.SchemaDefRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.ShellCommandRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.SoftwareRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.StepInputExpressionRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.SubworkflowFeatureRequirement
+
+
This method returns the value of class_value.
+
+
getclass() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of class_value.
+
+
getCommandLineToolInstance() - Method in class org.commonwl.util.CWLReader
+
+
Purpose: Returns the populated CommandLineTool instance.
+
+
getcontents() - Method in class org.commonwl.lang.File
+
+
This method returns the value of contents.
+
+
getcoresMax() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of coresMax.
+
+
getcoresMin() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of coresMin.
+
+
getcwlVersion() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of cwlVersion.
+
+
getcwlVersion() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of cwlVersion.
+
+
getcwlVersion() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of cwlVersion.
+
+
getcwlVersion() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of cwlVersion.
+
+
getdefault() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of default_value.
+
+
getdefault() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of default_value.
+
+
getdefault() - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method returns the value of default_value.
+
+
getdirname() - Method in class org.commonwl.lang.File
+
+
This method returns the value of dirname.
+
+
getdoc() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method returns the value of doc.
+
+
getdoc() - Method in interface org.commonwl.lang.DocType
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.Documentation
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.InputRecordField
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.OutputRecordField
+
+
This method returns the value of doc.
+
+
getdoc() - Method in interface org.commonwl.lang.Parameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.RecordField
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.SaladRecordField
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of doc.
+
+
getdoc() - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of doc.
+
+
getdoc() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of doc.
+
+
getdocAfter() - Method in interface org.commonwl.lang.DocType
+
+
This method returns the value of docAfter.
+
+
getdocAfter() - Method in class org.commonwl.lang.Documentation
+
+
This method returns the value of docAfter.
+
+
getdocAfter() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of docAfter.
+
+
getdocAfter() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of docAfter.
+
+
getdocAfter() - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method returns the value of docAfter.
+
+
getdocChild() - Method in interface org.commonwl.lang.DocType
+
+
This method returns the value of docChild.
+
+
getdocChild() - Method in class org.commonwl.lang.Documentation
+
+
This method returns the value of docChild.
+
+
getdocChild() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of docChild.
+
+
getdocChild() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of docChild.
+
+
getdocChild() - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method returns the value of docChild.
+
+
getdockerFile() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of dockerFile.
+
+
getdockerImageId() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of dockerImageId.
+
+
getdockerImport() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of dockerImport.
+
+
getdockerLoad() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of dockerLoad.
+
+
getdockerOutputDirectory() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of dockerOutputDirectory.
+
+
getdockerPull() - Method in class org.commonwl.lang.DockerRequirement
+
+
This method returns the value of dockerPull.
+
+
getdocParent() - Method in interface org.commonwl.lang.DocType
+
+
This method returns the value of docParent.
+
+
getdocParent() - Method in class org.commonwl.lang.Documentation
+
+
This method returns the value of docParent.
+
+
getdocParent() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of docParent.
+
+
getdocParent() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of docParent.
+
+
getdocParent() - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method returns the value of docParent.
+
+
getdocumentRoot() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of documentRoot.
+
+
getdocumentRoot() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of documentRoot.
+
+
getdocumentRoot() - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method returns the value of documentRoot.
+
+
getentry() - Method in class org.commonwl.lang.Dirent
+
+
This method returns the value of entry.
+
+
getentryname() - Method in class org.commonwl.lang.Dirent
+
+
This method returns the value of entryname.
+
+
getenvDef() - Method in class org.commonwl.lang.EnvVarRequirement
+
+
This method returns the value of envDef.
+
+
getenvName() - Method in class org.commonwl.lang.EnvironmentDef
+
+
This method returns the value of envName.
+
+
getenvValue() - Method in class org.commonwl.lang.EnvironmentDef
+
+
This method returns the value of envValue.
+
+
getexpression() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of expression.
+
+
getexpressionLib() - Method in class org.commonwl.lang.InlineJavascriptRequirement
+
+
This method returns the value of expressionLib.
+
+
getextends() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of extends_value.
+
+
getextends() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of extends_value.
+
+
getFirstElementOfArrayList(ArrayList) - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
Purpose: Returns the first element of an ArrayList as a String.
+
+
getFirstElementOfArrayList(ArrayList) - Method in class org.commonwl.util.CWLReader
+
+
Purpose: Returns the first element of an ArrayList as a String.
+
+
getformat() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of format.
+
+
getformat() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of format.
+
+
getformat() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of format.
+
+
getformat() - Method in class org.commonwl.lang.File
+
+
This method returns the value of format.
+
+
getformat() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of format.
+
+
getformat() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of format.
+
+
getformat() - Method in interface org.commonwl.lang.Parameter
+
+
This method returns the value of format.
+
+
getformat() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of format.
+
+
getglob() - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method returns the value of glob.
+
+
gethints() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of hints.
+
+
gethints() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of hints.
+
+
gethints() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of hints.
+
+
gethints() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of hints.
+
+
gethints() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of hints.
+
+
getid() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of id.
+
+
getid() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method returns the value of id.
+
+
getid() - Method in class org.commonwl.lang.WorkflowStepOutput
+
+
This method returns the value of id.
+
+
getidentity() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of identity.
+
+
getin() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of in.
+
+
getinputBinding() - Method in class org.commonwl.lang.CommandInputArraySchema
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.CommandInputEnumSchema
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.InputArraySchema
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.InputEnumSchema
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of inputBinding.
+
+
getinputBinding() - Method in class org.commonwl.lang.InputRecordField
+
+
This method returns the value of inputBinding.
+
+
getinputs() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of inputs.
+
+
getinputs() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of inputs.
+
+
getinputs() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of inputs.
+
+
getinputs() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of inputs.
+
+
getitemSeparator() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of itemSeparator.
+
+
getjsonldPredicate() - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method returns the value of jsonldPredicate.
+
+
getjsonldPredicate() - Method in class org.commonwl.lang.SaladRecordField
+
+
This method returns the value of jsonldPredicate.
+
+
getjsonldPredicate() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of jsonldPredicate.
+
+
getjsonldPredicate() - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method returns the value of jsonldPredicate.
+
+
getlabel() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.InputArraySchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.InputEnumSchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.InputRecordField
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.InputRecordSchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in interface org.commonwl.lang.InputSchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.OutputArraySchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.OutputEnumSchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.OutputRecordSchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in interface org.commonwl.lang.OutputSchema
+
+
This method returns the value of label.
+
+
getlabel() - Method in interface org.commonwl.lang.Parameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of label.
+
+
getlabel() - Method in interface org.commonwl.lang.SchemaBase
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of label.
+
+
getlabel() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of label.
+
+
getlinkMerge() - Method in interface org.commonwl.lang.Sink
+
+
This method returns the value of linkMerge.
+
+
getlinkMerge() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of linkMerge.
+
+
getlinkMerge() - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method returns the value of linkMerge.
+
+
getlisting() - Method in class org.commonwl.lang.Directory
+
+
This method returns the value of listing.
+
+
getlisting() - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method returns the value of listing.
+
+
getloadContents() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of loadContents.
+
+
getloadContents() - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method returns the value of loadContents.
+
+
getloadContents() - Method in interface org.commonwl.lang.InputBinding
+
+
This method returns the value of loadContents.
+
+
getlocation() - Method in class org.commonwl.lang.Directory
+
+
This method returns the value of location.
+
+
getlocation() - Method in class org.commonwl.lang.File
+
+
This method returns the value of location.
+
+
getmapPredicate() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of mapPredicate.
+
+
getmapSubject() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of mapSubject.
+
+
getname() - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.Documentation
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.InputRecordField
+
+
This method returns the value of name.
+
+
getname() - Method in interface org.commonwl.lang.NamedType
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.OutputRecordField
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.RecordField
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.SaladRecordField
+
+
This method returns the value of name.
+
+
getname() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of name.
+
+
getnameext() - Method in class org.commonwl.lang.File
+
+
This method returns the value of nameext.
+
+
getnameroot() - Method in class org.commonwl.lang.File
+
+
This method returns the value of nameroot.
+
+
getnoLinkCheck() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of noLinkCheck.
+
+
getout() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of out.
+
+
getoutdirMax() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of outdirMax.
+
+
getoutdirMin() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of outdirMin.
+
+
getoutputBinding() - Method in class org.commonwl.lang.CommandOutputArraySchema
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.CommandOutputEnumSchema
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.OutputArraySchema
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.OutputEnumSchema
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.OutputRecordField
+
+
This method returns the value of outputBinding.
+
+
getoutputBinding() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of outputBinding.
+
+
getoutputEval() - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method returns the value of outputEval.
+
+
getoutputs() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of outputs.
+
+
getoutputs() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of outputs.
+
+
getoutputs() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of outputs.
+
+
getoutputs() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of outputs.
+
+
getoutputSource() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of outputSource.
+
+
getpackage() - Method in class org.commonwl.lang.SoftwarePackage
+
+
This method returns the value of package_value.
+
+
getpackages() - Method in class org.commonwl.lang.SoftwareRequirement
+
+
This method returns the value of packages.
+
+
getpath() - Method in class org.commonwl.lang.Directory
+
+
This method returns the value of path.
+
+
getpath() - Method in class org.commonwl.lang.File
+
+
This method returns the value of path.
+
+
getpermanentFailCodes() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of permanentFailCodes.
+
+
getposition() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of position.
+
+
getprefix() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of prefix.
+
+
getramMax() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of ramMax.
+
+
getramMin() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of ramMin.
+
+
getrefScope() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of refScope.
+
+
getrequirements() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of requirements.
+
+
getrequirements() - Method in class org.commonwl.lang.ExpressionTool
+
+
This method returns the value of requirements.
+
+
getrequirements() - Method in interface org.commonwl.lang.Process
+
+
This method returns the value of requirements.
+
+
getrequirements() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of requirements.
+
+
getrequirements() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of requirements.
+
+
getrun() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of run.
+
+
getscatter() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of scatter.
+
+
getscatterMethod() - Method in class org.commonwl.lang.WorkflowStep
+
+
This method returns the value of scatterMethod.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.File
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in interface org.commonwl.lang.Parameter
+
+
This method returns the value of secondaryFiles.
+
+
getsecondaryFiles() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of secondaryFiles.
+
+
getseparate() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of separate.
+
+
getshellQuote() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of shellQuote.
+
+
getsize() - Method in class org.commonwl.lang.File
+
+
This method returns the value of size.
+
+
getsource() - Method in interface org.commonwl.lang.Sink
+
+
This method returns the value of source.
+
+
getsource() - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method returns the value of source.
+
+
getspecialize() - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method returns the value of specialize.
+
+
getspecializeFrom() - Method in class org.commonwl.lang.SpecializeDef
+
+
This method returns the value of specializeFrom.
+
+
getspecializeTo() - Method in class org.commonwl.lang.SpecializeDef
+
+
This method returns the value of specializeTo.
+
+
getspecs() - Method in class org.commonwl.lang.SoftwarePackage
+
+
This method returns the value of specs.
+
+
getStandardError() - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method returns the last value of the standard error.
+
+
getStandardInput() - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method returns the last value of the standard input.
+
+
getStandardOutput() - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method returns the last value of the standard output.
+
+
getStatusCode() - Method in class org.commonwl.util.SystemCommandExecution
+
 
+
getstderr() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of stderr.
+
+
getstdin() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of stdin.
+
+
getstdout() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of stdout.
+
+
getsteps() - Method in class org.commonwl.lang.Workflow
+
+
This method returns the value of steps.
+
+
getstreamable() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of streamable.
+
+
getstreamable() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of streamable.
+
+
getstreamable() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of streamable.
+
+
getstreamable() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of streamable.
+
+
getstreamable() - Method in class org.commonwl.lang.OutputParameter
+
+
This method returns the value of streamable.
+
+
getstreamable() - Method in interface org.commonwl.lang.Parameter
+
+
This method returns the value of streamable.
+
+
getstreamable() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of streamable.
+
+
getsuccessCodes() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of successCodes.
+
+
gettemporaryFailCodes() - Method in class org.commonwl.lang.CommandLineTool
+
+
This method returns the value of temporaryFailCodes.
+
+
gettmpdirMax() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of tmpdirMax.
+
+
gettmpdirMin() - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method returns the value of tmpdirMin.
+
+
gettype() - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.Documentation
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.InputParameter
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.InputRecordField
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.OutputRecordField
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.RecordField
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.SaladRecordField
+
+
This method returns the value of type.
+
+
gettype() - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method returns the value of type.
+
+
gettypeDSL() - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method returns the value of typeDSL.
+
+
gettypes() - Method in class org.commonwl.lang.SchemaDefRequirement
+
+
This method returns the value of types.
+
+
getValue(String) - Method in class org.commonwl.util.JSONReader
+
+
This method is used to request the value using a key in the processed JSON file.
+
+
getvalueFrom() - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method returns the value of valueFrom.
+
+
getvalueFrom() - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method returns the value of valueFrom.
+
+
getversion() - Method in class org.commonwl.lang.SoftwarePackage
+
+
This method returns the value of version.
+
+
getwritable() - Method in class org.commonwl.lang.Dirent
+
+
This method returns the value of writable.
+
+
glob - Variable in class org.commonwl.lang.CommandOutputBinding
+
+
Find files relative to the output directory, using POSIX glob(3) pathname matching.
+
+
+ + + +

H

+
+
hints - Variable in class org.commonwl.lang.CommandLineTool
+
+
Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process.
+
+
hints - Variable in class org.commonwl.lang.ExpressionTool
+
+
Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process.
+
+
hints - Static variable in interface org.commonwl.lang.Process
+
+
Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process.
+
+
hints - Variable in class org.commonwl.lang.Workflow
+
+
Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process.
+
+
hints - Variable in class org.commonwl.lang.WorkflowStep
+
+
Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this workflow step.
+
+
+ + + +

I

+
+
id - Variable in class org.commonwl.lang.CommandInputParameter
+
+
The unique identifier for this parameter object.
+
+
id - Variable in class org.commonwl.lang.CommandLineTool
+
+
The unique identifier for this process object.
+
+
id - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
The unique identifier for this parameter object.
+
+
id - Variable in class org.commonwl.lang.ExpressionTool
+
+
The unique identifier for this process object.
+
+
id - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
The unique identifier for this parameter object.
+
+
id - Variable in class org.commonwl.lang.InputParameter
+
+
The unique identifier for this parameter object.
+
+
id - Variable in class org.commonwl.lang.OutputParameter
+
+
The unique identifier for this parameter object.
+
+
id - Static variable in interface org.commonwl.lang.Process
+
+
The unique identifier for this process object.
+
+
id - Variable in class org.commonwl.lang.Workflow
+
+
The unique identifier for this process object.
+
+
id - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
The unique identifier for this parameter object.
+
+
id - Variable in class org.commonwl.lang.WorkflowStep
+
+
The unique identifier for this workflow step.
+
+
id - Variable in class org.commonwl.lang.WorkflowStepInput
+
+
A unique identifier for this workflow input parameter.
+
+
id - Variable in class org.commonwl.lang.WorkflowStepOutput
+
+
A unique identifier for this workflow output parameter.
+
+
identity - Variable in class org.commonwl.lang.JsonldPredicate
+
+
If true and `_type` is `@id` this indicates that the parent field must be resolved according to identity resolution rules instead of link resolution rules.
+
+
in - Variable in class org.commonwl.lang.WorkflowStep
+
+
Defines the input parameters of the workflow step.
+
+
InitialWorkDirRequirement - Class in org.commonwl.lang
+
+
Define a list of files and subdirectories that must be created by the workflow platform in the designated output directory prior to executing the command line tool.
+
+
InitialWorkDirRequirement() - Constructor for class org.commonwl.lang.InitialWorkDirRequirement
+
 
+
InlineJavascriptRequirement - Class in org.commonwl.lang
+
+
Indicates that the workflow platform must support inline Javascript expressions.
+
+
InlineJavascriptRequirement() - Constructor for class org.commonwl.lang.InlineJavascriptRequirement
+
 
+
InputArraySchema - Class in org.commonwl.lang
+
 
+
InputArraySchema() - Constructor for class org.commonwl.lang.InputArraySchema
+
 
+
inputBinding - Variable in class org.commonwl.lang.CommandInputArraySchema
+
 
+
inputBinding - Variable in class org.commonwl.lang.CommandInputEnumSchema
+
 
+
inputBinding - Variable in class org.commonwl.lang.CommandInputParameter
+
+
Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
+
+
inputBinding - Variable in class org.commonwl.lang.CommandInputRecordField
+
 
+
inputBinding - Variable in class org.commonwl.lang.InputArraySchema
+
 
+
InputBinding - Interface in org.commonwl.lang
+
 
+
inputBinding - Variable in class org.commonwl.lang.InputEnumSchema
+
 
+
inputBinding - Variable in class org.commonwl.lang.InputParameter
+
+
Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
+
+
inputBinding - Variable in class org.commonwl.lang.InputRecordField
+
 
+
InputEnumSchema - Class in org.commonwl.lang
+
 
+
InputEnumSchema() - Constructor for class org.commonwl.lang.InputEnumSchema
+
 
+
InputParameter - Class in org.commonwl.lang
+
 
+
InputParameter() - Constructor for class org.commonwl.lang.InputParameter
+
 
+
InputRecordField - Class in org.commonwl.lang
+
 
+
InputRecordField() - Constructor for class org.commonwl.lang.InputRecordField
+
 
+
InputRecordSchema - Class in org.commonwl.lang
+
 
+
InputRecordSchema() - Constructor for class org.commonwl.lang.InputRecordSchema
+
 
+
inputs - Variable in class org.commonwl.lang.CommandLineTool
+
+
Defines the input parameters of the process.
+
+
inputs - Variable in class org.commonwl.lang.ExpressionTool
+
+
Defines the input parameters of the process.
+
+
inputs - Static variable in interface org.commonwl.lang.Process
+
+
Defines the input parameters of the process.
+
+
inputs - Variable in class org.commonwl.lang.Workflow
+
+
Defines the input parameters of the process.
+
+
INPUTS - Variable in class org.commonwl.util.CWLReader
+
+
The CommandInputParameter used for storing inputs in the CWL file.
+
+
InputSchema - Interface in org.commonwl.lang
+
 
+
itemSeparator - Variable in class org.commonwl.lang.CommandLineBinding
+
+
Join the array elements into a single string with the elements separated by by `itemSeparator`.
+
+
+ + + +

J

+
+
JSON_FILE - Variable in class org.commonwl.util.JSONReader
+
+
The String used for storing the JSON filename.
+
+
JsonldPredicate - Class in org.commonwl.lang
+
+
Attached to a record field to define how the parent record field is handled for URI resolution and JSON-LD context generation.
+
+
JsonldPredicate() - Constructor for class org.commonwl.lang.JsonldPredicate
+
 
+
jsonldPredicate - Variable in class org.commonwl.lang.SaladEnumSchema
+
+
Annotate this type with linked data context.
+
+
jsonldPredicate - Variable in class org.commonwl.lang.SaladRecordField
+
+
Annotate this type with linked data context.
+
+
jsonldPredicate - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
Annotate this type with linked data context.
+
+
jsonldPredicate - Static variable in interface org.commonwl.lang.SchemaDefinedType
+
+
Annotate this type with linked data context.
+
+
jsonMap - Variable in class org.commonwl.util.JSONReader
+
+
The key-value pairs in a JSON file that sit underneath the root key in a JSON file.
+
+
JSONReader - Class in org.commonwl.util
+
+
This is used reading and processing a JSON file.
+
+
JSONReader(String) - Constructor for class org.commonwl.util.JSONReader
+
 
+
+ + + +

L

+
+
label - Variable in class org.commonwl.lang.CommandInputParameter
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.CommandInputRecordField
+
+
A short, human-readable label of this process object.
+
+
label - Variable in class org.commonwl.lang.CommandLineTool
+
+
A short, human-readable label of this process object.
+
+
label - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.ExpressionTool
+
+
A short, human-readable label of this process object.
+
+
label - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.InputArraySchema
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.InputEnumSchema
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.InputParameter
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.InputRecordField
+
+
A short, human-readable label of this process object.
+
+
label - Variable in class org.commonwl.lang.InputRecordSchema
+
+
A short, human-readable label of this object.
+
+
label - Static variable in interface org.commonwl.lang.InputSchema
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.OutputArraySchema
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.OutputEnumSchema
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.OutputParameter
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.OutputRecordSchema
+
+
A short, human-readable label of this object.
+
+
label - Static variable in interface org.commonwl.lang.OutputSchema
+
+
A short, human-readable label of this object.
+
+
label - Static variable in interface org.commonwl.lang.Parameter
+
+
A short, human-readable label of this object.
+
+
label - Static variable in interface org.commonwl.lang.Process
+
+
A short, human-readable label of this process object.
+
+
label - Static variable in interface org.commonwl.lang.SchemaBase
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.Workflow
+
+
A short, human-readable label of this process object.
+
+
label - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
A short, human-readable label of this object.
+
+
label - Variable in class org.commonwl.lang.WorkflowStep
+
+
A short, human-readable label of this process object.
+
+
linkMerge - Static variable in interface org.commonwl.lang.Sink
+
+
The method to use to merge multiple inbound links into a single array.
+
+
linkMerge - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
The method to use to merge multiple sources into a single array.
+
+
linkMerge - Variable in class org.commonwl.lang.WorkflowStepInput
+
+
The method to use to merge multiple inbound links into a single array.
+
+
LinkMergeMethod - Enum in org.commonwl.lang
+
+
The input link merge method, described in [WorkflowStepInput](#WorkflowStepInput).
+
+
LinkMergeMethod() - Constructor for enum org.commonwl.lang.LinkMergeMethod
+
 
+
listing - Variable in class org.commonwl.lang.Directory
+
+
List of files or subdirectories contained in this directory.
+
+
listing - Variable in class org.commonwl.lang.InitialWorkDirRequirement
+
+
The list of files or subdirectories that must be placed in the designated output directory prior to executing the command line tool.
+
+
loadContents - Variable in class org.commonwl.lang.CommandLineBinding
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
loadContents - Variable in class org.commonwl.lang.CommandOutputBinding
+
+
For each file matched in `glob`, read up to the first 64 KiB of text from the file and place it in the `contents` field of the file object for manipulation by `outputEval`.
+
+
loadContents - Static variable in interface org.commonwl.lang.InputBinding
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
location - Variable in class org.commonwl.lang.Directory
+
+
An IRI that identifies the directory resource.
+
+
location - Variable in class org.commonwl.lang.File
+
+
An IRI that identifies the file resource.
+
+
+ + + +

M

+
+
mapPredicate - Variable in class org.commonwl.lang.JsonldPredicate
+
+
Only applies if `mapSubject` is also provided.
+
+
mapSubject - Variable in class org.commonwl.lang.JsonldPredicate
+
+
If the value of the field is a JSON object, it must be transformed into an array of JSON objects, where each key-value pair from the source JSON object is a list item, the list items must be JSON objects, and the key is assigned to the field specified by `mapSubject`.
+
+
MultipleInputFeatureRequirement - Class in org.commonwl.lang
+
+
Indicates that the workflow platform must support multiple inbound data links listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).
+
+
MultipleInputFeatureRequirement() - Constructor for class org.commonwl.lang.MultipleInputFeatureRequirement
+
 
+
+ + + +

N

+
+
name - Variable in class org.commonwl.lang.CommandInputRecordField
+
+
The name of the field
+
+
name - Variable in class org.commonwl.lang.CommandOutputRecordField
+
+
The name of the field
+
+
name - Variable in class org.commonwl.lang.Documentation
+
+
The identifier for this type
+
+
name - Variable in class org.commonwl.lang.InputRecordField
+
+
The name of the field
+
+
name - Static variable in interface org.commonwl.lang.NamedType
+
+
The identifier for this type
+
+
name - Variable in class org.commonwl.lang.OutputRecordField
+
+
The name of the field
+
+
name - Variable in class org.commonwl.lang.RecordField
+
+
The name of the field
+
+
name - Variable in class org.commonwl.lang.SaladRecordField
+
+
The name of the field
+
+
name - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
The identifier for this type
+
+
NamedType - Interface in org.commonwl.lang
+
 
+
nameext - Variable in class org.commonwl.lang.File
+
+
The basename extension such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period.
+
+
nameroot - Variable in class org.commonwl.lang.File
+
+
The basename root such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period.
+
+
newExecutionCommand() - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method resets the standard input String.
+
+
noLinkCheck - Variable in class org.commonwl.lang.JsonldPredicate
+
+
If true, this indicates that link validation traversal must stop at this field.
+
+
+ + + +

O

+
+
org.commonwl.lang - package org.commonwl.lang
+
 
+
org.commonwl.util - package org.commonwl.util
+
 
+
out - Variable in class org.commonwl.lang.WorkflowStep
+
+
Defines the parameters representing the output of the process.
+
+
outdirMax - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
+
+
outdirMin - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
+
+
OutputArraySchema - Class in org.commonwl.lang
+
 
+
OutputArraySchema() - Constructor for class org.commonwl.lang.OutputArraySchema
+
 
+
outputBinding - Variable in class org.commonwl.lang.CommandOutputArraySchema
+
 
+
outputBinding - Variable in class org.commonwl.lang.CommandOutputEnumSchema
+
 
+
outputBinding - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
Describes how to handle the outputs of a process.
+
+
outputBinding - Variable in class org.commonwl.lang.CommandOutputRecordField
+
 
+
outputBinding - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
Describes how to handle the outputs of a process.
+
+
outputBinding - Variable in class org.commonwl.lang.OutputArraySchema
+
 
+
OutputBinding - Interface in org.commonwl.lang
+
 
+
outputBinding - Variable in class org.commonwl.lang.OutputEnumSchema
+
 
+
outputBinding - Variable in class org.commonwl.lang.OutputParameter
+
+
Describes how to handle the outputs of a process.
+
+
outputBinding - Variable in class org.commonwl.lang.OutputRecordField
+
 
+
outputBinding - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
Describes how to handle the outputs of a process.
+
+
OutputEnumSchema - Class in org.commonwl.lang
+
 
+
OutputEnumSchema() - Constructor for class org.commonwl.lang.OutputEnumSchema
+
 
+
outputEval - Variable in class org.commonwl.lang.CommandOutputBinding
+
+
Evaluate an expression to generate the output value.
+
+
OutputParameter - Class in org.commonwl.lang
+
 
+
OutputParameter() - Constructor for class org.commonwl.lang.OutputParameter
+
 
+
OutputRecordField - Class in org.commonwl.lang
+
 
+
OutputRecordField() - Constructor for class org.commonwl.lang.OutputRecordField
+
 
+
OutputRecordSchema - Class in org.commonwl.lang
+
 
+
OutputRecordSchema() - Constructor for class org.commonwl.lang.OutputRecordSchema
+
 
+
outputs - Variable in class org.commonwl.lang.CommandLineTool
+
+
Defines the parameters representing the output of the process.
+
+
outputs - Variable in class org.commonwl.lang.ExpressionTool
+
+
Defines the parameters representing the output of the process.
+
+
outputs - Static variable in interface org.commonwl.lang.Process
+
+
Defines the parameters representing the output of the process.
+
+
outputs - Variable in class org.commonwl.lang.Workflow
+
+
Defines the parameters representing the output of the process.
+
+
OUTPUTS - Variable in class org.commonwl.util.CWLReader
+
+
The CommandOutputParameter used for storing outputs in the CWL file.
+
+
OutputSchema - Interface in org.commonwl.lang
+
 
+
outputSource - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
Specifies one or more workflow parameters that supply the value of to the output parameter.
+
+
+ + + +

P

+
+
package_value - Variable in class org.commonwl.lang.SoftwarePackage
+
+
The common name of the software to be configured.
+
+
packages - Variable in class org.commonwl.lang.SoftwareRequirement
+
+
The list of software to be configured.
+
+
Parameter - Interface in org.commonwl.lang
+
+
Define an input or output parameter to a process.
+
+
path - Variable in class org.commonwl.lang.Directory
+
+
The local path where the Directory is made available prior to executing a CommandLineTool.
+
+
path - Variable in class org.commonwl.lang.File
+
+
The local host path where the File is available when a CommandLineTool is executed.
+
+
permanentFailCodes - Variable in class org.commonwl.lang.CommandLineTool
+
+
Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail.
+
+
position - Variable in class org.commonwl.lang.CommandLineBinding
+
+
The sorting key.
+
+
prefix - Variable in class org.commonwl.lang.CommandLineBinding
+
+
Command line prefix to add before the value.
+
+
PrimitiveType - Class in org.commonwl.lang
+
+
Salad data types are based on Avro schema declarations.
+
+
PrimitiveType(Object) - Constructor for class org.commonwl.lang.PrimitiveType
+
 
+
Process - Interface in org.commonwl.lang
+
 
+
processClass(String) - Method in class org.commonwl.util.CWLReader
+
+
This method processes the class in a CWL file, and updates the CommandLineTool contents.
+
+
processContents(Map) - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
This method processing of the contents of a CWL file for populating a CommandLineTool instance.
+
+
processContents(String, Object) - Method in class org.commonwl.util.CWLReader
+
+
This method processing of the contents of a CWL file for populating a CommandLineTool instance.
+
+
processFile() - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
This method starts the processing of the CWL file for populating the contents in a CommandLineTool.
+
+
processFile() - Method in class org.commonwl.util.CWLReader
+
+
This method starts the processing of the CWL file for populating the contents in a CommandLineTool.
+
+
processFile() - Method in class org.commonwl.util.JSONReader
+
+
This method will process a JSON file an store it's contents.
+
+
processInputs(Map) - Method in class org.commonwl.util.CWLReader
+
+
This method processes the intputs in a CWL file, and updates the CommandLineTool contents.
+
+
processOutputs(Map) - Method in class org.commonwl.util.CWLReader
+
+
This method processes the outputs in a CWL file, and updates the CommandLineTool contents.
+
+
ProcessRequirement - Interface in org.commonwl.lang
+
+
A process requirement declares a prerequisite that may or must be fulfilled before executing a process.
+
+
+ + + +

R

+
+
ramMax - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Maximum reserved RAM in mebibytes (2**20)
+
+
ramMin - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Minimum reserved RAM in mebibytes (2**20)
+
+
RecordField - Class in org.commonwl.lang
+
+
A field of a record.
+
+
RecordField() - Constructor for class org.commonwl.lang.RecordField
+
 
+
RecordSchema - Class in org.commonwl.lang
+
 
+
RecordSchema() - Constructor for class org.commonwl.lang.RecordSchema
+
 
+
refScope - Variable in class org.commonwl.lang.JsonldPredicate
+
+
If the field contains a relative reference, it must be resolved by searching for valid document references in each successive parent scope in the document fragment.
+
+
removeBrackets(String) - Method in class org.commonwl.util.CWLJavaCodeGenerator
+
+
Purpose: To remove the brackets ([]) in a baseCommand.
+
+
removeBrackets(String) - Method in class org.commonwl.util.CWLReader
+
+
Purpose: To remove the brackets ([]) in a baseCommand.
+
+
requirements - Variable in class org.commonwl.lang.CommandLineTool
+
+
Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process.
+
+
requirements - Variable in class org.commonwl.lang.ExpressionTool
+
+
Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process.
+
+
requirements - Static variable in interface org.commonwl.lang.Process
+
+
Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process.
+
+
requirements - Variable in class org.commonwl.lang.Workflow
+
+
Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process.
+
+
requirements - Variable in class org.commonwl.lang.WorkflowStep
+
+
Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this workflow step.
+
+
ResourceRequirement - Class in org.commonwl.lang
+
+
Specify basic hardware resource requirements.
+
+
ResourceRequirement() - Constructor for class org.commonwl.lang.ResourceRequirement
+
 
+
ROOT_KEY - Variable in class org.commonwl.util.JSONReader
+
+
The String used for storing the key of the root of a JSON file's contents.
+
+
run - Variable in class org.commonwl.lang.WorkflowStep
+
+
Specifies the process to run.
+
+
+ + + +

S

+
+
SaladEnumSchema - Class in org.commonwl.lang
+
+
Define an enumerated type.
+
+
SaladEnumSchema() - Constructor for class org.commonwl.lang.SaladEnumSchema
+
 
+
SaladRecordField - Class in org.commonwl.lang
+
+
A field of a record.
+
+
SaladRecordField() - Constructor for class org.commonwl.lang.SaladRecordField
+
 
+
SaladRecordSchema - Class in org.commonwl.lang
+
 
+
SaladRecordSchema() - Constructor for class org.commonwl.lang.SaladRecordSchema
+
 
+
scatter - Variable in class org.commonwl.lang.WorkflowStep
+
 
+
ScatterFeatureRequirement - Class in org.commonwl.lang
+
+
Indicates that the workflow platform must support the `scatter` and `scatterMethod` fields of [WorkflowStep](#WorkflowStep).
+
+
ScatterFeatureRequirement() - Constructor for class org.commonwl.lang.ScatterFeatureRequirement
+
 
+
ScatterMethod - Enum in org.commonwl.lang
+
+
The scatter method, as described in [workflow step scatter](#WorkflowStep).
+
+
ScatterMethod() - Constructor for enum org.commonwl.lang.ScatterMethod
+
 
+
scatterMethod - Variable in class org.commonwl.lang.WorkflowStep
+
+
Required if `scatter` is an array of more than one element.
+
+
SchemaBase - Interface in org.commonwl.lang
+
 
+
SchemaDefinedType - Interface in org.commonwl.lang
+
+
Abstract base for schema-defined types.
+
+
SchemaDefRequirement - Class in org.commonwl.lang
+
+
This field consists of an array of type definitions which must be used when interpreting the `inputs` and `outputs` fields.
+
+
SchemaDefRequirement() - Constructor for class org.commonwl.lang.SchemaDefRequirement
+
 
+
secondaryFiles - Variable in class org.commonwl.lang.CommandInputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
secondaryFiles - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
secondaryFiles - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
secondaryFiles - Variable in class org.commonwl.lang.File
+
+
A list of additional files that are associated with the primary file and must be transferred alongside the primary file.
+
+
secondaryFiles - Variable in class org.commonwl.lang.InputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
secondaryFiles - Variable in class org.commonwl.lang.OutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
secondaryFiles - Static variable in interface org.commonwl.lang.Parameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
secondaryFiles - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
separate - Variable in class org.commonwl.lang.CommandLineBinding
+
+
If true (default), then the prefix and value must be added as separate command line arguments; if false, prefix and value must be concatenated into a single command line argument.
+
+
set(Object) - Method in class org.commonwl.lang.Any
+
+
This method sets the value of Any.
+
+
set(Boolean) - Method in class org.commonwl.lang.PrimitiveType
+
+
This method sets the value of PrimitiveType.
+
+
set(Integer) - Method in class org.commonwl.lang.PrimitiveType
+
+
This method sets the value of PrimitiveType.
+
+
set(Long) - Method in class org.commonwl.lang.PrimitiveType
+
+
This method sets the value of PrimitiveType.
+
+
set(Float) - Method in class org.commonwl.lang.PrimitiveType
+
+
This method sets the value of PrimitiveType.
+
+
set(Double) - Method in class org.commonwl.lang.PrimitiveType
+
+
This method sets the value of PrimitiveType.
+
+
set(String) - Method in class org.commonwl.lang.PrimitiveType
+
+
This method sets the value of PrimitiveType.
+
+
set_container(String) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of _container.
+
+
set_id(String) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of _id.
+
+
set_type(String) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of _type.
+
+
setabstract(Boolean) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of abstract_value.
+
+
setarguments(Expression[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of arguments.
+
+
setarguments(CommandLineBinding[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of arguments.
+
+
setarguments(String[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of arguments.
+
+
setbaseCommand(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of baseCommand.
+
+
setbaseCommand(String[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of baseCommand.
+
+
setbasename(String) - Method in class org.commonwl.lang.Directory
+
+
This method sets the value of basename.
+
+
setbasename(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of basename.
+
+
setchecksum(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of checksum.
+
+
setclass(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of class_value.
+
+
setclass(Directory) - Method in class org.commonwl.lang.Directory
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.EnvVarRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of class_value.
+
+
setclass(File) - Method in class org.commonwl.lang.File
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.InlineJavascriptRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.MultipleInputFeatureRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.ScatterFeatureRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.SchemaDefRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.ShellCommandRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.SoftwareRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.StepInputExpressionRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.SubworkflowFeatureRequirement
+
+
This method sets the value of class_value.
+
+
setclass(String) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of class_value.
+
+
setcontents(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of contents.
+
+
setcoresMax(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of coresMax.
+
+
setcoresMax(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of coresMax.
+
+
setcoresMax(Integer) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of coresMax.
+
+
setcoresMin(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of coresMin.
+
+
setcoresMin(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of coresMin.
+
+
setcoresMin(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of coresMin.
+
+
setcwlVersion(CWLVersion) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of cwlVersion.
+
+
setcwlVersion(CWLVersion) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of cwlVersion.
+
+
setcwlVersion(CWLVersion) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of cwlVersion.
+
+
setcwlVersion(CWLVersion) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of cwlVersion.
+
+
setdefault(Any) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of default_value.
+
+
setdefault(Any) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of default_value.
+
+
setdefault(Any) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of default_value.
+
+
setdirname(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of dirname.
+
+
setdoc(String) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in interface org.commonwl.lang.DocType
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in interface org.commonwl.lang.DocType
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of doc.
+
+
setdoc(String) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of doc.
+
+
setdocAfter(String) - Method in interface org.commonwl.lang.DocType
+
+
This method sets the value of docAfter.
+
+
setdocAfter(String) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of docAfter.
+
+
setdocAfter(String) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of docAfter.
+
+
setdocAfter(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of docAfter.
+
+
setdocAfter(String) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of docAfter.
+
+
setdocChild(String) - Method in interface org.commonwl.lang.DocType
+
+
This method sets the value of docChild.
+
+
setdocChild(String[]) - Method in interface org.commonwl.lang.DocType
+
+
This method sets the value of docChild.
+
+
setdocChild(String) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of docChild.
+
+
setdocChild(String[]) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of docChild.
+
+
setdocChild(String) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of docChild.
+
+
setdocChild(String[]) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of docChild.
+
+
setdocChild(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of docChild.
+
+
setdocChild(String[]) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of docChild.
+
+
setdocChild(String) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of docChild.
+
+
setdocChild(String[]) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of docChild.
+
+
setdockerFile(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of dockerFile.
+
+
setdockerImageId(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of dockerImageId.
+
+
setdockerImport(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of dockerImport.
+
+
setdockerLoad(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of dockerLoad.
+
+
setdockerOutputDirectory(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of dockerOutputDirectory.
+
+
setdockerPull(String) - Method in class org.commonwl.lang.DockerRequirement
+
+
This method sets the value of dockerPull.
+
+
setdocParent(String) - Method in interface org.commonwl.lang.DocType
+
+
This method sets the value of docParent.
+
+
setdocParent(String) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of docParent.
+
+
setdocParent(String) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of docParent.
+
+
setdocParent(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of docParent.
+
+
setdocParent(String) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of docParent.
+
+
setdocumentRoot(Boolean) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of documentRoot.
+
+
setdocumentRoot(Boolean) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of documentRoot.
+
+
setdocumentRoot(Boolean) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of documentRoot.
+
+
setentry(String) - Method in class org.commonwl.lang.Dirent
+
+
This method sets the value of entry.
+
+
setentry(Expression) - Method in class org.commonwl.lang.Dirent
+
+
This method sets the value of entry.
+
+
setentryname(String) - Method in class org.commonwl.lang.Dirent
+
+
This method sets the value of entryname.
+
+
setentryname(Expression) - Method in class org.commonwl.lang.Dirent
+
+
This method sets the value of entryname.
+
+
setenvDef(EnvironmentDef) - Method in class org.commonwl.lang.EnvVarRequirement
+
+
This method sets the value of envDef.
+
+
setenvName(String) - Method in class org.commonwl.lang.EnvironmentDef
+
+
This method sets the value of envName.
+
+
setenvValue(String) - Method in class org.commonwl.lang.EnvironmentDef
+
+
This method sets the value of envValue.
+
+
setenvValue(Expression) - Method in class org.commonwl.lang.EnvironmentDef
+
+
This method sets the value of envValue.
+
+
setexpression(String) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of expression.
+
+
setexpression(Expression) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of expression.
+
+
setexpressionLib(String) - Method in class org.commonwl.lang.InlineJavascriptRequirement
+
+
This method sets the value of expressionLib.
+
+
setextends(String) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of extends_value.
+
+
setextends(String[]) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of extends_value.
+
+
setextends(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of extends_value.
+
+
setextends(String[]) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of extends_value.
+
+
setformat(Expression[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of format.
+
+
setformat(Expression[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of format.
+
+
setformat(Expression[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of format.
+
+
setformat(Expression[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of format.
+
+
setformat(Expression[]) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of format.
+
+
setformat(Expression[]) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of format.
+
+
setformat(Expression[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of format.
+
+
setformat(String[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of format.
+
+
setglob(String) - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method sets the value of glob.
+
+
setglob(String[]) - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method sets the value of glob.
+
+
setglob(Expression) - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method sets the value of glob.
+
+
sethints(Any) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of hints.
+
+
sethints(Any) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of hints.
+
+
sethints(Any) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of hints.
+
+
sethints(Any) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of hints.
+
+
sethints(Any) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of hints.
+
+
setid(String) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of id.
+
+
setid(String) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of id.
+
+
setid(String) - Method in class org.commonwl.lang.WorkflowStepOutput
+
+
This method sets the value of id.
+
+
setidentity(Boolean) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of identity.
+
+
setin(WorkflowStepInput) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of in.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.CommandInputArraySchema
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.CommandInputEnumSchema
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.InputArraySchema
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.InputEnumSchema
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of inputBinding.
+
+
setinputBinding(CommandLineBinding) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of inputBinding.
+
+
setinputs(CommandInputParameter[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of inputs.
+
+
setinputs(InputParameter[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
+
+
setinputs(InputParameter[]) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of inputs.
+
+
setinputs(InputParameter[]) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of inputs.
+
+
setinputs(InputParameter[]) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of inputs.
+
+
setitemSeparator(String) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of itemSeparator.
+
+
setjsonldPredicate(String) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(JsonldPredicate) - Method in class org.commonwl.lang.SaladEnumSchema
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(String) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(JsonldPredicate) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(JsonldPredicate) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(String) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of jsonldPredicate.
+
+
setjsonldPredicate(JsonldPredicate) - Method in interface org.commonwl.lang.SchemaDefinedType
+
+
This method sets the value of jsonldPredicate.
+
+
setlabel(String) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.InputArraySchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.InputEnumSchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.InputRecordSchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in interface org.commonwl.lang.InputSchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.OutputArraySchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.OutputEnumSchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.OutputRecordSchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in interface org.commonwl.lang.OutputSchema
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in interface org.commonwl.lang.SchemaBase
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of label.
+
+
setlabel(String) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of label.
+
+
setlinkMerge(LinkMergeMethod) - Method in interface org.commonwl.lang.Sink
+
+
This method sets the value of linkMerge.
+
+
setlinkMerge(LinkMergeMethod) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of linkMerge.
+
+
setlinkMerge(LinkMergeMethod) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of linkMerge.
+
+
setlisting(File[]) - Method in class org.commonwl.lang.Directory
+
+
This method sets the value of listing.
+
+
setlisting(Directory[]) - Method in class org.commonwl.lang.Directory
+
+
This method sets the value of listing.
+
+
setlisting(Dirent[]) - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method sets the value of listing.
+
+
setlisting(File[]) - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method sets the value of listing.
+
+
setlisting(Directory[]) - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method sets the value of listing.
+
+
setlisting(Expression[]) - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method sets the value of listing.
+
+
setlisting(String[]) - Method in class org.commonwl.lang.InitialWorkDirRequirement
+
+
This method sets the value of listing.
+
+
setloadContents(Boolean) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of loadContents.
+
+
setloadContents(Boolean) - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method sets the value of loadContents.
+
+
setloadContents(Boolean) - Method in interface org.commonwl.lang.InputBinding
+
+
This method sets the value of loadContents.
+
+
setlocation(String) - Method in class org.commonwl.lang.Directory
+
+
This method sets the value of location.
+
+
setlocation(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of location.
+
+
setmapPredicate(String) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of mapPredicate.
+
+
setmapSubject(String) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of mapSubject.
+
+
setname(String) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of name.
+
+
setname(String) - Method in interface org.commonwl.lang.NamedType
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of name.
+
+
setname(String) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of name.
+
+
setnameext(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of nameext.
+
+
setnameroot(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of nameroot.
+
+
setnoLinkCheck(Boolean) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of noLinkCheck.
+
+
setout(WorkflowStepOutput[]) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of out.
+
+
setout(String[]) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of out.
+
+
setoutdirMax(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of outdirMax.
+
+
setoutdirMax(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of outdirMax.
+
+
setoutdirMax(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of outdirMax.
+
+
setoutdirMin(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of outdirMin.
+
+
setoutdirMin(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of outdirMin.
+
+
setoutdirMin(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of outdirMin.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.CommandOutputArraySchema
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.CommandOutputEnumSchema
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.OutputArraySchema
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.OutputEnumSchema
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of outputBinding.
+
+
setoutputBinding(CommandOutputBinding) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of outputBinding.
+
+
setoutputEval(String) - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method sets the value of outputEval.
+
+
setoutputEval(Expression) - Method in class org.commonwl.lang.CommandOutputBinding
+
+
This method sets the value of outputEval.
+
+
setoutputs(CommandOutputParameter[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of outputs.
+
+
setoutputs(OutputParameter[]) - Method in class org.commonwl.lang.CommandLineTool
+
+
This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
+
+
setoutputs(ExpressionToolOutputParameter[]) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of outputs.
+
+
setoutputs(OutputParameter[]) - Method in class org.commonwl.lang.ExpressionTool
+
+
This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
+
+
setoutputs(OutputParameter[]) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of outputs.
+
+
setoutputs(WorkflowOutputParameter[]) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of outputs.
+
+
setoutputs(OutputParameter[]) - Method in class org.commonwl.lang.Workflow
+
+
This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
+
+
setoutputSource(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of outputSource.
+
+
setoutputSource(String[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of outputSource.
+
+
setpackage(String) - Method in class org.commonwl.lang.SoftwarePackage
+
+
This method sets the value of package_value.
+
+
setpackages(SoftwarePackage) - Method in class org.commonwl.lang.SoftwareRequirement
+
+
This method sets the value of packages.
+
+
setpath(String) - Method in class org.commonwl.lang.Directory
+
+
This method sets the value of path.
+
+
setpath(String) - Method in class org.commonwl.lang.File
+
+
This method sets the value of path.
+
+
setpermanentFailCodes(Integer) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of permanentFailCodes.
+
+
setposition(Integer) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of position.
+
+
setprefix(String) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of prefix.
+
+
setramMax(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of ramMax.
+
+
setramMax(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of ramMax.
+
+
setramMax(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of ramMax.
+
+
setramMin(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of ramMin.
+
+
setramMin(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of ramMin.
+
+
setramMin(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of ramMin.
+
+
setrefScope(Integer) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of refScope.
+
+
setrequirements(StepInputExpressionRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(MultipleInputFeatureRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(SoftwareRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(SchemaDefRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(InitialWorkDirRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(EnvVarRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(DockerRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(ResourceRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(InlineJavascriptRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(ShellCommandRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(ScatterFeatureRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(SubworkflowFeatureRequirement) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of requirements.
+
+
setrequirements(StepInputExpressionRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(MultipleInputFeatureRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(SoftwareRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(SchemaDefRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(InitialWorkDirRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(EnvVarRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(DockerRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(ResourceRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(InlineJavascriptRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(ShellCommandRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(ScatterFeatureRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(SubworkflowFeatureRequirement) - Method in class org.commonwl.lang.ExpressionTool
+
+
This method sets the value of requirements.
+
+
setrequirements(StepInputExpressionRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(MultipleInputFeatureRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(SoftwareRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(SchemaDefRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(InitialWorkDirRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(EnvVarRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(DockerRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(ResourceRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(InlineJavascriptRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(ShellCommandRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(ScatterFeatureRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(SubworkflowFeatureRequirement) - Method in interface org.commonwl.lang.Process
+
+
This method sets the value of requirements.
+
+
setrequirements(StepInputExpressionRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(MultipleInputFeatureRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(SoftwareRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(SchemaDefRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(InitialWorkDirRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(EnvVarRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(DockerRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(ResourceRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(InlineJavascriptRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(ShellCommandRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(ScatterFeatureRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(SubworkflowFeatureRequirement) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of requirements.
+
+
setrequirements(StepInputExpressionRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(MultipleInputFeatureRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(SoftwareRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(SchemaDefRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(InitialWorkDirRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(EnvVarRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(DockerRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(ResourceRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(InlineJavascriptRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(ShellCommandRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(ScatterFeatureRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrequirements(SubworkflowFeatureRequirement) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of requirements.
+
+
setrun(CommandLineTool) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of run.
+
+
setrun(String) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of run.
+
+
setrun(Workflow) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of run.
+
+
setrun(ExpressionTool) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of run.
+
+
setscatter(String) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of scatter.
+
+
setscatter(String[]) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of scatter.
+
+
setscatterMethod(ScatterMethod) - Method in class org.commonwl.lang.WorkflowStep
+
+
This method sets the value of scatterMethod.
+
+
setsecondaryFiles(Expression[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(File[]) - Method in class org.commonwl.lang.File
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Directory[]) - Method in class org.commonwl.lang.File
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression[]) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression[]) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(String[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setsecondaryFiles(Expression) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of secondaryFiles.
+
+
setseparate(Boolean) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of separate.
+
+
setshellQuote(Boolean) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of shellQuote.
+
+
setsize(Long) - Method in class org.commonwl.lang.File
+
+
This method sets the value of size.
+
+
setsource(String) - Method in interface org.commonwl.lang.Sink
+
+
This method sets the value of source.
+
+
setsource(String[]) - Method in interface org.commonwl.lang.Sink
+
+
This method sets the value of source.
+
+
setsource(String) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of source.
+
+
setsource(String[]) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of source.
+
+
setspecialize(SpecializeDef[]) - Method in class org.commonwl.lang.SaladRecordSchema
+
+
This method sets the value of specialize.
+
+
setspecializeFrom(String) - Method in class org.commonwl.lang.SpecializeDef
+
+
This method sets the value of specializeFrom.
+
+
setspecializeTo(String) - Method in class org.commonwl.lang.SpecializeDef
+
+
This method sets the value of specializeTo.
+
+
setspecs(String) - Method in class org.commonwl.lang.SoftwarePackage
+
+
This method sets the value of specs.
+
+
setStandardInput(String) - Method in class org.commonwl.util.SystemCommandExecution
+
+
This method sets the standard input String.
+
+
setStatusCode(Integer) - Method in class org.commonwl.util.SystemCommandExecution
+
 
+
setstderr(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of stderr.
+
+
setstderr(Expression) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of stderr.
+
+
setstdin(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of stdin.
+
+
setstdin(Expression) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of stdin.
+
+
setstdout(String) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of stdout.
+
+
setstdout(Expression) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of stdout.
+
+
setsteps(WorkflowStep[]) - Method in class org.commonwl.lang.Workflow
+
+
This method sets the value of steps.
+
+
setstreamable(Boolean) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of streamable.
+
+
setstreamable(Boolean) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of streamable.
+
+
setstreamable(Boolean) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of streamable.
+
+
setstreamable(Boolean) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of streamable.
+
+
setstreamable(Boolean) - Method in class org.commonwl.lang.OutputParameter
+
+
This method sets the value of streamable.
+
+
setstreamable(Boolean) - Method in interface org.commonwl.lang.Parameter
+
+
This method sets the value of streamable.
+
+
setstreamable(Boolean) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of streamable.
+
+
setsuccessCodes(Integer) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of successCodes.
+
+
settemporaryFailCodes(Integer) - Method in class org.commonwl.lang.CommandLineTool
+
+
This method sets the value of temporaryFailCodes.
+
+
settmpdirMax(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of tmpdirMax.
+
+
settmpdirMax(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of tmpdirMax.
+
+
settmpdirMax(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of tmpdirMax.
+
+
settmpdirMin(Expression) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of tmpdirMin.
+
+
settmpdirMin(String) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of tmpdirMin.
+
+
settmpdirMin(Long) - Method in class org.commonwl.lang.ResourceRequirement
+
+
This method sets the value of tmpdirMin.
+
+
settype(CommandInputEnumSchema[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CommandInputEnumSchema) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CommandInputRecordSchema[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CommandInputRecordSchema) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CommandInputArraySchema) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(CommandInputArraySchema[]) - Method in class org.commonwl.lang.CommandInputParameter
+
+
This method sets the value of type.
+
+
settype(RecordSchema) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType[]) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(RecordSchema[]) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema[]) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema[]) - Method in class org.commonwl.lang.CommandInputRecordField
+
+
This method sets the value of type.
+
+
settype(CommandOutputArraySchema) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(stderr) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CommandOutputArraySchema[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CommandOutputRecordSchema[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(stdout) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CommandOutputEnumSchema) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CommandOutputRecordSchema) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(CommandOutputEnumSchema[]) - Method in class org.commonwl.lang.CommandOutputParameter
+
+
This method sets the value of type.
+
+
settype(RecordSchema) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType[]) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(RecordSchema[]) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema[]) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema[]) - Method in class org.commonwl.lang.CommandOutputRecordField
+
+
This method sets the value of type.
+
+
settype(Object) - Method in class org.commonwl.lang.Documentation
+
+
This method sets the value of type.
+
+
settype(OutputRecordSchema[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputEnumSchema[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputRecordSchema) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputEnumSchema) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputArraySchema) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputArraySchema[]) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
This method sets the value of type.
+
+
settype(InputEnumSchema[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(InputEnumSchema) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(InputRecordSchema[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(InputRecordSchema) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(InputArraySchema) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(InputArraySchema[]) - Method in class org.commonwl.lang.InputParameter
+
+
This method sets the value of type.
+
+
settype(InputRecordSchema) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(InputEnumSchema) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(InputArraySchema) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(InputRecordSchema[]) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(InputArraySchema[]) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(InputEnumSchema[]) - Method in class org.commonwl.lang.InputRecordField
+
+
This method sets the value of type.
+
+
settype(OutputRecordSchema) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(OutputEnumSchema) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(OutputArraySchema) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(OutputRecordSchema[]) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(OutputArraySchema[]) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(OutputEnumSchema[]) - Method in class org.commonwl.lang.OutputRecordField
+
+
This method sets the value of type.
+
+
settype(RecordSchema) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType[]) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(RecordSchema[]) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema[]) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema[]) - Method in class org.commonwl.lang.RecordField
+
+
This method sets the value of type.
+
+
settype(RecordSchema) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType[]) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(RecordSchema[]) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(PrimitiveType) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(ArraySchema[]) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(EnumSchema[]) - Method in class org.commonwl.lang.SaladRecordField
+
+
This method sets the value of type.
+
+
settype(OutputRecordSchema[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputEnumSchema[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(String[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputRecordSchema) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputEnumSchema) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputArraySchema) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(OutputArraySchema[]) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(CWLType) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settype(String) - Method in class org.commonwl.lang.WorkflowOutputParameter
+
+
This method sets the value of type.
+
+
settypeDSL(Boolean) - Method in class org.commonwl.lang.JsonldPredicate
+
+
This method sets the value of typeDSL.
+
+
settypes(InputEnumSchema[]) - Method in class org.commonwl.lang.SchemaDefRequirement
+
+
This method sets the value of types.
+
+
settypes(InputArraySchema[]) - Method in class org.commonwl.lang.SchemaDefRequirement
+
+
This method sets the value of types.
+
+
settypes(InputRecordSchema[]) - Method in class org.commonwl.lang.SchemaDefRequirement
+
+
This method sets the value of types.
+
+
setvalueFrom(String) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of valueFrom.
+
+
setvalueFrom(Expression) - Method in class org.commonwl.lang.CommandLineBinding
+
+
This method sets the value of valueFrom.
+
+
setvalueFrom(String) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of valueFrom.
+
+
setvalueFrom(Expression) - Method in class org.commonwl.lang.WorkflowStepInput
+
+
This method sets the value of valueFrom.
+
+
setversion(String) - Method in class org.commonwl.lang.SoftwarePackage
+
+
This method sets the value of version.
+
+
setwritable(Boolean) - Method in class org.commonwl.lang.Dirent
+
+
This method sets the value of writable.
+
+
ShellCommandRequirement - Class in org.commonwl.lang
+
+
Modify the behavior of CommandLineTool to generate a single string containing a shell command line.
+
+
ShellCommandRequirement() - Constructor for class org.commonwl.lang.ShellCommandRequirement
+
 
+
shellQuote - Variable in class org.commonwl.lang.CommandLineBinding
+
+
If `ShellCommandRequirement` is in the requirements for the current command, this controls whether the value is quoted on the command line (default is true).
+
+
Sink - Interface in org.commonwl.lang
+
 
+
size - Variable in class org.commonwl.lang.File
+
+
Optional file size
+
+
SoftwarePackage - Class in org.commonwl.lang
+
 
+
SoftwarePackage() - Constructor for class org.commonwl.lang.SoftwarePackage
+
 
+
SoftwareRequirement - Class in org.commonwl.lang
+
+
A list of software packages that should be configured in the environment of the defined process.
+
+
SoftwareRequirement() - Constructor for class org.commonwl.lang.SoftwareRequirement
+
 
+
source - Static variable in interface org.commonwl.lang.Sink
+
+
Specifies one or more workflow parameters that will provide input to the underlying step parameter.
+
+
source - Variable in class org.commonwl.lang.WorkflowStepInput
+
+
Specifies one or more workflow parameters that will provide input to the underlying step parameter.
+
+
specialize - Variable in class org.commonwl.lang.SaladRecordSchema
+
+
Only applies if `extends` is declared.
+
+
SpecializeDef - Class in org.commonwl.lang
+
 
+
SpecializeDef() - Constructor for class org.commonwl.lang.SpecializeDef
+
 
+
specializeFrom - Variable in class org.commonwl.lang.SpecializeDef
+
+
The data type to be replaced
+
+
specializeTo - Variable in class org.commonwl.lang.SpecializeDef
+
+
The new data type to replace with
+
+
specs - Variable in class org.commonwl.lang.SoftwarePackage
+
+
Must be one or more IRIs identifying resources for installing or enabling the software.
+
+
StandardError - Variable in class org.commonwl.util.SystemCommandExecution
+
+
The String used for storing the standard error.
+
+
StandardInput - Variable in class org.commonwl.util.SystemCommandExecution
+
+
The String used for storing the standard input.
+
+
StandardOutput - Variable in class org.commonwl.util.SystemCommandExecution
+
+
The String used for storing the standard output.
+
+
statusCode - Variable in class org.commonwl.util.SystemCommandExecution
+
+
The Integer used for storing the return status code.
+
+
stderr - Variable in class org.commonwl.lang.CommandLineTool
+
+
Capture the command's standard error stream to a file written to the designated output directory.
+
+
stderr - Enum in org.commonwl.lang
+
+
Only valid as a `type` for a `CommandLineTool` output with no `outputBinding` set.
+
+
stderr() - Constructor for enum org.commonwl.lang.stderr
+
 
+
stdin - Variable in class org.commonwl.lang.CommandLineTool
+
+
A path to a file whose contents must be piped into the command's standard input stream.
+
+
stdout - Variable in class org.commonwl.lang.CommandLineTool
+
+
Capture the command's standard output stream to a file written to the designated output directory.
+
+
stdout - Enum in org.commonwl.lang
+
+
Only valid as a `type` for a `CommandLineTool` output with no `outputBinding` set.
+
+
stdout() - Constructor for enum org.commonwl.lang.stdout
+
 
+
StepInputExpressionRequirement - Class in org.commonwl.lang
+
+
Indicate that the workflow platform must support the `valueFrom` field of [WorkflowStepInput](#WorkflowStepInput).
+
+
StepInputExpressionRequirement() - Constructor for class org.commonwl.lang.StepInputExpressionRequirement
+
 
+
steps - Variable in class org.commonwl.lang.Workflow
+
+
The individual steps that make up the workflow.
+
+
streamable - Variable in class org.commonwl.lang.CommandInputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
streamable - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
streamable - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
streamable - Variable in class org.commonwl.lang.InputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
streamable - Variable in class org.commonwl.lang.OutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
streamable - Static variable in interface org.commonwl.lang.Parameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
streamable - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
Only valid when `type: File` or is an array of `items: File`.
+
+
SubworkflowFeatureRequirement - Class in org.commonwl.lang
+
+
Indicates that the workflow platform must support nested workflows in the `run` field of [WorkflowStep](#WorkflowStep).
+
+
SubworkflowFeatureRequirement() - Constructor for class org.commonwl.lang.SubworkflowFeatureRequirement
+
 
+
successCodes - Variable in class org.commonwl.lang.CommandLineTool
+
+
Exit codes that indicate the process completed successfully.
+
+
SystemCommandExecution - Class in org.commonwl.util
+
+
This is used for executing commands on the system.
+
+
SystemCommandExecution() - Constructor for class org.commonwl.util.SystemCommandExecution
+
 
+
SystemCommandExecution(String) - Constructor for class org.commonwl.util.SystemCommandExecution
+
 
+
+ + + +

T

+
+
temporaryFailCodes - Variable in class org.commonwl.lang.CommandLineTool
+
+
Exit codes that indicate the process failed due to a possibly temporary condition, where executing the process with the same runtime environment and inputs may produce different results.
+
+
tmpdirMax - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
+
+
tmpdirMin - Variable in class org.commonwl.lang.ResourceRequirement
+
+
Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
+
+
TOOL_TYPE - Variable in class org.commonwl.util.CWLJavaCodeGenerator
+
+
The String used for storing if the CWL file is a CommandLineTool or Workflow.
+
+
type - Variable in class org.commonwl.lang.CommandInputParameter
+
+
Specify valid types of data that may be assigned to this parameter.
+
+
type - Variable in class org.commonwl.lang.CommandInputRecordField
+
+
The field type
+
+
type - Variable in class org.commonwl.lang.CommandOutputParameter
+
+
Specify valid types of data that may be assigned to this parameter.
+
+
type - Variable in class org.commonwl.lang.CommandOutputRecordField
+
+
The field type
+
+
type - Variable in class org.commonwl.lang.Documentation
+
+
Must be `documentation`
+
+
type - Variable in class org.commonwl.lang.ExpressionToolOutputParameter
+
+
Specify valid types of data that may be assigned to this parameter.
+
+
type - Variable in class org.commonwl.lang.InputParameter
+
+
Specify valid types of data that may be assigned to this parameter.
+
+
type - Variable in class org.commonwl.lang.InputRecordField
+
+
The field type
+
+
type - Variable in class org.commonwl.lang.OutputRecordField
+
+
The field type
+
+
type - Variable in class org.commonwl.lang.RecordField
+
+
The field type
+
+
type - Variable in class org.commonwl.lang.SaladRecordField
+
+
The field type
+
+
type - Variable in class org.commonwl.lang.WorkflowOutputParameter
+
+
Specify valid types of data that may be assigned to this parameter.
+
+
typeDSL - Variable in class org.commonwl.lang.JsonldPredicate
+
+
Field must be expanded based on the the Schema Salad type DSL.
+
+
types - Variable in class org.commonwl.lang.SchemaDefRequirement
+
+
The list of type definitions.
+
+
+ + + +

V

+
+
value - Variable in class org.commonwl.lang.Any
+
+
This is the value of Any.
+
+
value - Variable in class org.commonwl.lang.PrimitiveType
+
 
+
valueFrom - Variable in class org.commonwl.lang.CommandLineBinding
+
+
If `valueFrom` is a constant string value, use this as the value and apply the binding rules above.
+
+
valueFrom - Variable in class org.commonwl.lang.WorkflowStepInput
+
+
To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must be specified in the workflow or workflow step requirements.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.CWLType
+
+
Returns the enum constant of this type with the specified name.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.CWLVersion
+
+
Returns the enum constant of this type with the specified name.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.Expression
+
+
Returns the enum constant of this type with the specified name.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.LinkMergeMethod
+
+
Returns the enum constant of this type with the specified name.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.ScatterMethod
+
+
Returns the enum constant of this type with the specified name.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.stderr
+
+
Returns the enum constant of this type with the specified name.
+
+
valueOf(String) - Static method in enum org.commonwl.lang.stdout
+
+
Returns the enum constant of this type with the specified name.
+
+
values() - Static method in enum org.commonwl.lang.CWLType
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
values() - Static method in enum org.commonwl.lang.CWLVersion
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
values() - Static method in enum org.commonwl.lang.Expression
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
values() - Static method in enum org.commonwl.lang.LinkMergeMethod
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
values() - Static method in enum org.commonwl.lang.ScatterMethod
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
values() - Static method in enum org.commonwl.lang.stderr
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
values() - Static method in enum org.commonwl.lang.stdout
+
+
Returns an array containing the constants of this enum type, in +the order they are declared.
+
+
version - Variable in class org.commonwl.lang.SoftwarePackage
+
+
The (optional) version of the software to configured.
+
+
+ + + +

W

+
+
Workflow - Class in org.commonwl.lang
+
+
A workflow describes a set of **steps** and the **dependencies** between those steps.
+
+
Workflow() - Constructor for class org.commonwl.lang.Workflow
+
 
+
WorkflowOutputParameter - Class in org.commonwl.lang
+
+
Describe an output parameter of a workflow.
+
+
WorkflowOutputParameter() - Constructor for class org.commonwl.lang.WorkflowOutputParameter
+
 
+
WorkflowStep - Class in org.commonwl.lang
+
+
A workflow step is an executable element of a workflow.
+
+
WorkflowStep() - Constructor for class org.commonwl.lang.WorkflowStep
+
 
+
WorkflowStepInput - Class in org.commonwl.lang
+
+
The input of a workflow step connects an upstream parameter (from the workflow inputs, or the outputs of other workflows steps) with the input parameters of the underlying step.
+
+
WorkflowStepInput() - Constructor for class org.commonwl.lang.WorkflowStepInput
+
 
+
WorkflowStepOutput - Class in org.commonwl.lang
+
+
Associate an output parameter of the underlying process with a workflow parameter.
+
+
WorkflowStepOutput() - Constructor for class org.commonwl.lang.WorkflowStepOutput
+
 
+
writable - Variable in class org.commonwl.lang.Dirent
+
+
If true, the file or directory must be writable by the tool.
+
+
+ + + +

_

+
+
_container - Variable in class org.commonwl.lang.JsonldPredicate
+
+
Structure hint, corresponds to JSON-LD `@container` directive.
+
+
_id - Variable in class org.commonwl.lang.JsonldPredicate
+
+
The predicate URI that this field corresponds to.
+
+
_type - Variable in class org.commonwl.lang.JsonldPredicate
+
+
The context type hint, corresponds to JSON-LD `@type` directive.
+
+
+A B C D E F G H I J L M N O P R S T V W _ 
+ +
+ + +
Skip navigation links
+ + + + +
+
+
    +
  • Prev
    • +
  • Next
    • +
+ + +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/index.html b/sdk-and-javadoc-generation/javadoc/index.html new file mode 100644 index 00000000..5cce64e8 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/index.html @@ -0,0 +1,74 @@ + + + + + +Generated Documentation (Untitled) + + + + + + + + + +<noscript> +<div>JavaScript is disabled on your browser.</div> +</noscript> +<h2>Frame Alert</h2> +<p>This document is designed to be viewed using the frames feature. If you see this message, you are using a non-frame-capable web client. Link to <a href="overview-summary.html">Non-frame version</a>.</p> + + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Any.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Any.html new file mode 100644 index 00000000..ddaa346b --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Any.html @@ -0,0 +1,336 @@ + + + + + +Any + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class Any

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.Any
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class Any
+extends java.lang.Object
    +
    The Any type validates for any non-null value.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectvalue +
      This is the value of Any.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      Any(java.lang.Object objectInstance) 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectget() +
      This method returns the value of Any.
      +
      voidset(java.lang.Object objectInstance) +
      This method sets the value of Any.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        value

        +
        java.lang.Object value
        +
        This is the value of Any.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        Any

        +
        public Any(java.lang.Object objectInstance)
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        set

        +
        public void set(java.lang.Object objectInstance)
        +
        This method sets the value of Any.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of Any, and is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        get

        +
        public java.lang.Object get()
        +
        This method returns the value of Any.
        +
        +
        Returns:
        +
        This method will return the value of Any, which is an Any type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ArraySchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ArraySchema.html new file mode 100644 index 00000000..ad5f46fd --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ArraySchema.html @@ -0,0 +1,239 @@ + + + + + +ArraySchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Class ArraySchema

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.ArraySchema
      • +
    +
    • +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      ArraySchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        ArraySchema

        +
        public ArraySchema()
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CWLType.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CWLType.html new file mode 100644 index 00000000..a7c456e6 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CWLType.html @@ -0,0 +1,340 @@ + + + + + +CWLType + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Enum CWLType

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<CWLType>
      • +
    • +
        +
      • org.commonwl.lang.CWLType
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<CWLType>
    +
    +
    +
    +
    public enum CWLType
+extends java.lang.Enum<CWLType>
    +
    - Extends primitive types with the concept of a file and directory as a builtin type. - File: A File object - Directory: A Directory object
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Enum Constant Summary

      + + + + + + + + + + + +
      Enum Constants 
      Enum Constant and Description
      Directory 
      File 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Static Methods Concrete Methods 
      Modifier and TypeMethod and Description
      static CWLTypevalueOf(java.lang.String name) +
      Returns the enum constant of this type with the specified name.
      +
      static CWLType[]values() +
      Returns an array containing the constants of this enum type, in +the order they are declared.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Enum

        +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
        • +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +getClass, notify, notifyAll, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Enum Constant Detail

      + + + +
        +
      • +

        File

        +
        public static final CWLType File
        +
        • +
      + + + +
        +
      • +

        Directory

        +
        public static final CWLType Directory
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static CWLType[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (CWLType c : CWLType.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static CWLType valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CWLVersion.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CWLVersion.html new file mode 100644 index 00000000..34e03153 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CWLVersion.html @@ -0,0 +1,460 @@ + + + + + +CWLVersion + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Enum CWLVersion

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<CWLVersion>
      • +
    • +
        +
      • org.commonwl.lang.CWLVersion
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<CWLVersion>
    +
    +
    +
    +
    public enum CWLVersion
+extends java.lang.Enum<CWLVersion>
    +
    Version symbols for published CWL document versions.
    +
    • +
+
+
+ +
+
+
    +
  • + + + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static CWLVersion[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (CWLVersion c : CWLVersion.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static CWLVersion valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputArraySchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputArraySchema.html new file mode 100644 index 00000000..e4daeb1f --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputArraySchema.html @@ -0,0 +1,364 @@ + + + + + +CommandInputArraySchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandInputArraySchema

+
+
+ +
+ +
+
+ +
+
+
    +
  • + + + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandInputArraySchema

        +
        public CommandInputArraySchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Overrides:
        +
        setinputBinding in class InputArraySchema
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Overrides:
        +
        getinputBinding in class InputArraySchema
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputEnumSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputEnumSchema.html new file mode 100644 index 00000000..2ba101ba --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputEnumSchema.html @@ -0,0 +1,364 @@ + + + + + +CommandInputEnumSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandInputEnumSchema

+
+
+ +
+ +
+
+ +
+
+
    +
  • + + + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandInputEnumSchema

        +
        public CommandInputEnumSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Overrides:
        +
        setinputBinding in class InputEnumSchema
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Overrides:
        +
        getinputBinding in class InputEnumSchema
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      +
      • +
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+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputParameter.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputParameter.html new file mode 100644 index 00000000..a9bbe0b9 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputParameter.html @@ -0,0 +1,1190 @@ + + + + + +CommandInputParameter + + + + + + + + +
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+
org.commonwl.lang
+

Class CommandInputParameter

+
+
+ +
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Parameter, SchemaBase
    +
    +
    +
    +
    public class CommandInputParameter
+extends InputParameter
    +
    An input parameter for a CommandLineTool.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) Anydefault_value +
      The default value for this parameter if not provided in the input object.
      +
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this parameter object.
      +
      (package private) CommandLineBindinginputBinding +
      Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Objecttype +
      Specify valid types of data that may be assigned to this parameter.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      Anygetdefault() +
      This method returns the value of default_value.
      +
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      CommandLineBindinggetinputBinding() +
      This method returns the value of inputBinding.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdefault(Any value) +
      This method sets the value of default_value.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetinputBinding(CommandLineBinding value) +
      This method sets the value of inputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      voidsettype(CommandInputArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(CommandInputArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(CommandInputEnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(CommandInputEnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(CommandInputRecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(CommandInputRecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(CWLType value) +
      This method sets the value of type.
      +
      voidsettype(CWLType[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      + +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        default_value

        +
        Any default_value
        +
        The default value for this parameter if not provided in the input object.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this parameter object.
        +
        • +
      + + + +
        +
      • +

        inputBinding

        +
        CommandLineBinding inputBinding
        +
        Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        Specify valid types of data that may be assigned to this parameter.
        +
        • +
      + + + +
        +
      • +

        streamable

        +
        java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandInputParameter

        +
        public CommandInputParameter()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setdefault

        +
        public void setdefault(Any value)
        +
        This method sets the value of default_value.
        +
        +
        Overrides:
        +
        setdefault in class InputParameter
        +
        Parameters:
        +
        value - will update default_value, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        getdefault

        +
        public Any getdefault()
        +
        This method returns the value of default_value.
        +
        +
        Overrides:
        +
        getdefault in class InputParameter
        +
        Returns:
        +
        This method will return the value of default_value, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Overrides:
        +
        setid in class InputParameter
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Overrides:
        +
        getid in class InputParameter
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Overrides:
        +
        setinputBinding in class InputParameter
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Overrides:
        +
        getinputBinding in class InputParameter
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandInputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputEnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandInputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputEnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class InputParameter
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandInputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputRecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandInputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputRecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class InputParameter
        +
        Parameters:
        +
        value - will update type, which is a CWLType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class InputParameter
        +
        Parameters:
        +
        value - will update type, which is a CWLType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class InputParameter
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandInputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandInputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Overrides:
        +
        gettype in class InputParameter
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setstreamable

        +
        public void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Specified by:
        +
        setstreamable in interface Parameter
        +
        Overrides:
        +
        setstreamable in class InputParameter
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        public java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Specified by:
        +
        getstreamable in interface Parameter
        +
        Overrides:
        +
        getstreamable in class InputParameter
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class InputParameter
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class InputParameter
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class InputParameter
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Specified by:
        +
        getformat in interface Parameter
        +
        Overrides:
        +
        getformat in class InputParameter
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class InputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class InputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Parameter
        +
        Overrides:
        +
        getdoc in class InputParameter
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class InputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class InputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Specified by:
        +
        getsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        getsecondaryFiles in class InputParameter
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Parameter
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Overrides:
        +
        setlabel in class InputParameter
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Parameter
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Overrides:
        +
        getlabel in class InputParameter
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
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+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputRecordField.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputRecordField.html new file mode 100644 index 00000000..d4aac6ac --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputRecordField.html @@ -0,0 +1,791 @@ + + + + + +CommandInputRecordField + + + + + + + + +
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+
org.commonwl.lang
+

Class CommandInputRecordField

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringdoc +
      A documentation string for this field
      +
      (package private) CommandLineBindinginputBinding 
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this process object.
      +
      (package private) java.lang.Stringname +
      The name of the field
      +
      (package private) java.lang.Objecttype +
      The field type
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetdoc() +
      This method returns the value of doc.
      +
      CommandLineBindinggetinputBinding() +
      This method returns the value of inputBinding.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      java.lang.Stringgetname() +
      This method returns the value of name.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetinputBinding(CommandLineBinding value) +
      This method sets the value of inputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetname(java.lang.String value) +
      This method sets the value of name.
      +
      voidsettype(ArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(ArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(EnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(EnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(PrimitiveType value) +
      This method sets the value of type.
      +
      voidsettype(PrimitiveType[] value) +
      This method sets the value of type.
      +
      voidsettype(RecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(RecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      + +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      + + + + + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The name of the field
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A documentation string for this field
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        The field type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandInputRecordField

        +
        public CommandInputRecordField()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Overrides:
        +
        setlabel in class InputRecordField
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Overrides:
        +
        getlabel in class InputRecordField
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Overrides:
        +
        setinputBinding in class InputRecordField
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Overrides:
        +
        getinputBinding in class InputRecordField
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Overrides:
        +
        setname in class InputRecordField
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Overrides:
        +
        getname in class InputRecordField
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Overrides:
        +
        setdoc in class InputRecordField
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Overrides:
        +
        getdoc in class InputRecordField
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class InputRecordField
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class InputRecordField
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Overrides:
        +
        gettype in class InputRecordField
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputRecordSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputRecordSchema.html new file mode 100644 index 00000000..d677301d --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandInputRecordSchema.html @@ -0,0 +1,271 @@ + + + + + +CommandInputRecordSchema + + + + + + + + +
+ + +
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+ + + +
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    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandInputRecordSchema

+
+
+ +
+ +
+
+
    +
  • + + + + + +
      +
    • + + +

      Method Summary

      + +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandInputRecordSchema

        +
        public CommandInputRecordSchema()
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ +
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandLineBinding.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandLineBinding.html new file mode 100644 index 00000000..dd0ac4bb --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandLineBinding.html @@ -0,0 +1,700 @@ + + + + + +CommandLineBinding + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandLineBinding

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.CommandLineBinding
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    InputBinding
    +
    +
    +
    +
    public class CommandLineBinding
+extends java.lang.Object
+implements InputBinding
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.StringitemSeparator +
      Join the array elements into a single string with the elements separated by by `itemSeparator`.
      +
      (package private) java.lang.BooleanloadContents +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Integerposition +
      The sorting key.
      +
      (package private) java.lang.Stringprefix +
      Command line prefix to add before the value.
      +
      (package private) java.lang.Booleanseparate +
      If true (default), then the prefix and value must be added as separate command line arguments; if false, prefix and value must be concatenated into a single command line argument.
      +
      (package private) java.lang.BooleanshellQuote +
      If `ShellCommandRequirement` is in the requirements for the current command, this controls whether the value is quoted on the command line (default is true).
      +
      (package private) java.lang.ObjectvalueFrom +
      If `valueFrom` is a constant string value, use this as the value and apply the binding rules above.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      CommandLineBinding() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.StringgetitemSeparator() +
      This method returns the value of itemSeparator.
      +
      java.lang.BooleangetloadContents() +
      This method returns the value of loadContents.
      +
      java.lang.Integergetposition() +
      This method returns the value of position.
      +
      java.lang.Stringgetprefix() +
      This method returns the value of prefix.
      +
      java.lang.Booleangetseparate() +
      This method returns the value of separate.
      +
      java.lang.BooleangetshellQuote() +
      This method returns the value of shellQuote.
      +
      java.lang.ObjectgetvalueFrom() +
      This method returns the value of valueFrom.
      +
      voidsetitemSeparator(java.lang.String value) +
      This method sets the value of itemSeparator.
      +
      voidsetloadContents(java.lang.Boolean value) +
      This method sets the value of loadContents.
      +
      voidsetposition(java.lang.Integer value) +
      This method sets the value of position.
      +
      voidsetprefix(java.lang.String value) +
      This method sets the value of prefix.
      +
      voidsetseparate(java.lang.Boolean value) +
      This method sets the value of separate.
      +
      voidsetshellQuote(java.lang.Boolean value) +
      This method sets the value of shellQuote.
      +
      voidsetvalueFrom(Expression value) +
      This method sets the value of valueFrom.
      +
      voidsetvalueFrom(java.lang.String value) +
      This method sets the value of valueFrom.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        separate

        +
        java.lang.Boolean separate
        +
        If true (default), then the prefix and value must be added as separate command line arguments; if false, prefix and value must be concatenated into a single command line argument.
        +
        • +
      + + + +
        +
      • +

        itemSeparator

        +
        java.lang.String itemSeparator
        +
        Join the array elements into a single string with the elements separated by by `itemSeparator`.
        +
        • +
      + + + +
        +
      • +

        prefix

        +
        java.lang.String prefix
        +
        Command line prefix to add before the value.
        +
        • +
      + + + +
        +
      • +

        shellQuote

        +
        java.lang.Boolean shellQuote
        +
        If `ShellCommandRequirement` is in the requirements for the current command, this controls whether the value is quoted on the command line (default is true). Use `shellQuote: false` to inject metacharacters for operations such as pipes.
        +
        • +
      + + + +
        +
      • +

        position

        +
        java.lang.Integer position
        +
        The sorting key. Default position is 0.
        +
        • +
      + + + +
        +
      • +

        valueFrom

        +
        java.lang.Object valueFrom
        +
        If `valueFrom` is a constant string value, use this as the value and apply the binding rules above. If `valueFrom` is an expression, evaluate the expression to yield the actual value to use to build the command line and apply the binding rules above. If the inputBinding is associated with an input parameter, the value of `self` in the expression will be the value of the input parameter. When a binding is part of the `CommandLineTool.arguments` field, the `valueFrom` field is required.
        +
        • +
      + + + +
        +
      • +

        loadContents

        +
        java.lang.Boolean loadContents
        +
        Only valid when `type: File` or is an array of `items: File`. Read up to the first 64 KiB of text from the file and place it in the contents field of the file object for use by expressions.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandLineBinding

        +
        public CommandLineBinding()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setseparate

        +
        public void setseparate(java.lang.Boolean value)
        +
        This method sets the value of separate.
        +
        +
        Parameters:
        +
        value - will update separate, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getseparate

        +
        public java.lang.Boolean getseparate()
        +
        This method returns the value of separate.
        +
        +
        Returns:
        +
        This method will return the value of separate, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setitemSeparator

        +
        public void setitemSeparator(java.lang.String value)
        +
        This method sets the value of itemSeparator.
        +
        +
        Parameters:
        +
        value - will update itemSeparator, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getitemSeparator

        +
        public java.lang.String getitemSeparator()
        +
        This method returns the value of itemSeparator.
        +
        +
        Returns:
        +
        This method will return the value of itemSeparator, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setprefix

        +
        public void setprefix(java.lang.String value)
        +
        This method sets the value of prefix.
        +
        +
        Parameters:
        +
        value - will update prefix, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getprefix

        +
        public java.lang.String getprefix()
        +
        This method returns the value of prefix.
        +
        +
        Returns:
        +
        This method will return the value of prefix, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setshellQuote

        +
        public void setshellQuote(java.lang.Boolean value)
        +
        This method sets the value of shellQuote.
        +
        +
        Parameters:
        +
        value - will update shellQuote, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getshellQuote

        +
        public java.lang.Boolean getshellQuote()
        +
        This method returns the value of shellQuote.
        +
        +
        Returns:
        +
        This method will return the value of shellQuote, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setposition

        +
        public void setposition(java.lang.Integer value)
        +
        This method sets the value of position.
        +
        +
        Parameters:
        +
        value - will update position, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        getposition

        +
        public java.lang.Integer getposition()
        +
        This method returns the value of position.
        +
        +
        Returns:
        +
        This method will return the value of position, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        setvalueFrom

        +
        public void setvalueFrom(java.lang.String value)
        +
        This method sets the value of valueFrom.
        +
        +
        Parameters:
        +
        value - will update valueFrom, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setvalueFrom

        +
        public void setvalueFrom(Expression value)
        +
        This method sets the value of valueFrom.
        +
        +
        Parameters:
        +
        value - will update valueFrom, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getvalueFrom

        +
        public java.lang.Object getvalueFrom()
        +
        This method returns the value of valueFrom.
        +
        +
        Returns:
        +
        This method will return the value of valueFrom, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setloadContents

        +
        public void setloadContents(java.lang.Boolean value)
        +
        This method sets the value of loadContents.
        +
        +
        Specified by:
        +
        setloadContents in interface InputBinding
        +
        Parameters:
        +
        value - will update loadContents, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getloadContents

        +
        public java.lang.Boolean getloadContents()
        +
        This method returns the value of loadContents.
        +
        +
        Specified by:
        +
        getloadContents in interface InputBinding
        +
        Returns:
        +
        This method will return the value of loadContents, which is a Boolean type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
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+ + +
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org.commonwl.lang
+

Class CommandLineTool

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.CommandLineTool
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Process
    +
    +
    +
    +
    public class CommandLineTool
+extends java.lang.Object
+implements Process
    +
    This defines the schema of the CWL Command Line Tool Description document.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectarguments +
      Command line bindings which are not directly associated with input parameters.
      +
      (package private) java.lang.ObjectbaseCommand +
      Specifies the program to execute.
      +
      (package private) java.lang.Stringclass_value 
      (package private) CWLVersioncwlVersion +
      CWL document version.
      +
      (package private) java.lang.Stringdoc +
      A long, human-readable description of this process object.
      +
      (package private) Anyhints +
      Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this process object.
      +
      (package private) CommandInputParameter[]inputs +
      Defines the input parameters of the process.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this process object.
      +
      (package private) CommandOutputParameter[]outputs +
      Defines the parameters representing the output of the process.
      +
      (package private) java.lang.IntegerpermanentFailCodes +
      Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail.
      +
      (package private) java.lang.Objectrequirements +
      Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process.
      +
      (package private) java.lang.Objectstderr +
      Capture the command's standard error stream to a file written to the designated output directory.
      +
      (package private) java.lang.Objectstdin +
      A path to a file whose contents must be piped into the command's standard input stream.
      +
      (package private) java.lang.Objectstdout +
      Capture the command's standard output stream to a file written to the designated output directory.
      +
      (package private) java.lang.IntegersuccessCodes +
      Exit codes that indicate the process completed successfully.
      +
      (package private) java.lang.IntegertemporaryFailCodes +
      Exit codes that indicate the process failed due to a possibly temporary condition, where executing the process with the same runtime environment and inputs may produce different results.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      CommandLineTool() 
      +
      • +
    + + +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        stdin

        +
        java.lang.Object stdin
        +
        A path to a file whose contents must be piped into the command's standard input stream.
        +
        • +
      + + + +
        +
      • +

        stdout

        +
        java.lang.Object stdout
        +
        Capture the command's standard output stream to a file written to the designated output directory. If `stdout` is a string, it specifies the file name to use. If `stdout` is an expression, the expression is evaluated and must return a string with the file name to use to capture stdout. If the return value is not a string, or the resulting path contains illegal characters (such as the path separator `/`) it is an error.
        +
        • +
      + + + +
        +
      • +

        successCodes

        +
        java.lang.Integer successCodes
        +
        Exit codes that indicate the process completed successfully.
        +
        • +
      + + + +
        +
      • +

        temporaryFailCodes

        +
        java.lang.Integer temporaryFailCodes
        +
        Exit codes that indicate the process failed due to a possibly temporary condition, where executing the process with the same runtime environment and inputs may produce different results.
        +
        • +
      + + + +
        +
      • +

        baseCommand

        +
        java.lang.Object baseCommand
        +
        Specifies the program to execute. If an array, the first element of the array is the command to execute, and subsequent elements are mandatory command line arguments. The elements in `baseCommand` must appear before any command line bindings from `inputBinding` or `arguments`. If `baseCommand` is not provided or is an empty array, the first element of the command line produced after processing `inputBinding` or `arguments` must be used as the program to execute. If the program includes a path separator character it must be an absolute path, otherwise it is an error. If the program does not include a path separator, search the `$PATH` variable in the runtime environment of the workflow runner find the absolute path of the executable.
        +
        • +
      + + + +
        +
      • +

        arguments

        +
        java.lang.Object arguments
        +
        Command line bindings which are not directly associated with input parameters.
        +
        • +
      + + + +
        +
      • +

        stderr

        +
        java.lang.Object stderr
        +
        Capture the command's standard error stream to a file written to the designated output directory. If `stderr` is a string, it specifies the file name to use. If `stderr` is an expression, the expression is evaluated and must return a string with the file name to use to capture stderr. If the return value is not a string, or the resulting path contains illegal characters (such as the path separator `/`) it is an error.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        • +
      + + + +
        +
      • +

        permanentFailCodes

        +
        java.lang.Integer permanentFailCodes
        +
        Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail.
        +
        • +
      + + + +
        +
      • +

        outputs

        +
        CommandOutputParameter[] outputs
        +
        Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.
        +
        • +
      + + + +
        +
      • +

        requirements

        +
        java.lang.Object requirements
        +
        Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
        +
        • +
      + + + +
        +
      • +

        cwlVersion

        +
        CWLVersion cwlVersion
        +
        CWL document version. Always required at the document root. Not required for a Process embedded inside another Process.
        +
        • +
      + + + +
        +
      • +

        inputs

        +
        CommandInputParameter[] inputs
        +
        Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object.
        +
        • +
      + + + +
        +
      • +

        hints

        +
        Any hints
        +
        Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A long, human-readable description of this process object.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this process object.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandLineTool

        +
        public CommandLineTool()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setstdin

        +
        public void setstdin(java.lang.String value)
        +
        This method sets the value of stdin.
        +
        +
        Parameters:
        +
        value - will update stdin, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstdin

        +
        public void setstdin(Expression value)
        +
        This method sets the value of stdin.
        +
        +
        Parameters:
        +
        value - will update stdin, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getstdin

        +
        public java.lang.Object getstdin()
        +
        This method returns the value of stdin.
        +
        +
        Returns:
        +
        This method will return the value of stdin, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setstdout

        +
        public void setstdout(java.lang.String value)
        +
        This method sets the value of stdout.
        +
        +
        Parameters:
        +
        value - will update stdout, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstdout

        +
        public void setstdout(Expression value)
        +
        This method sets the value of stdout.
        +
        +
        Parameters:
        +
        value - will update stdout, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getstdout

        +
        public java.lang.Object getstdout()
        +
        This method returns the value of stdout.
        +
        +
        Returns:
        +
        This method will return the value of stdout, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setsuccessCodes

        +
        public void setsuccessCodes(java.lang.Integer value)
        +
        This method sets the value of successCodes.
        +
        +
        Parameters:
        +
        value - will update successCodes, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        getsuccessCodes

        +
        public java.lang.Integer getsuccessCodes()
        +
        This method returns the value of successCodes.
        +
        +
        Returns:
        +
        This method will return the value of successCodes, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        settemporaryFailCodes

        +
        public void settemporaryFailCodes(java.lang.Integer value)
        +
        This method sets the value of temporaryFailCodes.
        +
        +
        Parameters:
        +
        value - will update temporaryFailCodes, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        gettemporaryFailCodes

        +
        public java.lang.Integer gettemporaryFailCodes()
        +
        This method returns the value of temporaryFailCodes.
        +
        +
        Returns:
        +
        This method will return the value of temporaryFailCodes, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        setbaseCommand

        +
        public void setbaseCommand(java.lang.String value)
        +
        This method sets the value of baseCommand.
        +
        +
        Parameters:
        +
        value - will update baseCommand, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setbaseCommand

        +
        public void setbaseCommand(java.lang.String[] value)
        +
        This method sets the value of baseCommand.
        +
        +
        Parameters:
        +
        value - will update baseCommand, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getbaseCommand

        +
        public java.lang.Object getbaseCommand()
        +
        This method returns the value of baseCommand.
        +
        +
        Returns:
        +
        This method will return the value of baseCommand, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setarguments

        +
        public void setarguments(Expression[] value)
        +
        This method sets the value of arguments.
        +
        +
        Parameters:
        +
        value - will update arguments, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setarguments

        +
        public void setarguments(CommandLineBinding[] value)
        +
        This method sets the value of arguments.
        +
        +
        Parameters:
        +
        value - will update arguments, which is a CommandLineBinding array.
        +
        +
        • +
      + + + +
        +
      • +

        setarguments

        +
        public void setarguments(java.lang.String[] value)
        +
        This method sets the value of arguments.
        +
        +
        Parameters:
        +
        value - will update arguments, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getarguments

        +
        public java.lang.Object getarguments()
        +
        This method returns the value of arguments.
        +
        +
        Returns:
        +
        This method will return the value of arguments, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setstderr

        +
        public void setstderr(java.lang.String value)
        +
        This method sets the value of stderr.
        +
        +
        Parameters:
        +
        value - will update stderr, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstderr

        +
        public void setstderr(Expression value)
        +
        This method sets the value of stderr.
        +
        +
        Parameters:
        +
        value - will update stderr, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getstderr

        +
        public java.lang.Object getstderr()
        +
        This method returns the value of stderr.
        +
        +
        Returns:
        +
        This method will return the value of stderr, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setpermanentFailCodes

        +
        public void setpermanentFailCodes(java.lang.Integer value)
        +
        This method sets the value of permanentFailCodes.
        +
        +
        Parameters:
        +
        value - will update permanentFailCodes, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        getpermanentFailCodes

        +
        public java.lang.Integer getpermanentFailCodes()
        +
        This method returns the value of permanentFailCodes.
        +
        +
        Returns:
        +
        This method will return the value of permanentFailCodes, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputs

        +
        public void setoutputs(CommandOutputParameter[] value)
        +
        This method sets the value of outputs.
        +
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputs

        +
        public void setoutputs(OutputParameter[] value)
        +
        This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
        +
        +
        Specified by:
        +
        setoutputs in interface Process
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputs

        +
        public CommandOutputParameter[] getoutputs()
        +
        This method returns the value of outputs.
        +
        +
        Specified by:
        +
        getoutputs in interface Process
        +
        Returns:
        +
        This method will return the value of outputs, which is a CommandOutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(StepInputExpressionRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a StepInputExpressionRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(MultipleInputFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a MultipleInputFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SoftwareRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SoftwareRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SchemaDefRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SchemaDefRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InitialWorkDirRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a InitialWorkDirRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(EnvVarRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a EnvVarRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(DockerRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a DockerRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ResourceRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ResourceRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InlineJavascriptRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a InlineJavascriptRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ShellCommandRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ShellCommandRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ScatterFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ScatterFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SubworkflowFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SubworkflowFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        getrequirements

        +
        public java.lang.Object getrequirements()
        +
        This method returns the value of requirements.
        +
        +
        Specified by:
        +
        getrequirements in interface Process
        +
        Returns:
        +
        This method will return the value of requirements, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setcwlVersion

        +
        public void setcwlVersion(CWLVersion value)
        +
        This method sets the value of cwlVersion.
        +
        +
        Specified by:
        +
        setcwlVersion in interface Process
        +
        Parameters:
        +
        value - will update cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        getcwlVersion

        +
        public CWLVersion getcwlVersion()
        +
        This method returns the value of cwlVersion.
        +
        +
        Specified by:
        +
        getcwlVersion in interface Process
        +
        Returns:
        +
        This method will return the value of cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputs

        +
        public void setinputs(CommandInputParameter[] value)
        +
        This method sets the value of inputs.
        +
        +
        Parameters:
        +
        value - will update inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setinputs

        +
        public void setinputs(InputParameter[] value)
        +
        This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
        +
        +
        Specified by:
        +
        setinputs in interface Process
        +
        Parameters:
        +
        value - will update inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getinputs

        +
        public CommandInputParameter[] getinputs()
        +
        This method returns the value of inputs.
        +
        +
        Specified by:
        +
        getinputs in interface Process
        +
        Returns:
        +
        This method will return the value of inputs, which is a CommandInputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        sethints

        +
        public void sethints(Any value)
        +
        This method sets the value of hints.
        +
        +
        Specified by:
        +
        sethints in interface Process
        +
        Parameters:
        +
        value - will update hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        gethints

        +
        public Any gethints()
        +
        This method returns the value of hints.
        +
        +
        Specified by:
        +
        gethints in interface Process
        +
        Returns:
        +
        This method will return the value of hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Process
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Process
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Specified by:
        +
        setid in interface Process
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Specified by:
        +
        getid in interface Process
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Process
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Process
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputArraySchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputArraySchema.html new file mode 100644 index 00000000..7bb2aba9 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputArraySchema.html @@ -0,0 +1,364 @@ + + + + + +CommandOutputArraySchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandOutputArraySchema

+
+
+ +
+ +
+
+ +
+
+
    +
  • + + + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandOutputArraySchema

        +
        public CommandOutputArraySchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Overrides:
        +
        setoutputBinding in class OutputArraySchema
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Overrides:
        +
        getoutputBinding in class OutputArraySchema
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputBinding.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputBinding.html new file mode 100644 index 00000000..1b03aef0 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputBinding.html @@ -0,0 +1,513 @@ + + + + + +CommandOutputBinding + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandOutputBinding

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.CommandOutputBinding
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    OutputBinding
    +
    +
    +
    +
    public class CommandOutputBinding
+extends java.lang.Object
+implements OutputBinding
    +
    Describes how to generate an output parameter based on the files produced by a CommandLineTool.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectglob +
      Find files relative to the output directory, using POSIX glob(3) pathname matching.
      +
      (package private) java.lang.BooleanloadContents +
      For each file matched in `glob`, read up to the first 64 KiB of text from the file and place it in the `contents` field of the file object for manipulation by `outputEval`.
      +
      (package private) java.lang.ObjectoutputEval +
      Evaluate an expression to generate the output value.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetglob() +
      This method returns the value of glob.
      +
      java.lang.BooleangetloadContents() +
      This method returns the value of loadContents.
      +
      java.lang.ObjectgetoutputEval() +
      This method returns the value of outputEval.
      +
      voidsetglob(Expression value) +
      This method sets the value of glob.
      +
      voidsetglob(java.lang.String value) +
      This method sets the value of glob.
      +
      voidsetglob(java.lang.String[] value) +
      This method sets the value of glob.
      +
      voidsetloadContents(java.lang.Boolean value) +
      This method sets the value of loadContents.
      +
      voidsetoutputEval(Expression value) +
      This method sets the value of outputEval.
      +
      voidsetoutputEval(java.lang.String value) +
      This method sets the value of outputEval.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        loadContents

        +
        java.lang.Boolean loadContents
        +
        For each file matched in `glob`, read up to the first 64 KiB of text from the file and place it in the `contents` field of the file object for manipulation by `outputEval`.
        +
        • +
      + + + +
        +
      • +

        outputEval

        +
        java.lang.Object outputEval
        +
        Evaluate an expression to generate the output value. If `glob` was specified, the value of `self` must be an array containing file objects that were matched. If no files were matched, `self` must be a zero length array; if a single file was matched, the value of `self` is an array of a single element. Additionally, if `loadContents` is `true`, the File objects must include up to the first 64 KiB of file contents in the `contents` field.
        +
        • +
      + + + +
        +
      • +

        glob

        +
        java.lang.Object glob
        +
        Find files relative to the output directory, using POSIX glob(3) pathname matching. If an array is provided, find files that match any pattern in the array. If an expression is provided, the expression must return a string or an array of strings, which will then be evaluated as one or more glob patterns. Must only match and return files which actually exist.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandOutputBinding

        +
        public CommandOutputBinding()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setloadContents

        +
        public void setloadContents(java.lang.Boolean value)
        +
        This method sets the value of loadContents.
        +
        +
        Parameters:
        +
        value - will update loadContents, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getloadContents

        +
        public java.lang.Boolean getloadContents()
        +
        This method returns the value of loadContents.
        +
        +
        Returns:
        +
        This method will return the value of loadContents, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputEval

        +
        public void setoutputEval(java.lang.String value)
        +
        This method sets the value of outputEval.
        +
        +
        Parameters:
        +
        value - will update outputEval, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputEval

        +
        public void setoutputEval(Expression value)
        +
        This method sets the value of outputEval.
        +
        +
        Parameters:
        +
        value - will update outputEval, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputEval

        +
        public java.lang.Object getoutputEval()
        +
        This method returns the value of outputEval.
        +
        +
        Returns:
        +
        This method will return the value of outputEval, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setglob

        +
        public void setglob(java.lang.String value)
        +
        This method sets the value of glob.
        +
        +
        Parameters:
        +
        value - will update glob, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setglob

        +
        public void setglob(java.lang.String[] value)
        +
        This method sets the value of glob.
        +
        +
        Parameters:
        +
        value - will update glob, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        setglob

        +
        public void setglob(Expression value)
        +
        This method sets the value of glob.
        +
        +
        Parameters:
        +
        value - will update glob, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getglob

        +
        public java.lang.Object getglob()
        +
        This method returns the value of glob.
        +
        +
        Returns:
        +
        This method will return the value of glob, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputEnumSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputEnumSchema.html new file mode 100644 index 00000000..4e619059 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputEnumSchema.html @@ -0,0 +1,364 @@ + + + + + +CommandOutputEnumSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandOutputEnumSchema

+
+
+ +
+ +
+
+ +
+
+
    +
  • + + + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandOutputEnumSchema

        +
        public CommandOutputEnumSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Overrides:
        +
        setoutputBinding in class OutputEnumSchema
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Overrides:
        +
        getoutputBinding in class OutputEnumSchema
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputParameter.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputParameter.html new file mode 100644 index 00000000..5cc87fd1 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputParameter.html @@ -0,0 +1,1153 @@ + + + + + +CommandOutputParameter + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandOutputParameter

+
+
+ +
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Parameter, SchemaBase
    +
    +
    +
    +
    public class CommandOutputParameter
+extends OutputParameter
    +
    An output parameter for a CommandLineTool.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this parameter object.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) CommandOutputBindingoutputBinding +
      Describes how to handle the outputs of a process.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Objecttype +
      Specify valid types of data that may be assigned to this parameter.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      CommandOutputBindinggetoutputBinding() +
      This method returns the value of outputBinding.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetoutputBinding(CommandOutputBinding value) +
      This method sets the value of outputBinding.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      voidsettype(CommandOutputArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(CommandOutputArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(CommandOutputEnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(CommandOutputEnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(CommandOutputRecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(CommandOutputRecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(CWLType value) +
      This method sets the value of type.
      +
      voidsettype(CWLType[] value) +
      This method sets the value of type.
      +
      voidsettype(stderr value) +
      This method sets the value of type.
      +
      voidsettype(stdout value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        Specify valid types of data that may be assigned to this parameter.
        +
        • +
      + + + +
        +
      • +

        outputBinding

        +
        CommandOutputBinding outputBinding
        +
        Describes how to handle the outputs of a process.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this parameter object.
        +
        • +
      + + + +
        +
      • +

        streamable

        +
        java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandOutputParameter

        +
        public CommandOutputParameter()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        settype

        +
        public void settype(CommandOutputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CommandOutputArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(stderr value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a stderr type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandOutputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CommandOutputArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandOutputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CommandOutputRecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(stdout value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a stdout type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandOutputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CommandOutputEnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandOutputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CommandOutputRecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CommandOutputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CommandOutputEnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Overrides:
        +
        setoutputBinding in class OutputParameter
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Overrides:
        +
        getoutputBinding in class OutputParameter
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Overrides:
        +
        setid in class OutputParameter
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Overrides:
        +
        getid in class OutputParameter
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstreamable

        +
        public void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Specified by:
        +
        setstreamable in interface Parameter
        +
        Overrides:
        +
        setstreamable in class OutputParameter
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        public java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Specified by:
        +
        getstreamable in interface Parameter
        +
        Overrides:
        +
        getstreamable in class OutputParameter
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Specified by:
        +
        getformat in interface Parameter
        +
        Overrides:
        +
        getformat in class OutputParameter
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class OutputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class OutputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Parameter
        +
        Overrides:
        +
        getdoc in class OutputParameter
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class OutputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class OutputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Specified by:
        +
        getsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        getsecondaryFiles in class OutputParameter
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Parameter
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Overrides:
        +
        setlabel in class OutputParameter
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Parameter
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Overrides:
        +
        getlabel in class OutputParameter
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputRecordField.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputRecordField.html new file mode 100644 index 00000000..c74603cf --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputRecordField.html @@ -0,0 +1,731 @@ + + + + + +CommandOutputRecordField + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandOutputRecordField

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringdoc +
      A documentation string for this field
      +
      (package private) java.lang.Stringname +
      The name of the field
      +
      (package private) CommandOutputBindingoutputBinding 
      (package private) java.lang.Objecttype +
      The field type
      +
      +
      • +
    + + + + +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + + + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The name of the field
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A documentation string for this field
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        The field type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandOutputRecordField

        +
        public CommandOutputRecordField()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Overrides:
        +
        setoutputBinding in class OutputRecordField
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Overrides:
        +
        getoutputBinding in class OutputRecordField
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Overrides:
        +
        setname in class OutputRecordField
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Overrides:
        +
        getname in class OutputRecordField
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Overrides:
        +
        setdoc in class OutputRecordField
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Overrides:
        +
        getdoc in class OutputRecordField
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class OutputRecordField
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class OutputRecordField
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Overrides:
        +
        gettype in class OutputRecordField
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputRecordSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputRecordSchema.html new file mode 100644 index 00000000..53878acc --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/CommandOutputRecordSchema.html @@ -0,0 +1,271 @@ + + + + + +CommandOutputRecordSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ +
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Class CommandOutputRecordSchema

+
+
+ +
+ +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CommandOutputRecordSchema

        +
        public CommandOutputRecordSchema()
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ +
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Directory.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Directory.html new file mode 100644 index 00000000..e49140fa --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Directory.html @@ -0,0 +1,580 @@ + + + + + +Directory + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class Directory

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.Directory
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class Directory
+extends java.lang.Object
    +
    Represents a directory to present to a command line tool.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringbasename +
      The base name of the directory, that is, the name of the file without any leading directory path.
      +
      (package private) Directoryclass_value +
      Must be `Directory` to indicate this object describes a Directory.
      +
      (package private) java.lang.Objectlisting +
      List of files or subdirectories contained in this directory.
      +
      (package private) java.lang.Stringlocation +
      An IRI that identifies the directory resource.
      +
      (package private) java.lang.Stringpath +
      The local path where the Directory is made available prior to executing a CommandLineTool.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      Directory() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetbasename() +
      This method returns the value of basename.
      +
      Directorygetclass() +
      This method returns the value of class_value.
      +
      java.lang.Objectgetlisting() +
      This method returns the value of listing.
      +
      java.lang.Stringgetlocation() +
      This method returns the value of location.
      +
      java.lang.Stringgetpath() +
      This method returns the value of path.
      +
      voidsetbasename(java.lang.String value) +
      This method sets the value of basename.
      +
      voidsetclass(Directory value) +
      This method sets the value of class_value.
      +
      voidsetlisting(Directory[] value) +
      This method sets the value of listing.
      +
      voidsetlisting(File[] value) +
      This method sets the value of listing.
      +
      voidsetlocation(java.lang.String value) +
      This method sets the value of location.
      +
      voidsetpath(java.lang.String value) +
      This method sets the value of path.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        path

        +
        java.lang.String path
        +
        The local path where the Directory is made available prior to executing a CommandLineTool. This must be set by the implementation. This field must not be used in any other context. The command line tool being executed must be able to to access the directory at `path` using the POSIX `opendir(2)` syscall. If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) (`|`,`&`, `;`, `(`, `)`, `(`,`)`, `$`,`` ` ``, `\`, ``, `'`, `(space)`, `(tab)`, and `(newline)`) or characters [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) then implementations may terminate the process with a `permanentFailure`.
        +
        • +
      + + + +
        +
      • +

        basename

        +
        java.lang.String basename
        +
        The base name of the directory, that is, the name of the file without any leading directory path. The base name must not contain a slash `/`. If not provided, the implementation must set this field based on the `location` field by taking the final path component after parsing `location` as an IRI. If `basename` is provided, it is not required to match the value from `location`. When this file is made available to a CommandLineTool, it must be named with `basename`, i.e. the final component of the `path` field must match `basename`.
        +
        • +
      + + + +
        +
      • +

        location

        +
        java.lang.String location
        +
        An IRI that identifies the directory resource. This may be a relative reference, in which case it must be resolved using the base IRI of the document. The location may refer to a local or remote resource. If the `listing` field is not set, the implementation must use the location IRI to retrieve directory listing. If an implementation is unable to retrieve the directory listing stored at a remote resource (due to unsupported protocol, access denied, or other issue) it must signal an error. If the `location` field is not provided, the `listing` field must be provided. The implementation must assign a unique identifier for the `location` field. If the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, then follow the rules above.
        +
        • +
      + + + +
        +
      • +

        listing

        +
        java.lang.Object listing
        +
        List of files or subdirectories contained in this directory. The name of each file or subdirectory is determined by the `basename` field of each `File` or `Directory` object. It is an error if a `File` shares a `basename` with any other entry in `listing`. If two or more `Directory` object share the same `basename`, this must be treated as equivalent to a single subdirectory with the listings recursively merged.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        Directory class_value
        +
        Must be `Directory` to indicate this object describes a Directory.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        Directory

        +
        public Directory()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setpath

        +
        public void setpath(java.lang.String value)
        +
        This method sets the value of path.
        +
        +
        Parameters:
        +
        value - will update path, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getpath

        +
        public java.lang.String getpath()
        +
        This method returns the value of path.
        +
        +
        Returns:
        +
        This method will return the value of path, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setbasename

        +
        public void setbasename(java.lang.String value)
        +
        This method sets the value of basename.
        +
        +
        Parameters:
        +
        value - will update basename, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getbasename

        +
        public java.lang.String getbasename()
        +
        This method returns the value of basename.
        +
        +
        Returns:
        +
        This method will return the value of basename, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlocation

        +
        public void setlocation(java.lang.String value)
        +
        This method sets the value of location.
        +
        +
        Parameters:
        +
        value - will update location, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlocation

        +
        public java.lang.String getlocation()
        +
        This method returns the value of location.
        +
        +
        Returns:
        +
        This method will return the value of location, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(File[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a File array.
        +
        +
        • +
      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(Directory[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a Directory array.
        +
        +
        • +
      + + + +
        +
      • +

        getlisting

        +
        public java.lang.Object getlisting()
        +
        This method returns the value of listing.
        +
        +
        Returns:
        +
        This method will return the value of listing, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(Directory value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a Directory type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public Directory getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a Directory type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Dirent.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Dirent.html new file mode 100644 index 00000000..700b6834 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Dirent.html @@ -0,0 +1,488 @@ + + + + + +Dirent + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class Dirent

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.Dirent
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class Dirent
+extends java.lang.Object
    +
    Define a file or subdirectory that must be placed in the designated output directory prior to executing the command line tool. May be the result of executing an expression, such as building a configuration file from a template.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectentry +
      If the value is a string literal or an expression which evaluates to a string, a new file must be created with the string as the file contents.
      +
      (package private) java.lang.Objectentryname +
      The name of the file or subdirectory to create in the output directory.
      +
      (package private) java.lang.Booleanwritable +
      If true, the file or directory must be writable by the tool.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      Dirent() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetentry() +
      This method returns the value of entry.
      +
      java.lang.Objectgetentryname() +
      This method returns the value of entryname.
      +
      java.lang.Booleangetwritable() +
      This method returns the value of writable.
      +
      voidsetentry(Expression value) +
      This method sets the value of entry.
      +
      voidsetentry(java.lang.String value) +
      This method sets the value of entry.
      +
      voidsetentryname(Expression value) +
      This method sets the value of entryname.
      +
      voidsetentryname(java.lang.String value) +
      This method sets the value of entryname.
      +
      voidsetwritable(java.lang.Boolean value) +
      This method sets the value of writable.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        entry

        +
        java.lang.Object entry
        +
        If the value is a string literal or an expression which evaluates to a string, a new file must be created with the string as the file contents. If the value is an expression that evaluates to a `File` object, this indicates the referenced file should be added to the designated output directory prior to executing the tool. If the value is an expression that evaluates to a `Dirent` object, this indicates that the File or Directory in `entry` should be added to the designated output directory with the name in `entryname`. If `writable` is false, the file may be made available using a bind mount or file system link to avoid unnecessary copying of the input file.
        +
        • +
      + + + +
        +
      • +

        entryname

        +
        java.lang.Object entryname
        +
        The name of the file or subdirectory to create in the output directory. If `entry` is a File or Directory, this overrides `basename`. Optional.
        +
        • +
      + + + +
        +
      • +

        writable

        +
        java.lang.Boolean writable
        +
        If true, the file or directory must be writable by the tool. Changes to the file or directory must be isolated and not visible by any other CommandLineTool process. This may be implemented by making a copy of the original file or directory. Default false (files and directories read-only by default).
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        Dirent

        +
        public Dirent()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setentry

        +
        public void setentry(java.lang.String value)
        +
        This method sets the value of entry.
        +
        +
        Parameters:
        +
        value - will update entry, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setentry

        +
        public void setentry(Expression value)
        +
        This method sets the value of entry.
        +
        +
        Parameters:
        +
        value - will update entry, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getentry

        +
        public java.lang.Object getentry()
        +
        This method returns the value of entry.
        +
        +
        Returns:
        +
        This method will return the value of entry, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setentryname

        +
        public void setentryname(java.lang.String value)
        +
        This method sets the value of entryname.
        +
        +
        Parameters:
        +
        value - will update entryname, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setentryname

        +
        public void setentryname(Expression value)
        +
        This method sets the value of entryname.
        +
        +
        Parameters:
        +
        value - will update entryname, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getentryname

        +
        public java.lang.Object getentryname()
        +
        This method returns the value of entryname.
        +
        +
        Returns:
        +
        This method will return the value of entryname, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setwritable

        +
        public void setwritable(java.lang.Boolean value)
        +
        This method sets the value of writable.
        +
        +
        Parameters:
        +
        value - will update writable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getwritable

        +
        public java.lang.Boolean getwritable()
        +
        This method returns the value of writable.
        +
        +
        Returns:
        +
        This method will return the value of writable, which is a Boolean type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/DocType.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/DocType.html new file mode 100644 index 00000000..9c0c941c --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/DocType.html @@ -0,0 +1,501 @@ + + + + + +DocType + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface DocType

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      static java.lang.StringdocAfter +
      Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
      +
      static java.lang.ObjectdocChild +
      Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
      +
      static java.lang.StringdocParent +
      Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.StringgetdocAfter() +
      This method returns the value of docAfter.
      +
      java.lang.ObjectgetdocChild() +
      This method returns the value of docChild.
      +
      java.lang.StringgetdocParent() +
      This method returns the value of docParent.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetdocAfter(java.lang.String value) +
      This method sets the value of docAfter.
      +
      voidsetdocChild(java.lang.String value) +
      This method sets the value of docChild.
      +
      voidsetdocChild(java.lang.String[] value) +
      This method sets the value of docChild.
      +
      voidsetdocParent(java.lang.String value) +
      This method sets the value of docParent.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        docParent

        +
        static final java.lang.String docParent
        +
        Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        static final java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        docAfter

        +
        static final java.lang.String docAfter
        +
        Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
        +
        • +
      + + + +
        +
      • +

        docChild

        +
        static final java.lang.Object docChild
        +
        Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setdocParent

        +
        void setdocParent(java.lang.String value)
        +
        This method sets the value of docParent.
        +
        +
        Parameters:
        +
        value - will update docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocParent

        +
        java.lang.String getdocParent()
        +
        This method returns the value of docParent.
        +
        +
        Returns:
        +
        This method will return the value of docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocAfter

        +
        void setdocAfter(java.lang.String value)
        +
        This method sets the value of docAfter.
        +
        +
        Parameters:
        +
        value - will update docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocAfter

        +
        java.lang.String getdocAfter()
        +
        This method returns the value of docAfter.
        +
        +
        Returns:
        +
        This method will return the value of docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        void setdocChild(java.lang.String value)
        +
        This method sets the value of docChild.
        +
        +
        Parameters:
        +
        value - will update docChild, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        void setdocChild(java.lang.String[] value)
        +
        This method sets the value of docChild.
        +
        +
        Parameters:
        +
        value - will update docChild, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdocChild

        +
        java.lang.Object getdocChild()
        +
        This method returns the value of docChild.
        +
        +
        Returns:
        +
        This method will return the value of docChild, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/DockerRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/DockerRequirement.html new file mode 100644 index 00000000..9b7ccc13 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/DockerRequirement.html @@ -0,0 +1,677 @@ + + + + + +DockerRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class DockerRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.DockerRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class DockerRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Indicates that a workflow component should be run in a [Docker](http://docker.com) container, and specifies how to fetch or build the image.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'DockerRequirement'
      +
      (package private) java.lang.StringdockerFile +
      Supply the contents of a Dockerfile which will be built using `docker build`.
      +
      (package private) java.lang.StringdockerImageId +
      The image id that will be used for `docker run`.
      +
      (package private) java.lang.StringdockerImport +
      Provide HTTP URL to download and gunzip a Docker images using `docker import.
      +
      (package private) java.lang.StringdockerLoad +
      Specify a HTTP URL from which to download a Docker image using `docker load`.
      +
      (package private) java.lang.StringdockerOutputDirectory +
      Set the designated output directory to a specific location inside the Docker container.
      +
      (package private) java.lang.StringdockerPull +
      Specify a Docker image to retrieve using `docker pull`.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      DockerRequirement() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      java.lang.StringgetdockerFile() +
      This method returns the value of dockerFile.
      +
      java.lang.StringgetdockerImageId() +
      This method returns the value of dockerImageId.
      +
      java.lang.StringgetdockerImport() +
      This method returns the value of dockerImport.
      +
      java.lang.StringgetdockerLoad() +
      This method returns the value of dockerLoad.
      +
      java.lang.StringgetdockerOutputDirectory() +
      This method returns the value of dockerOutputDirectory.
      +
      java.lang.StringgetdockerPull() +
      This method returns the value of dockerPull.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsetdockerFile(java.lang.String value) +
      This method sets the value of dockerFile.
      +
      voidsetdockerImageId(java.lang.String value) +
      This method sets the value of dockerImageId.
      +
      voidsetdockerImport(java.lang.String value) +
      This method sets the value of dockerImport.
      +
      voidsetdockerLoad(java.lang.String value) +
      This method sets the value of dockerLoad.
      +
      voidsetdockerOutputDirectory(java.lang.String value) +
      This method sets the value of dockerOutputDirectory.
      +
      voidsetdockerPull(java.lang.String value) +
      This method sets the value of dockerPull.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        dockerFile

        +
        java.lang.String dockerFile
        +
        Supply the contents of a Dockerfile which will be built using `docker build`.
        +
        • +
      + + + +
        +
      • +

        dockerPull

        +
        java.lang.String dockerPull
        +
        Specify a Docker image to retrieve using `docker pull`.
        +
        • +
      + + + +
        +
      • +

        dockerImport

        +
        java.lang.String dockerImport
        +
        Provide HTTP URL to download and gunzip a Docker images using `docker import.
        +
        • +
      + + + +
        +
      • +

        dockerOutputDirectory

        +
        java.lang.String dockerOutputDirectory
        +
        Set the designated output directory to a specific location inside the Docker container.
        +
        • +
      + + + +
        +
      • +

        dockerLoad

        +
        java.lang.String dockerLoad
        +
        Specify a HTTP URL from which to download a Docker image using `docker load`.
        +
        • +
      + + + +
        +
      • +

        dockerImageId

        +
        java.lang.String dockerImageId
        +
        The image id that will be used for `docker run`. May be a human-readable image name or the image identifier hash. May be skipped if `dockerPull` is specified, in which case the `dockerPull` image id must be used.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'DockerRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        DockerRequirement

        +
        public DockerRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setdockerFile

        +
        public void setdockerFile(java.lang.String value)
        +
        This method sets the value of dockerFile.
        +
        +
        Parameters:
        +
        value - will update dockerFile, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdockerFile

        +
        public java.lang.String getdockerFile()
        +
        This method returns the value of dockerFile.
        +
        +
        Returns:
        +
        This method will return the value of dockerFile, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdockerPull

        +
        public void setdockerPull(java.lang.String value)
        +
        This method sets the value of dockerPull.
        +
        +
        Parameters:
        +
        value - will update dockerPull, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdockerPull

        +
        public java.lang.String getdockerPull()
        +
        This method returns the value of dockerPull.
        +
        +
        Returns:
        +
        This method will return the value of dockerPull, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdockerImport

        +
        public void setdockerImport(java.lang.String value)
        +
        This method sets the value of dockerImport.
        +
        +
        Parameters:
        +
        value - will update dockerImport, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdockerImport

        +
        public java.lang.String getdockerImport()
        +
        This method returns the value of dockerImport.
        +
        +
        Returns:
        +
        This method will return the value of dockerImport, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdockerOutputDirectory

        +
        public void setdockerOutputDirectory(java.lang.String value)
        +
        This method sets the value of dockerOutputDirectory.
        +
        +
        Parameters:
        +
        value - will update dockerOutputDirectory, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdockerOutputDirectory

        +
        public java.lang.String getdockerOutputDirectory()
        +
        This method returns the value of dockerOutputDirectory.
        +
        +
        Returns:
        +
        This method will return the value of dockerOutputDirectory, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdockerLoad

        +
        public void setdockerLoad(java.lang.String value)
        +
        This method sets the value of dockerLoad.
        +
        +
        Parameters:
        +
        value - will update dockerLoad, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdockerLoad

        +
        public java.lang.String getdockerLoad()
        +
        This method returns the value of dockerLoad.
        +
        +
        Returns:
        +
        This method will return the value of dockerLoad, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdockerImageId

        +
        public void setdockerImageId(java.lang.String value)
        +
        This method sets the value of dockerImageId.
        +
        +
        Parameters:
        +
        value - will update dockerImageId, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdockerImageId

        +
        public java.lang.String getdockerImageId()
        +
        This method returns the value of dockerImageId.
        +
        +
        Returns:
        +
        This method will return the value of dockerImageId, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Documentation.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Documentation.html new file mode 100644 index 00000000..2c0286be --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Documentation.html @@ -0,0 +1,685 @@ + + + + + +Documentation + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class Documentation

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.Documentation
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    DocType, NamedType
    +
    +
    +
    +
    public class Documentation
+extends java.lang.Object
+implements NamedType, DocType
    +
    A documentation section. This type exists to facilitate self-documenting schemas but has no role in formal validation.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.StringdocAfter +
      Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
      +
      (package private) java.lang.ObjectdocChild +
      Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
      +
      (package private) java.lang.StringdocParent +
      Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
      +
      (package private) java.lang.Stringname +
      The identifier for this type
      +
      (package private) java.lang.Objecttype +
      Must be `documentation`
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      Documentation() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.StringgetdocAfter() +
      This method returns the value of docAfter.
      +
      java.lang.ObjectgetdocChild() +
      This method returns the value of docChild.
      +
      java.lang.StringgetdocParent() +
      This method returns the value of docParent.
      +
      java.lang.Stringgetname() +
      This method returns the value of name.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetdocAfter(java.lang.String value) +
      This method sets the value of docAfter.
      +
      voidsetdocChild(java.lang.String value) +
      This method sets the value of docChild.
      +
      voidsetdocChild(java.lang.String[] value) +
      This method sets the value of docChild.
      +
      voidsetdocParent(java.lang.String value) +
      This method sets the value of docParent.
      +
      voidsetname(java.lang.String value) +
      This method sets the value of name.
      +
      voidsettype(java.lang.Object value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        Must be `documentation`
        +
        • +
      + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The identifier for this type
        +
        • +
      + + + +
        +
      • +

        docParent

        +
        java.lang.String docParent
        +
        Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        docAfter

        +
        java.lang.String docAfter
        +
        Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
        +
        • +
      + + + +
        +
      • +

        docChild

        +
        java.lang.Object docChild
        +
        Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        Documentation

        +
        public Documentation()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.Object value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Specified by:
        +
        setname in interface NamedType
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Specified by:
        +
        getname in interface NamedType
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocParent

        +
        public void setdocParent(java.lang.String value)
        +
        This method sets the value of docParent.
        +
        +
        Specified by:
        +
        setdocParent in interface DocType
        +
        Parameters:
        +
        value - will update docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocParent

        +
        public java.lang.String getdocParent()
        +
        This method returns the value of docParent.
        +
        +
        Specified by:
        +
        getdocParent in interface DocType
        +
        Returns:
        +
        This method will return the value of docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface DocType
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocAfter

        +
        public void setdocAfter(java.lang.String value)
        +
        This method sets the value of docAfter.
        +
        +
        Specified by:
        +
        setdocAfter in interface DocType
        +
        Parameters:
        +
        value - will update docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocAfter

        +
        public java.lang.String getdocAfter()
        +
        This method returns the value of docAfter.
        +
        +
        Specified by:
        +
        getdocAfter in interface DocType
        +
        Returns:
        +
        This method will return the value of docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        public void setdocChild(java.lang.String value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Parameters:
        +
        value - will update docChild, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        public void setdocChild(java.lang.String[] value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Parameters:
        +
        value - will update docChild, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdocChild

        +
        public java.lang.Object getdocChild()
        +
        This method returns the value of docChild.
        +
        +
        Specified by:
        +
        getdocChild in interface DocType
        +
        Returns:
        +
        This method will return the value of docChild, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/EnumSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/EnumSchema.html new file mode 100644 index 00000000..e44a3899 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/EnumSchema.html @@ -0,0 +1,240 @@ + + + + + +EnumSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Class EnumSchema

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.EnumSchema
      • +
    +
    • +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      EnumSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        EnumSchema

        +
        public EnumSchema()
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/EnvVarRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/EnvVarRequirement.html new file mode 100644 index 00000000..18790e89 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/EnvVarRequirement.html @@ -0,0 +1,397 @@ + + + + + +EnvVarRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class EnvVarRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.EnvVarRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class EnvVarRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Define a list of environment variables which will be set in the execution environment of the tool. See `EnvironmentDef` for details.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'EnvVarRequirement'
      +
      (package private) EnvironmentDefenvDef +
      The list of environment variables.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      EnvVarRequirement() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      EnvironmentDefgetenvDef() +
      This method returns the value of envDef.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsetenvDef(EnvironmentDef value) +
      This method sets the value of envDef.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        envDef

        +
        EnvironmentDef envDef
        +
        The list of environment variables.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'EnvVarRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        EnvVarRequirement

        +
        public EnvVarRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setenvDef

        +
        public void setenvDef(EnvironmentDef value)
        +
        This method sets the value of envDef.
        +
        +
        Parameters:
        +
        value - will update envDef, which is a EnvironmentDef type.
        +
        +
        • +
      + + + +
        +
      • +

        getenvDef

        +
        public EnvironmentDef getenvDef()
        +
        This method returns the value of envDef.
        +
        +
        Returns:
        +
        This method will return the value of envDef, which is a EnvironmentDef type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/EnvironmentDef.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/EnvironmentDef.html new file mode 100644 index 00000000..947dcaa1 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/EnvironmentDef.html @@ -0,0 +1,412 @@ + + + + + +EnvironmentDef + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class EnvironmentDef

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.EnvironmentDef
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class EnvironmentDef
+extends java.lang.Object
    +
    Define an environment variable that will be set in the runtime environment by the workflow platform when executing the command line tool. May be the result of executing an expression, such as getting a parameter from input.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.StringenvName +
      The environment variable name
      +
      (package private) java.lang.ObjectenvValue +
      The environment variable value
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      EnvironmentDef() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.StringgetenvName() +
      This method returns the value of envName.
      +
      java.lang.ObjectgetenvValue() +
      This method returns the value of envValue.
      +
      voidsetenvName(java.lang.String value) +
      This method sets the value of envName.
      +
      voidsetenvValue(Expression value) +
      This method sets the value of envValue.
      +
      voidsetenvValue(java.lang.String value) +
      This method sets the value of envValue.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        envName

        +
        java.lang.String envName
        +
        The environment variable name
        +
        • +
      + + + +
        +
      • +

        envValue

        +
        java.lang.Object envValue
        +
        The environment variable value
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        EnvironmentDef

        +
        public EnvironmentDef()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setenvName

        +
        public void setenvName(java.lang.String value)
        +
        This method sets the value of envName.
        +
        +
        Parameters:
        +
        value - will update envName, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getenvName

        +
        public java.lang.String getenvName()
        +
        This method returns the value of envName.
        +
        +
        Returns:
        +
        This method will return the value of envName, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setenvValue

        +
        public void setenvValue(java.lang.String value)
        +
        This method sets the value of envValue.
        +
        +
        Parameters:
        +
        value - will update envValue, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setenvValue

        +
        public void setenvValue(Expression value)
        +
        This method sets the value of envValue.
        +
        +
        Parameters:
        +
        value - will update envValue, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getenvValue

        +
        public java.lang.Object getenvValue()
        +
        This method returns the value of envValue.
        +
        +
        Returns:
        +
        This method will return the value of envValue, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Expression.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Expression.html new file mode 100644 index 00000000..ede1ef96 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Expression.html @@ -0,0 +1,328 @@ + + + + + +Expression + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Enum Expression

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<Expression>
      • +
    • +
        +
      • org.commonwl.lang.Expression
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<Expression>
    +
    +
    +
    +
    public enum Expression
+extends java.lang.Enum<Expression>
    +
    'Expression' is not a real type. It indicates that a field must allow runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement) is declared and supported by the platform, the field must also allow Javascript expressions.
    +
    • +
+
+
+
    +
  • + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Static Methods Concrete Methods 
      Modifier and TypeMethod and Description
      static ExpressionvalueOf(java.lang.String name) +
      Returns the enum constant of this type with the specified name.
      +
      static Expression[]values() +
      Returns an array containing the constants of this enum type, in +the order they are declared.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Enum

        +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
        • +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +getClass, notify, notifyAll, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Enum Constant Detail

      + + + +
        +
      • +

        ExpressionPlaceholder

        +
        public static final Expression ExpressionPlaceholder
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static Expression[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (Expression c : Expression.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static Expression valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ExpressionTool.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ExpressionTool.html new file mode 100644 index 00000000..4a198491 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ExpressionTool.html @@ -0,0 +1,1158 @@ + + + + + +ExpressionTool + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class ExpressionTool

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.ExpressionTool
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Process
    +
    +
    +
    +
    public class ExpressionTool
+extends java.lang.Object
+implements Process
    +
    Execute an expression as a Workflow step.
    +
    • +
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        expression

        +
        java.lang.Object expression
        +
        The expression to execute. The expression must return a JSON object which matches the output parameters of the ExpressionTool.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        • +
      + + + +
        +
      • +

        outputs

        +
        ExpressionToolOutputParameter[] outputs
        +
        Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.
        +
        • +
      + + + +
        +
      • +

        requirements

        +
        java.lang.Object requirements
        +
        Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
        +
        • +
      + + + +
        +
      • +

        cwlVersion

        +
        CWLVersion cwlVersion
        +
        CWL document version. Always required at the document root. Not required for a Process embedded inside another Process.
        +
        • +
      + + + +
        +
      • +

        inputs

        +
        InputParameter[] inputs
        +
        Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object.
        +
        • +
      + + + +
        +
      • +

        hints

        +
        Any hints
        +
        Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A long, human-readable description of this process object.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this process object.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        ExpressionTool

        +
        public ExpressionTool()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setexpression

        +
        public void setexpression(java.lang.String value)
        +
        This method sets the value of expression.
        +
        +
        Parameters:
        +
        value - will update expression, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setexpression

        +
        public void setexpression(Expression value)
        +
        This method sets the value of expression.
        +
        +
        Parameters:
        +
        value - will update expression, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getexpression

        +
        public java.lang.Object getexpression()
        +
        This method returns the value of expression.
        +
        +
        Returns:
        +
        This method will return the value of expression, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputs

        +
        public void setoutputs(ExpressionToolOutputParameter[] value)
        +
        This method sets the value of outputs.
        +
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputs

        +
        public void setoutputs(OutputParameter[] value)
        +
        This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
        +
        +
        Specified by:
        +
        setoutputs in interface Process
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputs

        +
        public ExpressionToolOutputParameter[] getoutputs()
        +
        This method returns the value of outputs.
        +
        +
        Specified by:
        +
        getoutputs in interface Process
        +
        Returns:
        +
        This method will return the value of outputs, which is a ExpressionToolOutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(StepInputExpressionRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a StepInputExpressionRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(MultipleInputFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a MultipleInputFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SoftwareRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SoftwareRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SchemaDefRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SchemaDefRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InitialWorkDirRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a InitialWorkDirRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(EnvVarRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a EnvVarRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(DockerRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a DockerRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ResourceRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ResourceRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InlineJavascriptRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a InlineJavascriptRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ShellCommandRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ShellCommandRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ScatterFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ScatterFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SubworkflowFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SubworkflowFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        getrequirements

        +
        public java.lang.Object getrequirements()
        +
        This method returns the value of requirements.
        +
        +
        Specified by:
        +
        getrequirements in interface Process
        +
        Returns:
        +
        This method will return the value of requirements, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setcwlVersion

        +
        public void setcwlVersion(CWLVersion value)
        +
        This method sets the value of cwlVersion.
        +
        +
        Specified by:
        +
        setcwlVersion in interface Process
        +
        Parameters:
        +
        value - will update cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        getcwlVersion

        +
        public CWLVersion getcwlVersion()
        +
        This method returns the value of cwlVersion.
        +
        +
        Specified by:
        +
        getcwlVersion in interface Process
        +
        Returns:
        +
        This method will return the value of cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputs

        +
        public void setinputs(InputParameter[] value)
        +
        This method sets the value of inputs.
        +
        +
        Specified by:
        +
        setinputs in interface Process
        +
        Parameters:
        +
        value - will update inputs, which is a InputParameter array.
        +
        +
        • +
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        +
      • +

        getinputs

        +
        public InputParameter[] getinputs()
        +
        This method returns the value of inputs.
        +
        +
        Specified by:
        +
        getinputs in interface Process
        +
        Returns:
        +
        This method will return the value of inputs, which is a InputParameter array.
        +
        +
        • +
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      • +

        sethints

        +
        public void sethints(Any value)
        +
        This method sets the value of hints.
        +
        +
        Specified by:
        +
        sethints in interface Process
        +
        Parameters:
        +
        value - will update hints, which is a Any type.
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        gethints

        +
        public Any gethints()
        +
        This method returns the value of hints.
        +
        +
        Specified by:
        +
        gethints in interface Process
        +
        Returns:
        +
        This method will return the value of hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Process
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Process
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Specified by:
        +
        setid in interface Process
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Specified by:
        +
        getid in interface Process
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Process
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Process
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
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+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ExpressionToolOutputParameter.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ExpressionToolOutputParameter.html new file mode 100644 index 00000000..57a6116d --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ExpressionToolOutputParameter.html @@ -0,0 +1,1112 @@ + + + + + +ExpressionToolOutputParameter + + + + + + + + +
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org.commonwl.lang
+

Class ExpressionToolOutputParameter

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    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this parameter object.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) CommandOutputBindingoutputBinding +
      Describes how to handle the outputs of a process.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Objecttype +
      Specify valid types of data that may be assigned to this parameter.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

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      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      CommandOutputBindinggetoutputBinding() +
      This method returns the value of outputBinding.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetoutputBinding(CommandOutputBinding value) +
      This method sets the value of outputBinding.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      voidsettype(CWLType value) +
      This method sets the value of type.
      +
      voidsettype(CWLType[] value) +
      This method sets the value of type.
      +
      voidsettype(OutputArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(OutputArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(OutputEnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(OutputEnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(OutputRecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(OutputRecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
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  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        Specify valid types of data that may be assigned to this parameter.
        +
        • +
      + + + +
        +
      • +

        outputBinding

        +
        CommandOutputBinding outputBinding
        +
        Describes how to handle the outputs of a process.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this parameter object.
        +
        • +
      + + + +
        +
      • +

        streamable

        +
        java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        ExpressionToolOutputParameter

        +
        public ExpressionToolOutputParameter()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        settype

        +
        public void settype(OutputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputRecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputEnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputRecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputEnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Overrides:
        +
        setoutputBinding in class OutputParameter
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Overrides:
        +
        getoutputBinding in class OutputParameter
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Overrides:
        +
        setid in class OutputParameter
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Overrides:
        +
        getid in class OutputParameter
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstreamable

        +
        public void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Specified by:
        +
        setstreamable in interface Parameter
        +
        Overrides:
        +
        setstreamable in class OutputParameter
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        public java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Specified by:
        +
        getstreamable in interface Parameter
        +
        Overrides:
        +
        getstreamable in class OutputParameter
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Specified by:
        +
        getformat in interface Parameter
        +
        Overrides:
        +
        getformat in class OutputParameter
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class OutputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class OutputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Parameter
        +
        Overrides:
        +
        getdoc in class OutputParameter
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class OutputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class OutputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Specified by:
        +
        getsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        getsecondaryFiles in class OutputParameter
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Parameter
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Overrides:
        +
        setlabel in class OutputParameter
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Parameter
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Overrides:
        +
        getlabel in class OutputParameter
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
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+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/File.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/File.html new file mode 100644 index 00000000..5a12d3ae --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/File.html @@ -0,0 +1,972 @@ + + + + + +File + + + + + + + + +
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org.commonwl.lang
+

Class File

+
+
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    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.File
      • +
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    • +
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  • +
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    +
    public class File
+extends java.lang.Object
    +
    Represents a file (or group of files if `secondaryFiles` is specified) that must be accessible by tools using standard POSIX file system call API such as open(2) and read(2).
    +
    • +
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    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringbasename +
      The base name of the file, that is, the name of the file without any leading directory path.
      +
      (package private) java.lang.Stringchecksum +
      Optional hash code for validating file integrity.
      +
      (package private) Fileclass_value +
      Must be `File` to indicate this object describes a file.
      +
      (package private) java.lang.Stringcontents +
      File contents literal.
      +
      (package private) java.lang.Stringdirname +
      The name of the directory containing file, that is, the path leading up to the final slash in the path such that `dirname + '/' + basename == path`.
      +
      (package private) java.lang.Stringformat +
      The format of the file: this must be an IRI of a concept node that represents the file format, preferrably defined within an ontology.
      +
      (package private) java.lang.Stringlocation +
      An IRI that identifies the file resource.
      +
      (package private) java.lang.Stringnameext +
      The basename extension such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period.
      +
      (package private) java.lang.Stringnameroot +
      The basename root such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period.
      +
      (package private) java.lang.Stringpath +
      The local host path where the File is available when a CommandLineTool is executed.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      A list of additional files that are associated with the primary file and must be transferred alongside the primary file.
      +
      (package private) java.lang.Longsize +
      Optional file size
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      File() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetbasename() +
      This method returns the value of basename.
      +
      java.lang.Stringgetchecksum() +
      This method returns the value of checksum.
      +
      Filegetclass() +
      This method returns the value of class_value.
      +
      java.lang.Stringgetcontents() +
      This method returns the value of contents.
      +
      java.lang.Stringgetdirname() +
      This method returns the value of dirname.
      +
      java.lang.Stringgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetlocation() +
      This method returns the value of location.
      +
      java.lang.Stringgetnameext() +
      This method returns the value of nameext.
      +
      java.lang.Stringgetnameroot() +
      This method returns the value of nameroot.
      +
      java.lang.Stringgetpath() +
      This method returns the value of path.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Longgetsize() +
      This method returns the value of size.
      +
      voidsetbasename(java.lang.String value) +
      This method sets the value of basename.
      +
      voidsetchecksum(java.lang.String value) +
      This method sets the value of checksum.
      +
      voidsetclass(File value) +
      This method sets the value of class_value.
      +
      voidsetcontents(java.lang.String value) +
      This method sets the value of contents.
      +
      voidsetdirname(java.lang.String value) +
      This method sets the value of dirname.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetlocation(java.lang.String value) +
      This method sets the value of location.
      +
      voidsetnameext(java.lang.String value) +
      This method sets the value of nameext.
      +
      voidsetnameroot(java.lang.String value) +
      This method sets the value of nameroot.
      +
      voidsetpath(java.lang.String value) +
      This method sets the value of path.
      +
      voidsetsecondaryFiles(Directory[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(File[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsize(java.lang.Long value) +
      This method sets the value of size.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
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      +
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      Field Detail

      + + + +
        +
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        path

        +
        java.lang.String path
        +
        The local host path where the File is available when a CommandLineTool is executed. This field must be set by the implementation. The final path component must match the value of `basename`. This field must not be used in any other context. The command line tool being executed must be able to to access the file at `path` using the POSIX `open(2)` syscall. As a special case, if the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, and remove the `path` field. If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) (`|`,`&`, `;`, `(`, `)`, `(`,`)`, `$`,`` ` ``, `\`, ``, `'`, `(space)`, `(tab)`, and `(newline)`) or characters [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) then implementations may terminate the process with a `permanentFailure`.
        +
        • +
      + + + +
        +
      • +

        basename

        +
        java.lang.String basename
        +
        The base name of the file, that is, the name of the file without any leading directory path. The base name must not contain a slash `/`. If not provided, the implementation must set this field based on the `location` field by taking the final path component after parsing `location` as an IRI. If `basename` is provided, it is not required to match the value from `location`. When this file is made available to a CommandLineTool, it must be named with `basename`, i.e. the final component of the `path` field must match `basename`.
        +
        • +
      + + + +
        +
      • +

        nameext

        +
        java.lang.String nameext
        +
        The basename extension such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period. Leading periods on the basename are ignored; a basename of `.cshrc` will have an empty `nameext`. The implementation must set this field automatically based on the value of `basename` prior to evaluating parameter references or expressions.
        +
        • +
      + + + +
        +
      • +

        size

        +
        java.lang.Long size
        +
        Optional file size
        +
        • +
      + + + +
        +
      • +

        contents

        +
        java.lang.String contents
        +
        File contents literal. Maximum of 64 KiB. If neither `location` nor `path` is provided, `contents` must be non-null. The implementation must assign a unique identifier for the `location` field. When the file is staged as input to CommandLineTool, the value of `contents` must be written to a file. If `loadContents` of `inputBinding` or `outputBinding` is true and `location` is valid, the implementation must read up to the first 64 KiB of text from the file and place it in the contents field.
        +
        • +
      + + + +
        +
      • +

        checksum

        +
        java.lang.String checksum
        +
        Optional hash code for validating file integrity. Currently must be in the form sha1$ + hexadecimal string using the SHA-1 algorithm.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.String format
        +
        The format of the file: this must be an IRI of a concept node that represents the file format, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. Reasoning about format compatability must be done by checking that an input file format is the same, `owl:equivalentClass` or `rdfs:subClassOf` the format required by the input parameter. `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if `(B) owl:equivalentClass (C)` and `(B) owl:subclassOf (A)` then infer `(C) owl:subclassOf (A)`. File format ontologies may be provided in the $schema metadata at the root of the document. If no ontologies are specified in `$schema`, the runtime may perform exact file format matches.
        +
        • +
      + + + +
        +
      • +

        location

        +
        java.lang.String location
        +
        An IRI that identifies the file resource. This may be a relative reference, in which case it must be resolved using the base IRI of the document. The location may refer to a local or remote resource; the implementation must use the IRI to retrieve file content. If an implementation is unable to retrieve the file content stored at a remote resource (due to unsupported protocol, access denied, or other issue) it must signal an error. If the `location` field is not provided, the `contents` field must be provided. The implementation must assign a unique identifier for the `location` field. If the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, then follow the rules above.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        A list of additional files that are associated with the primary file and must be transferred alongside the primary file. Examples include indexes of the primary file, or external references which must be included when loading primary document. A file object listed in `secondaryFiles` may itself include `secondaryFiles` for which the same rules apply.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        File class_value
        +
        Must be `File` to indicate this object describes a file.
        +
        • +
      + + + +
        +
      • +

        dirname

        +
        java.lang.String dirname
        +
        The name of the directory containing file, that is, the path leading up to the final slash in the path such that `dirname + '/' + basename == path`. The implementation must set this field based on the value of `path` prior to evaluating parameter references or expressions in a CommandLineTool document. This field must not be used in any other context.
        +
        • +
      + + + +
        +
      • +

        nameroot

        +
        java.lang.String nameroot
        +
        The basename root such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period. For the purposess of path splitting leading periods on the basename are ignored; a basename of `.cshrc` will have a nameroot of `.cshrc`. The implementation must set this field automatically based on the value of `basename` prior to evaluating parameter references or expressions.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        File

        +
        public File()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setpath

        +
        public void setpath(java.lang.String value)
        +
        This method sets the value of path.
        +
        +
        Parameters:
        +
        value - will update path, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getpath

        +
        public java.lang.String getpath()
        +
        This method returns the value of path.
        +
        +
        Returns:
        +
        This method will return the value of path, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setbasename

        +
        public void setbasename(java.lang.String value)
        +
        This method sets the value of basename.
        +
        +
        Parameters:
        +
        value - will update basename, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getbasename

        +
        public java.lang.String getbasename()
        +
        This method returns the value of basename.
        +
        +
        Returns:
        +
        This method will return the value of basename, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setnameext

        +
        public void setnameext(java.lang.String value)
        +
        This method sets the value of nameext.
        +
        +
        Parameters:
        +
        value - will update nameext, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getnameext

        +
        public java.lang.String getnameext()
        +
        This method returns the value of nameext.
        +
        +
        Returns:
        +
        This method will return the value of nameext, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsize

        +
        public void setsize(java.lang.Long value)
        +
        This method sets the value of size.
        +
        +
        Parameters:
        +
        value - will update size, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        getsize

        +
        public java.lang.Long getsize()
        +
        This method returns the value of size.
        +
        +
        Returns:
        +
        This method will return the value of size, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        setcontents

        +
        public void setcontents(java.lang.String value)
        +
        This method sets the value of contents.
        +
        +
        Parameters:
        +
        value - will update contents, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getcontents

        +
        public java.lang.String getcontents()
        +
        This method returns the value of contents.
        +
        +
        Returns:
        +
        This method will return the value of contents, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setchecksum

        +
        public void setchecksum(java.lang.String value)
        +
        This method sets the value of checksum.
        +
        +
        Parameters:
        +
        value - will update checksum, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getchecksum

        +
        public java.lang.String getchecksum()
        +
        This method returns the value of checksum.
        +
        +
        Returns:
        +
        This method will return the value of checksum, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.String getformat()
        +
        This method returns the value of format.
        +
        +
        Returns:
        +
        This method will return the value of format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlocation

        +
        public void setlocation(java.lang.String value)
        +
        This method sets the value of location.
        +
        +
        Parameters:
        +
        value - will update location, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlocation

        +
        public java.lang.String getlocation()
        +
        This method returns the value of location.
        +
        +
        Returns:
        +
        This method will return the value of location, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(File[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a File array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(Directory[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Directory array.
        +
        +
        • +
      + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(File value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a File type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public File getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a File type.
        +
        +
        • +
      + + + +
        +
      • +

        setdirname

        +
        public void setdirname(java.lang.String value)
        +
        This method sets the value of dirname.
        +
        +
        Parameters:
        +
        value - will update dirname, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdirname

        +
        public java.lang.String getdirname()
        +
        This method returns the value of dirname.
        +
        +
        Returns:
        +
        This method will return the value of dirname, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setnameroot

        +
        public void setnameroot(java.lang.String value)
        +
        This method sets the value of nameroot.
        +
        +
        Parameters:
        +
        value - will update nameroot, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getnameroot

        +
        public java.lang.String getnameroot()
        +
        This method returns the value of nameroot.
        +
        +
        Returns:
        +
        This method will return the value of nameroot, which is a String type.
        +
        +
        • +
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+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InitialWorkDirRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InitialWorkDirRequirement.html new file mode 100644 index 00000000..f5198023 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InitialWorkDirRequirement.html @@ -0,0 +1,477 @@ + + + + + +InitialWorkDirRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
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+ + + +
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+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InitialWorkDirRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.InitialWorkDirRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class InitialWorkDirRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Define a list of files and subdirectories that must be created by the workflow platform in the designated output directory prior to executing the command line tool.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      InitialWorkDirRequirement
      +
      (package private) java.lang.Objectlisting +
      The list of files or subdirectories that must be placed in the designated output directory prior to executing the command line tool.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      java.lang.Objectgetlisting() +
      This method returns the value of listing.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsetlisting(Directory[] value) +
      This method sets the value of listing.
      +
      voidsetlisting(Dirent[] value) +
      This method sets the value of listing.
      +
      voidsetlisting(Expression[] value) +
      This method sets the value of listing.
      +
      voidsetlisting(File[] value) +
      This method sets the value of listing.
      +
      voidsetlisting(java.lang.String[] value) +
      This method sets the value of listing.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        listing

        +
        java.lang.Object listing
        +
        The list of files or subdirectories that must be placed in the designated output directory prior to executing the command line tool. May be an expression. If so, the expression return value must validate as `{type: array, items: [File, Directory]}`.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        InitialWorkDirRequirement
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InitialWorkDirRequirement

        +
        public InitialWorkDirRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(Dirent[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a Dirent array.
        +
        +
        • +
      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(File[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a File array.
        +
        +
        • +
      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(Directory[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a Directory array.
        +
        +
        • +
      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(Expression[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setlisting

        +
        public void setlisting(java.lang.String[] value)
        +
        This method sets the value of listing.
        +
        +
        Parameters:
        +
        value - will update listing, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getlisting

        +
        public java.lang.Object getlisting()
        +
        This method returns the value of listing.
        +
        +
        Returns:
        +
        This method will return the value of listing, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InlineJavascriptRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InlineJavascriptRequirement.html new file mode 100644 index 00000000..96d08d8f --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InlineJavascriptRequirement.html @@ -0,0 +1,397 @@ + + + + + +InlineJavascriptRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InlineJavascriptRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.InlineJavascriptRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class InlineJavascriptRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Indicates that the workflow platform must support inline Javascript expressions. If this requirement is not present, the workflow platform must not perform expression interpolatation.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'InlineJavascriptRequirement'
      +
      (package private) java.lang.StringexpressionLib +
      Additional code fragments that will also be inserted before executing the expression code.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      java.lang.StringgetexpressionLib() +
      This method returns the value of expressionLib.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsetexpressionLib(java.lang.String value) +
      This method sets the value of expressionLib.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        expressionLib

        +
        java.lang.String expressionLib
        +
        Additional code fragments that will also be inserted before executing the expression code. Allows for function definitions that may be called from CWL expressions.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'InlineJavascriptRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InlineJavascriptRequirement

        +
        public InlineJavascriptRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setexpressionLib

        +
        public void setexpressionLib(java.lang.String value)
        +
        This method sets the value of expressionLib.
        +
        +
        Parameters:
        +
        value - will update expressionLib, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getexpressionLib

        +
        public java.lang.String getexpressionLib()
        +
        This method returns the value of expressionLib.
        +
        +
        Returns:
        +
        This method will return the value of expressionLib, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputArraySchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputArraySchema.html new file mode 100644 index 00000000..b7b72bdd --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputArraySchema.html @@ -0,0 +1,410 @@ + + + + + +InputArraySchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InputArraySchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) CommandLineBindinginputBinding 
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      InputArraySchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      CommandLineBindinggetinputBinding() +
      This method returns the value of inputBinding.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetinputBinding(CommandLineBinding value) +
      This method sets the value of inputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + + + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InputArraySchema

        +
        public InputArraySchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface InputSchema
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface InputSchema
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputBinding.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputBinding.html new file mode 100644 index 00000000..7c039bb9 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputBinding.html @@ -0,0 +1,289 @@ + + + + + +InputBinding + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface InputBinding

+
+
+
+
    +
  • +
    +
    All Known Implementing Classes:
    +
    CommandLineBinding
    +
    +
    +
    +
    public interface InputBinding
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.BooleanloadContents +
      Only valid when `type: File` or is an array of `items: File`.
      +
      +
      • +
    + + +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        loadContents

        +
        static final java.lang.Boolean loadContents
        +
        Only valid when `type: File` or is an array of `items: File`. Read up to the first 64 KiB of text from the file and place it in the contents field of the file object for use by expressions.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setloadContents

        +
        void setloadContents(java.lang.Boolean value)
        +
        This method sets the value of loadContents.
        +
        +
        Parameters:
        +
        value - will update loadContents, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getloadContents

        +
        java.lang.Boolean getloadContents()
        +
        This method returns the value of loadContents.
        +
        +
        Returns:
        +
        This method will return the value of loadContents, which is a Boolean type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputEnumSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputEnumSchema.html new file mode 100644 index 00000000..bfc8c1ef --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputEnumSchema.html @@ -0,0 +1,410 @@ + + + + + +InputEnumSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InputEnumSchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) CommandLineBindinginputBinding 
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      InputEnumSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      CommandLineBindinggetinputBinding() +
      This method returns the value of inputBinding.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetinputBinding(CommandLineBinding value) +
      This method sets the value of inputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + + + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InputEnumSchema

        +
        public InputEnumSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface InputSchema
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface InputSchema
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputParameter.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputParameter.html new file mode 100644 index 00000000..4fc7ee6d --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputParameter.html @@ -0,0 +1,1128 @@ + + + + + +InputParameter + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InputParameter

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.InputParameter
      • +
    +
    • +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) Anydefault_value +
      The default value for this parameter if not provided in the input object.
      +
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this parameter object.
      +
      (package private) CommandLineBindinginputBinding +
      Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Objecttype +
      Specify valid types of data that may be assigned to this parameter.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      InputParameter() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      Anygetdefault() +
      This method returns the value of default_value.
      +
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      CommandLineBindinggetinputBinding() +
      This method returns the value of inputBinding.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdefault(Any value) +
      This method sets the value of default_value.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetinputBinding(CommandLineBinding value) +
      This method sets the value of inputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      voidsettype(CWLType value) +
      This method sets the value of type.
      +
      voidsettype(CWLType[] value) +
      This method sets the value of type.
      +
      voidsettype(InputArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(InputArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(InputEnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(InputEnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(InputRecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(InputRecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        default_value

        +
        Any default_value
        +
        The default value for this parameter if not provided in the input object.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this parameter object.
        +
        • +
      + + + +
        +
      • +

        inputBinding

        +
        CommandLineBinding inputBinding
        +
        Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        Specify valid types of data that may be assigned to this parameter.
        +
        • +
      + + + +
        +
      • +

        streamable

        +
        java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InputParameter

        +
        public InputParameter()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setdefault

        +
        public void setdefault(Any value)
        +
        This method sets the value of default_value.
        +
        +
        Parameters:
        +
        value - will update default_value, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        getdefault

        +
        public Any getdefault()
        +
        This method returns the value of default_value.
        +
        +
        Returns:
        +
        This method will return the value of default_value, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputEnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputEnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputRecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputRecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a InputArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setstreamable

        +
        public void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Specified by:
        +
        setstreamable in interface Parameter
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        public java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Specified by:
        +
        getstreamable in interface Parameter
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Specified by:
        +
        getformat in interface Parameter
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Parameter
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(Expression[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(Expression value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Specified by:
        +
        getsecondaryFiles in interface Parameter
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Parameter
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Parameter
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
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Skip navigation links
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+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputRecordField.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputRecordField.html new file mode 100644 index 00000000..b65ce7ed --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputRecordField.html @@ -0,0 +1,766 @@ + + + + + +InputRecordField + + + + + + + + +
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+
org.commonwl.lang
+

Class InputRecordField

+
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+ +
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    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringdoc +
      A documentation string for this field
      +
      (package private) CommandLineBindinginputBinding 
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this process object.
      +
      (package private) java.lang.Stringname +
      The name of the field
      +
      (package private) java.lang.Objecttype +
      The field type
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      InputRecordField() 
      +
      • +
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    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      + + + + + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The name of the field
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A documentation string for this field
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        The field type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InputRecordField

        +
        public InputRecordField()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputBinding

        +
        public void setinputBinding(CommandLineBinding value)
        +
        This method sets the value of inputBinding.
        +
        +
        Parameters:
        +
        value - will update inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getinputBinding

        +
        public CommandLineBinding getinputBinding()
        +
        This method returns the value of inputBinding.
        +
        +
        Returns:
        +
        This method will return the value of inputBinding, which is a CommandLineBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Overrides:
        +
        setname in class RecordField
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Overrides:
        +
        getname in class RecordField
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Overrides:
        +
        setdoc in class RecordField
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Overrides:
        +
        getdoc in class RecordField
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(InputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Overrides:
        +
        gettype in class RecordField
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      +
      • +
    +
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+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputRecordSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputRecordSchema.html new file mode 100644 index 00000000..ef08c1a6 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputRecordSchema.html @@ -0,0 +1,357 @@ + + + + + +InputRecordSchema + + + + + + + + +
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+ +
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+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class InputRecordSchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      InputRecordSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        InputRecordSchema

        +
        public InputRecordSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface InputSchema
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface InputSchema
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputSchema.html new file mode 100644 index 00000000..662cc9b2 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/InputSchema.html @@ -0,0 +1,298 @@ + + + + + +InputSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface InputSchema

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        static final java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/JsonldPredicate.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/JsonldPredicate.html new file mode 100644 index 00000000..017c4429 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/JsonldPredicate.html @@ -0,0 +1,784 @@ + + + + + +JsonldPredicate + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class JsonldPredicate

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.JsonldPredicate
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class JsonldPredicate
+extends java.lang.Object
    +
    Attached to a record field to define how the parent record field is handled for URI resolution and JSON-LD context generation.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.String_container +
      Structure hint, corresponds to JSON-LD `@container` directive.
      +
      (package private) java.lang.String_id +
      The predicate URI that this field corresponds to.
      +
      (package private) java.lang.String_type +
      The context type hint, corresponds to JSON-LD `@type` directive.
      +
      (package private) java.lang.Booleanidentity +
      If true and `_type` is `@id` this indicates that the parent field must be resolved according to identity resolution rules instead of link resolution rules.
      +
      (package private) java.lang.StringmapPredicate +
      Only applies if `mapSubject` is also provided.
      +
      (package private) java.lang.StringmapSubject +
      If the value of the field is a JSON object, it must be transformed into an array of JSON objects, where each key-value pair from the source JSON object is a list item, the list items must be JSON objects, and the key is assigned to the field specified by `mapSubject`.
      +
      (package private) java.lang.BooleannoLinkCheck +
      If true, this indicates that link validation traversal must stop at this field.
      +
      (package private) java.lang.IntegerrefScope +
      If the field contains a relative reference, it must be resolved by searching for valid document references in each successive parent scope in the document fragment.
      +
      (package private) java.lang.BooleantypeDSL +
      Field must be expanded based on the the Schema Salad type DSL.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      JsonldPredicate() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringget_container() +
      This method returns the value of _container.
      +
      java.lang.Stringget_id() +
      This method returns the value of _id.
      +
      java.lang.Stringget_type() +
      This method returns the value of _type.
      +
      java.lang.Booleangetidentity() +
      This method returns the value of identity.
      +
      java.lang.StringgetmapPredicate() +
      This method returns the value of mapPredicate.
      +
      java.lang.StringgetmapSubject() +
      This method returns the value of mapSubject.
      +
      java.lang.BooleangetnoLinkCheck() +
      This method returns the value of noLinkCheck.
      +
      java.lang.IntegergetrefScope() +
      This method returns the value of refScope.
      +
      java.lang.BooleangettypeDSL() +
      This method returns the value of typeDSL.
      +
      voidset_container(java.lang.String value) +
      This method sets the value of _container.
      +
      voidset_id(java.lang.String value) +
      This method sets the value of _id.
      +
      voidset_type(java.lang.String value) +
      This method sets the value of _type.
      +
      voidsetidentity(java.lang.Boolean value) +
      This method sets the value of identity.
      +
      voidsetmapPredicate(java.lang.String value) +
      This method sets the value of mapPredicate.
      +
      voidsetmapSubject(java.lang.String value) +
      This method sets the value of mapSubject.
      +
      voidsetnoLinkCheck(java.lang.Boolean value) +
      This method sets the value of noLinkCheck.
      +
      voidsetrefScope(java.lang.Integer value) +
      This method sets the value of refScope.
      +
      voidsettypeDSL(java.lang.Boolean value) +
      This method sets the value of typeDSL.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        _container

        +
        java.lang.String _container
        +
        Structure hint, corresponds to JSON-LD `@container` directive.
        +
        • +
      + + + +
        +
      • +

        noLinkCheck

        +
        java.lang.Boolean noLinkCheck
        +
        If true, this indicates that link validation traversal must stop at this field. This field (it is is a URI) or any fields under it (if it is an object or array) are not subject to link checking.
        +
        • +
      + + + +
        +
      • +

        typeDSL

        +
        java.lang.Boolean typeDSL
        +
        Field must be expanded based on the the Schema Salad type DSL.
        +
        • +
      + + + +
        +
      • +

        identity

        +
        java.lang.Boolean identity
        +
        If true and `_type` is `@id` this indicates that the parent field must be resolved according to identity resolution rules instead of link resolution rules. In addition, the field value is considered an assertion that the linked value exists; absence of an object in the loaded document with the URI is not an error.
        +
        • +
      + + + +
        +
      • +

        _type

        +
        java.lang.String _type
        +
        The context type hint, corresponds to JSON-LD `@type` directive. * If the value of this field is `@id` and `identity` is false or unspecified, the parent field must be resolved using the link resolution rules. If `identity` is true, the parent field must be resolved using the identifier expansion rules. * If the value of this field is `@vocab`, the parent field must be resolved using the vocabulary resolution rules.
        +
        • +
      + + + +
        +
      • +

        refScope

        +
        java.lang.Integer refScope
        +
        If the field contains a relative reference, it must be resolved by searching for valid document references in each successive parent scope in the document fragment. For example, a reference of `foo` in the context `#foo/bar/baz` will first check for the existence of `#foo/bar/baz/foo`, followed by `#foo/bar/foo`, then `#foo/foo` and then finally `#foo`. The first valid URI in the search order shall be used as the fully resolved value of the identifier. The value of the refScope field is the specified number of levels from the containing identifer scope before starting the search, so if `refScope: 2` then baz and bar must be stripped to get the base `#foo` and search `#foo/foo` and the `#foo`. The last scope searched must be the top level scope before determining if the identifier cannot be resolved.
        +
        • +
      + + + +
        +
      • +

        mapSubject

        +
        java.lang.String mapSubject
        +
        If the value of the field is a JSON object, it must be transformed into an array of JSON objects, where each key-value pair from the source JSON object is a list item, the list items must be JSON objects, and the key is assigned to the field specified by `mapSubject`.
        +
        • +
      + + + +
        +
      • +

        _id

        +
        java.lang.String _id
        +
        The predicate URI that this field corresponds to. Corresponds to JSON-LD `@id` directive.
        +
        • +
      + + + +
        +
      • +

        mapPredicate

        +
        java.lang.String mapPredicate
        +
        Only applies if `mapSubject` is also provided. If the value of the field is a JSON object, it is transformed as described in `mapSubject`, with the addition that when the value of a map item is not an object, the item is transformed to a JSON object with the key assigned to the field specified by `mapSubject` and the value assigned to the field specified by `mapPredicate`.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        JsonldPredicate

        +
        public JsonldPredicate()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        set_container

        +
        public void set_container(java.lang.String value)
        +
        This method sets the value of _container.
        +
        +
        Parameters:
        +
        value - will update _container, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        get_container

        +
        public java.lang.String get_container()
        +
        This method returns the value of _container.
        +
        +
        Returns:
        +
        This method will return the value of _container, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setnoLinkCheck

        +
        public void setnoLinkCheck(java.lang.Boolean value)
        +
        This method sets the value of noLinkCheck.
        +
        +
        Parameters:
        +
        value - will update noLinkCheck, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getnoLinkCheck

        +
        public java.lang.Boolean getnoLinkCheck()
        +
        This method returns the value of noLinkCheck.
        +
        +
        Returns:
        +
        This method will return the value of noLinkCheck, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        settypeDSL

        +
        public void settypeDSL(java.lang.Boolean value)
        +
        This method sets the value of typeDSL.
        +
        +
        Parameters:
        +
        value - will update typeDSL, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        gettypeDSL

        +
        public java.lang.Boolean gettypeDSL()
        +
        This method returns the value of typeDSL.
        +
        +
        Returns:
        +
        This method will return the value of typeDSL, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setidentity

        +
        public void setidentity(java.lang.Boolean value)
        +
        This method sets the value of identity.
        +
        +
        Parameters:
        +
        value - will update identity, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getidentity

        +
        public java.lang.Boolean getidentity()
        +
        This method returns the value of identity.
        +
        +
        Returns:
        +
        This method will return the value of identity, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        set_type

        +
        public void set_type(java.lang.String value)
        +
        This method sets the value of _type.
        +
        +
        Parameters:
        +
        value - will update _type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        get_type

        +
        public java.lang.String get_type()
        +
        This method returns the value of _type.
        +
        +
        Returns:
        +
        This method will return the value of _type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setrefScope

        +
        public void setrefScope(java.lang.Integer value)
        +
        This method sets the value of refScope.
        +
        +
        Parameters:
        +
        value - will update refScope, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        getrefScope

        +
        public java.lang.Integer getrefScope()
        +
        This method returns the value of refScope.
        +
        +
        Returns:
        +
        This method will return the value of refScope, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        setmapSubject

        +
        public void setmapSubject(java.lang.String value)
        +
        This method sets the value of mapSubject.
        +
        +
        Parameters:
        +
        value - will update mapSubject, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getmapSubject

        +
        public java.lang.String getmapSubject()
        +
        This method returns the value of mapSubject.
        +
        +
        Returns:
        +
        This method will return the value of mapSubject, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        set_id

        +
        public void set_id(java.lang.String value)
        +
        This method sets the value of _id.
        +
        +
        Parameters:
        +
        value - will update _id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        get_id

        +
        public java.lang.String get_id()
        +
        This method returns the value of _id.
        +
        +
        Returns:
        +
        This method will return the value of _id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setmapPredicate

        +
        public void setmapPredicate(java.lang.String value)
        +
        This method sets the value of mapPredicate.
        +
        +
        Parameters:
        +
        value - will update mapPredicate, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getmapPredicate

        +
        public java.lang.String getmapPredicate()
        +
        This method returns the value of mapPredicate.
        +
        +
        Returns:
        +
        This method will return the value of mapPredicate, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/LinkMergeMethod.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/LinkMergeMethod.html new file mode 100644 index 00000000..60e4d37c --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/LinkMergeMethod.html @@ -0,0 +1,340 @@ + + + + + +LinkMergeMethod + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Enum LinkMergeMethod

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<LinkMergeMethod>
      • +
    • +
        +
      • org.commonwl.lang.LinkMergeMethod
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<LinkMergeMethod>
    +
    +
    +
    +
    public enum LinkMergeMethod
+extends java.lang.Enum<LinkMergeMethod>
    +
    The input link merge method, described in [WorkflowStepInput](#WorkflowStepInput).
    +
    • +
+
+
+
    +
  • + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Static Methods Concrete Methods 
      Modifier and TypeMethod and Description
      static LinkMergeMethodvalueOf(java.lang.String name) +
      Returns the enum constant of this type with the specified name.
      +
      static LinkMergeMethod[]values() +
      Returns an array containing the constants of this enum type, in +the order they are declared.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Enum

        +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
        • +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +getClass, notify, notifyAll, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + + + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static LinkMergeMethod[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (LinkMergeMethod c : LinkMergeMethod.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static LinkMergeMethod valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/MultipleInputFeatureRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/MultipleInputFeatureRequirement.html new file mode 100644 index 00000000..babbf79b --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/MultipleInputFeatureRequirement.html @@ -0,0 +1,341 @@ + + + + + +MultipleInputFeatureRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class MultipleInputFeatureRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.MultipleInputFeatureRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class MultipleInputFeatureRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Indicates that the workflow platform must support multiple inbound data links listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'MultipleInputFeatureRequirement'
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'MultipleInputFeatureRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        MultipleInputFeatureRequirement

        +
        public MultipleInputFeatureRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/NamedType.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/NamedType.html new file mode 100644 index 00000000..bb09cce9 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/NamedType.html @@ -0,0 +1,289 @@ + + + + + +NamedType + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface NamedType

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Stringname +
      The identifier for this type
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetname() +
      This method returns the value of name.
      +
      voidsetname(java.lang.String value) +
      This method sets the value of name.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        name

        +
        static final java.lang.String name
        +
        The identifier for this type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setname

        +
        void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputArraySchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputArraySchema.html new file mode 100644 index 00000000..89a85053 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputArraySchema.html @@ -0,0 +1,410 @@ + + + + + +OutputArraySchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class OutputArraySchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) CommandOutputBindingoutputBinding 
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      OutputArraySchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      CommandOutputBindinggetoutputBinding() +
      This method returns the value of outputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetoutputBinding(CommandOutputBinding value) +
      This method sets the value of outputBinding.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + + + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        OutputArraySchema

        +
        public OutputArraySchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface OutputSchema
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface OutputSchema
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputBinding.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputBinding.html new file mode 100644 index 00000000..5f8eacb6 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputBinding.html @@ -0,0 +1,169 @@ + + + + + +OutputBinding + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Interface OutputBinding

+
+
+
+
    +
  • +
    +
    All Known Implementing Classes:
    +
    CommandOutputBinding
    +
    +
    +
    +
    public interface OutputBinding
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputEnumSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputEnumSchema.html new file mode 100644 index 00000000..3a3edfc6 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputEnumSchema.html @@ -0,0 +1,410 @@ + + + + + +OutputEnumSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class OutputEnumSchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) CommandOutputBindingoutputBinding 
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      OutputEnumSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      CommandOutputBindinggetoutputBinding() +
      This method returns the value of outputBinding.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetoutputBinding(CommandOutputBinding value) +
      This method sets the value of outputBinding.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + + + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        OutputEnumSchema

        +
        public OutputEnumSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface OutputSchema
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface OutputSchema
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputParameter.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputParameter.html new file mode 100644 index 00000000..9960303f --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputParameter.html @@ -0,0 +1,836 @@ + + + + + +OutputParameter + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class OutputParameter

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.OutputParameter
      • +
    +
    • +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this parameter object.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) CommandOutputBindingoutputBinding +
      Describes how to handle the outputs of a process.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      OutputParameter() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      CommandOutputBindinggetoutputBinding() +
      This method returns the value of outputBinding.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetoutputBinding(CommandOutputBinding value) +
      This method sets the value of outputBinding.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        outputBinding

        +
        CommandOutputBinding outputBinding
        +
        Describes how to handle the outputs of a process.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this parameter object.
        +
        • +
      + + + +
        +
      • +

        streamable

        +
        java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        OutputParameter

        +
        public OutputParameter()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstreamable

        +
        public void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Specified by:
        +
        setstreamable in interface Parameter
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        public java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Specified by:
        +
        getstreamable in interface Parameter
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Specified by:
        +
        getformat in interface Parameter
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Parameter
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(Expression[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(Expression value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Specified by:
        +
        getsecondaryFiles in interface Parameter
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Parameter
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Parameter
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputRecordField.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputRecordField.html new file mode 100644 index 00000000..d9d56dbb --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputRecordField.html @@ -0,0 +1,710 @@ + + + + + +OutputRecordField + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class OutputRecordField

+
+
+ +
+ +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + + + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The name of the field
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A documentation string for this field
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        The field type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        OutputRecordField

        +
        public OutputRecordField()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Overrides:
        +
        setname in class RecordField
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Overrides:
        +
        getname in class RecordField
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Overrides:
        +
        setdoc in class RecordField
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Overrides:
        +
        getdoc in class RecordField
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Overrides:
        +
        gettype in class RecordField
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputRecordSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputRecordSchema.html new file mode 100644 index 00000000..4223270c --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputRecordSchema.html @@ -0,0 +1,357 @@ + + + + + +OutputRecordSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class OutputRecordSchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      OutputRecordSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        OutputRecordSchema

        +
        public OutputRecordSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface OutputSchema
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface OutputSchema
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputSchema.html new file mode 100644 index 00000000..7ce7e130 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/OutputSchema.html @@ -0,0 +1,298 @@ + + + + + +OutputSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface OutputSchema

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        static final java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Parameter.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Parameter.html new file mode 100644 index 00000000..40bc2504 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Parameter.html @@ -0,0 +1,643 @@ + + + + + +Parameter + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface Parameter

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      static java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      static java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      static java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      static java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        streamable

        +
        static final java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        static final java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        static final java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        static final java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        static final java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setstreamable

        +
        void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        void setsecondaryFiles(Expression[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        void setsecondaryFiles(Expression value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getsecondaryFiles

        +
        java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
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+ + + +
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+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/PrimitiveType.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/PrimitiveType.html new file mode 100644 index 00000000..426d6ee4 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/PrimitiveType.html @@ -0,0 +1,442 @@ + + + + + +PrimitiveType + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class PrimitiveType

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.PrimitiveType
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class PrimitiveType
+extends java.lang.Object
    +
    Salad data types are based on Avro schema declarations. Refer to the + [Avro schema declaration documentation](https://avro.apache.org/docs/current/spec.html#schemas) for + detailed information. + The types are: 1) null: no value, + 2) boolean: a binary value, + 3) int: 32-bit signed integer, + 4) long: 64-bit signed integer, + 5) float: single precision (32-bit) IEEE 754 floating-point number, + 6) double: double precision (64-bit) IEEE 754 floating-point number, and + 7) string: Unicode character sequence.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectvalue 
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      PrimitiveType(java.lang.Object objectInstance) 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectget() +
      This method returns the value of PrimitiveType.
      +
      voidset(java.lang.Boolean objectInstance) +
      This method sets the value of PrimitiveType.
      +
      voidset(java.lang.Double objectInstance) +
      This method sets the value of PrimitiveType.
      +
      voidset(java.lang.Float objectInstance) +
      This method sets the value of PrimitiveType.
      +
      voidset(java.lang.Integer objectInstance) +
      This method sets the value of PrimitiveType.
      +
      voidset(java.lang.Long objectInstance) +
      This method sets the value of PrimitiveType.
      +
      voidset(java.lang.String objectInstance) +
      This method sets the value of PrimitiveType.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        value

        +
        java.lang.Object value
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        PrimitiveType

        +
        public PrimitiveType(java.lang.Object objectInstance)
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        set

        +
        public void set(java.lang.Boolean objectInstance)
        +
        This method sets the value of PrimitiveType.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of PrimitiveType, and is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        set

        +
        public void set(java.lang.Integer objectInstance)
        +
        This method sets the value of PrimitiveType.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of PrimitiveType, and is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        set

        +
        public void set(java.lang.Long objectInstance)
        +
        This method sets the value of PrimitiveType.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of PrimitiveType, and is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        set

        +
        public void set(java.lang.Float objectInstance)
        +
        This method sets the value of PrimitiveType.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of PrimitiveType, and is a Float type.
        +
        +
        • +
      + + + +
        +
      • +

        set

        +
        public void set(java.lang.Double objectInstance)
        +
        This method sets the value of PrimitiveType.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of PrimitiveType, and is a Double type.
        +
        +
        • +
      + + + +
        +
      • +

        set

        +
        public void set(java.lang.String objectInstance)
        +
        This method sets the value of PrimitiveType.
        +
        +
        Parameters:
        +
        objectInstance - sets the value of PrimitiveType, and is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        get

        +
        public java.lang.Object get()
        +
        This method returns the value of PrimitiveType.
        +
        +
        Returns:
        +
        This method will return the value of PrimitiveType, which is an Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Process.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Process.html new file mode 100644 index 00000000..ceda44f4 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Process.html @@ -0,0 +1,901 @@ + + + + + +Process + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface Process

+
+
+
+ +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        outputs

        +
        static final OutputParameter[] outputs
        +
        Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.
        +
        • +
      + + + +
        +
      • +

        requirements

        +
        static final java.lang.Object requirements
        +
        Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
        +
        • +
      + + + +
        +
      • +

        cwlVersion

        +
        static final CWLVersion cwlVersion
        +
        CWL document version. Always required at the document root. Not required for a Process embedded inside another Process.
        +
        • +
      + + + +
        +
      • +

        inputs

        +
        static final InputParameter[] inputs
        +
        Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object.
        +
        • +
      + + + +
        +
      • +

        hints

        +
        static final Any hints
        +
        Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        static final java.lang.String doc
        +
        A long, human-readable description of this process object.
        +
        • +
      + + + +
        +
      • +

        id

        +
        static final java.lang.String id
        +
        The unique identifier for this process object.
        +
        • +
      + + + +
        +
      • +

        label

        +
        static final java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setoutputs

        +
        void setoutputs(OutputParameter[] value)
        +
        This method sets the value of outputs.
        +
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputs

        +
        OutputParameter[] getoutputs()
        +
        This method returns the value of outputs.
        +
        +
        Returns:
        +
        This method will return the value of outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(StepInputExpressionRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a StepInputExpressionRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(MultipleInputFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a MultipleInputFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(SoftwareRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a SoftwareRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(SchemaDefRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a SchemaDefRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(InitialWorkDirRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a InitialWorkDirRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(EnvVarRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a EnvVarRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(DockerRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a DockerRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(ResourceRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a ResourceRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(InlineJavascriptRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a InlineJavascriptRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(ShellCommandRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a ShellCommandRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(ScatterFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a ScatterFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        void setrequirements(SubworkflowFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a SubworkflowFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        getrequirements

        +
        java.lang.Object getrequirements()
        +
        This method returns the value of requirements.
        +
        +
        Returns:
        +
        This method will return the value of requirements, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setcwlVersion

        +
        void setcwlVersion(CWLVersion value)
        +
        This method sets the value of cwlVersion.
        +
        +
        Parameters:
        +
        value - will update cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        getcwlVersion

        +
        CWLVersion getcwlVersion()
        +
        This method returns the value of cwlVersion.
        +
        +
        Returns:
        +
        This method will return the value of cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputs

        +
        void setinputs(InputParameter[] value)
        +
        This method sets the value of inputs.
        +
        +
        Parameters:
        +
        value - will update inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getinputs

        +
        InputParameter[] getinputs()
        +
        This method returns the value of inputs.
        +
        +
        Returns:
        +
        This method will return the value of inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        sethints

        +
        void sethints(Any value)
        +
        This method sets the value of hints.
        +
        +
        Parameters:
        +
        value - will update hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        gethints

        +
        Any gethints()
        +
        This method returns the value of hints.
        +
        +
        Returns:
        +
        This method will return the value of hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
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    • +
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    • +
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    • +
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    • +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ProcessRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ProcessRequirement.html new file mode 100644 index 00000000..7c38a9b4 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ProcessRequirement.html @@ -0,0 +1,170 @@ + + + + + +ProcessRequirement + + + + + + + + +
+ + +
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+ + + + +
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  • Summary: 
    • +
  • Nested | 
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    • +
+
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  • Detail: 
    • +
  • Field | 
    • +
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    • +
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    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Interface ProcessRequirement

+
+
+
+ +
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
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    +
  • Summary: 
    • +
  • Nested | 
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+
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  • Detail: 
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    • +
+
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/RecordField.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/RecordField.html new file mode 100644 index 00000000..d8711e09 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/RecordField.html @@ -0,0 +1,632 @@ + + + + + +RecordField + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class RecordField

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.RecordField
      • +
    +
    • +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringdoc +
      A documentation string for this field
      +
      (package private) java.lang.Stringname +
      The name of the field
      +
      (package private) java.lang.Objecttype +
      The field type
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      RecordField() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Stringgetname() +
      This method returns the value of name.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetname(java.lang.String value) +
      This method sets the value of name.
      +
      voidsettype(ArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(ArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(EnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(EnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(PrimitiveType value) +
      This method sets the value of type.
      +
      voidsettype(PrimitiveType[] value) +
      This method sets the value of type.
      +
      voidsettype(RecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(RecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The name of the field
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A documentation string for this field
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        The field type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        RecordField

        +
        public RecordField()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/RecordSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/RecordSchema.html new file mode 100644 index 00000000..eb36db2b --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/RecordSchema.html @@ -0,0 +1,239 @@ + + + + + +RecordSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Class RecordSchema

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.RecordSchema
      • +
    +
    • +
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      RecordSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        RecordSchema

        +
        public RecordSchema()
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ResourceRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ResourceRequirement.html new file mode 100644 index 00000000..bea01659 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ResourceRequirement.html @@ -0,0 +1,1109 @@ + + + + + +ResourceRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class ResourceRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.ResourceRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class ResourceRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Specify basic hardware resource requirements.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'ResourceRequirement'
      +
      (package private) java.lang.ObjectcoresMax +
      Maximum reserved number of CPU cores
      +
      (package private) java.lang.ObjectcoresMin +
      Minimum reserved number of CPU cores
      +
      (package private) java.lang.ObjectoutdirMax +
      Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
      +
      (package private) java.lang.ObjectoutdirMin +
      Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
      +
      (package private) java.lang.ObjectramMax +
      Maximum reserved RAM in mebibytes (2**20)
      +
      (package private) java.lang.ObjectramMin +
      Minimum reserved RAM in mebibytes (2**20)
      +
      (package private) java.lang.ObjecttmpdirMax +
      Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
      +
      (package private) java.lang.ObjecttmpdirMin +
      Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      java.lang.ObjectgetcoresMax() +
      This method returns the value of coresMax.
      +
      java.lang.ObjectgetcoresMin() +
      This method returns the value of coresMin.
      +
      java.lang.ObjectgetoutdirMax() +
      This method returns the value of outdirMax.
      +
      java.lang.ObjectgetoutdirMin() +
      This method returns the value of outdirMin.
      +
      java.lang.ObjectgetramMax() +
      This method returns the value of ramMax.
      +
      java.lang.ObjectgetramMin() +
      This method returns the value of ramMin.
      +
      java.lang.ObjectgettmpdirMax() +
      This method returns the value of tmpdirMax.
      +
      java.lang.ObjectgettmpdirMin() +
      This method returns the value of tmpdirMin.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsetcoresMax(Expression value) +
      This method sets the value of coresMax.
      +
      voidsetcoresMax(java.lang.Integer value) +
      This method sets the value of coresMax.
      +
      voidsetcoresMax(java.lang.String value) +
      This method sets the value of coresMax.
      +
      voidsetcoresMin(Expression value) +
      This method sets the value of coresMin.
      +
      voidsetcoresMin(java.lang.Long value) +
      This method sets the value of coresMin.
      +
      voidsetcoresMin(java.lang.String value) +
      This method sets the value of coresMin.
      +
      voidsetoutdirMax(Expression value) +
      This method sets the value of outdirMax.
      +
      voidsetoutdirMax(java.lang.Long value) +
      This method sets the value of outdirMax.
      +
      voidsetoutdirMax(java.lang.String value) +
      This method sets the value of outdirMax.
      +
      voidsetoutdirMin(Expression value) +
      This method sets the value of outdirMin.
      +
      voidsetoutdirMin(java.lang.Long value) +
      This method sets the value of outdirMin.
      +
      voidsetoutdirMin(java.lang.String value) +
      This method sets the value of outdirMin.
      +
      voidsetramMax(Expression value) +
      This method sets the value of ramMax.
      +
      voidsetramMax(java.lang.Long value) +
      This method sets the value of ramMax.
      +
      voidsetramMax(java.lang.String value) +
      This method sets the value of ramMax.
      +
      voidsetramMin(Expression value) +
      This method sets the value of ramMin.
      +
      voidsetramMin(java.lang.Long value) +
      This method sets the value of ramMin.
      +
      voidsetramMin(java.lang.String value) +
      This method sets the value of ramMin.
      +
      voidsettmpdirMax(Expression value) +
      This method sets the value of tmpdirMax.
      +
      voidsettmpdirMax(java.lang.Long value) +
      This method sets the value of tmpdirMax.
      +
      voidsettmpdirMax(java.lang.String value) +
      This method sets the value of tmpdirMax.
      +
      voidsettmpdirMin(Expression value) +
      This method sets the value of tmpdirMin.
      +
      voidsettmpdirMin(java.lang.Long value) +
      This method sets the value of tmpdirMin.
      +
      voidsettmpdirMin(java.lang.String value) +
      This method sets the value of tmpdirMin.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        tmpdirMin

        +
        java.lang.Object tmpdirMin
        +
        Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
        +
        • +
      + + + +
        +
      • +

        tmpdirMax

        +
        java.lang.Object tmpdirMax
        +
        Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
        +
        • +
      + + + +
        +
      • +

        ramMax

        +
        java.lang.Object ramMax
        +
        Maximum reserved RAM in mebibytes (2**20)
        +
        • +
      + + + +
        +
      • +

        coresMax

        +
        java.lang.Object coresMax
        +
        Maximum reserved number of CPU cores
        +
        • +
      + + + +
        +
      • +

        ramMin

        +
        java.lang.Object ramMin
        +
        Minimum reserved RAM in mebibytes (2**20)
        +
        • +
      + + + +
        +
      • +

        outdirMin

        +
        java.lang.Object outdirMin
        +
        Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
        +
        • +
      + + + +
        +
      • +

        coresMin

        +
        java.lang.Object coresMin
        +
        Minimum reserved number of CPU cores
        +
        • +
      + + + +
        +
      • +

        outdirMax

        +
        java.lang.Object outdirMax
        +
        Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'ResourceRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        ResourceRequirement

        +
        public ResourceRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        settmpdirMin

        +
        public void settmpdirMin(Expression value)
        +
        This method sets the value of tmpdirMin.
        +
        +
        Parameters:
        +
        value - will update tmpdirMin, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        settmpdirMin

        +
        public void settmpdirMin(java.lang.String value)
        +
        This method sets the value of tmpdirMin.
        +
        +
        Parameters:
        +
        value - will update tmpdirMin, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settmpdirMin

        +
        public void settmpdirMin(java.lang.Long value)
        +
        This method sets the value of tmpdirMin.
        +
        +
        Parameters:
        +
        value - will update tmpdirMin, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        gettmpdirMin

        +
        public java.lang.Object gettmpdirMin()
        +
        This method returns the value of tmpdirMin.
        +
        +
        Returns:
        +
        This method will return the value of tmpdirMin, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        settmpdirMax

        +
        public void settmpdirMax(Expression value)
        +
        This method sets the value of tmpdirMax.
        +
        +
        Parameters:
        +
        value - will update tmpdirMax, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        settmpdirMax

        +
        public void settmpdirMax(java.lang.String value)
        +
        This method sets the value of tmpdirMax.
        +
        +
        Parameters:
        +
        value - will update tmpdirMax, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settmpdirMax

        +
        public void settmpdirMax(java.lang.Long value)
        +
        This method sets the value of tmpdirMax.
        +
        +
        Parameters:
        +
        value - will update tmpdirMax, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        gettmpdirMax

        +
        public java.lang.Object gettmpdirMax()
        +
        This method returns the value of tmpdirMax.
        +
        +
        Returns:
        +
        This method will return the value of tmpdirMax, which is a Object type.
        +
        +
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      + + + +
        +
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        setramMax

        +
        public void setramMax(Expression value)
        +
        This method sets the value of ramMax.
        +
        +
        Parameters:
        +
        value - will update ramMax, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        setramMax

        +
        public void setramMax(java.lang.String value)
        +
        This method sets the value of ramMax.
        +
        +
        Parameters:
        +
        value - will update ramMax, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setramMax

        +
        public void setramMax(java.lang.Long value)
        +
        This method sets the value of ramMax.
        +
        +
        Parameters:
        +
        value - will update ramMax, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        getramMax

        +
        public java.lang.Object getramMax()
        +
        This method returns the value of ramMax.
        +
        +
        Returns:
        +
        This method will return the value of ramMax, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setcoresMax

        +
        public void setcoresMax(Expression value)
        +
        This method sets the value of coresMax.
        +
        +
        Parameters:
        +
        value - will update coresMax, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        setcoresMax

        +
        public void setcoresMax(java.lang.String value)
        +
        This method sets the value of coresMax.
        +
        +
        Parameters:
        +
        value - will update coresMax, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setcoresMax

        +
        public void setcoresMax(java.lang.Integer value)
        +
        This method sets the value of coresMax.
        +
        +
        Parameters:
        +
        value - will update coresMax, which is a Integer type.
        +
        +
        • +
      + + + +
        +
      • +

        getcoresMax

        +
        public java.lang.Object getcoresMax()
        +
        This method returns the value of coresMax.
        +
        +
        Returns:
        +
        This method will return the value of coresMax, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setramMin

        +
        public void setramMin(Expression value)
        +
        This method sets the value of ramMin.
        +
        +
        Parameters:
        +
        value - will update ramMin, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        setramMin

        +
        public void setramMin(java.lang.String value)
        +
        This method sets the value of ramMin.
        +
        +
        Parameters:
        +
        value - will update ramMin, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setramMin

        +
        public void setramMin(java.lang.Long value)
        +
        This method sets the value of ramMin.
        +
        +
        Parameters:
        +
        value - will update ramMin, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        getramMin

        +
        public java.lang.Object getramMin()
        +
        This method returns the value of ramMin.
        +
        +
        Returns:
        +
        This method will return the value of ramMin, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutdirMin

        +
        public void setoutdirMin(Expression value)
        +
        This method sets the value of outdirMin.
        +
        +
        Parameters:
        +
        value - will update outdirMin, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutdirMin

        +
        public void setoutdirMin(java.lang.String value)
        +
        This method sets the value of outdirMin.
        +
        +
        Parameters:
        +
        value - will update outdirMin, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutdirMin

        +
        public void setoutdirMin(java.lang.Long value)
        +
        This method sets the value of outdirMin.
        +
        +
        Parameters:
        +
        value - will update outdirMin, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutdirMin

        +
        public java.lang.Object getoutdirMin()
        +
        This method returns the value of outdirMin.
        +
        +
        Returns:
        +
        This method will return the value of outdirMin, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setcoresMin

        +
        public void setcoresMin(Expression value)
        +
        This method sets the value of coresMin.
        +
        +
        Parameters:
        +
        value - will update coresMin, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        setcoresMin

        +
        public void setcoresMin(java.lang.String value)
        +
        This method sets the value of coresMin.
        +
        +
        Parameters:
        +
        value - will update coresMin, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setcoresMin

        +
        public void setcoresMin(java.lang.Long value)
        +
        This method sets the value of coresMin.
        +
        +
        Parameters:
        +
        value - will update coresMin, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        getcoresMin

        +
        public java.lang.Object getcoresMin()
        +
        This method returns the value of coresMin.
        +
        +
        Returns:
        +
        This method will return the value of coresMin, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutdirMax

        +
        public void setoutdirMax(Expression value)
        +
        This method sets the value of outdirMax.
        +
        +
        Parameters:
        +
        value - will update outdirMax, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutdirMax

        +
        public void setoutdirMax(java.lang.String value)
        +
        This method sets the value of outdirMax.
        +
        +
        Parameters:
        +
        value - will update outdirMax, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutdirMax

        +
        public void setoutdirMax(java.lang.Long value)
        +
        This method sets the value of outdirMax.
        +
        +
        Parameters:
        +
        value - will update outdirMax, which is a Long type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutdirMax

        +
        public java.lang.Object getoutdirMax()
        +
        This method returns the value of outdirMax.
        +
        +
        Returns:
        +
        This method will return the value of outdirMax, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
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+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SaladEnumSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SaladEnumSchema.html new file mode 100644 index 00000000..2f788db3 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SaladEnumSchema.html @@ -0,0 +1,812 @@ + + + + + +SaladEnumSchema + + + + + + + + +
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+
org.commonwl.lang
+

Class SaladEnumSchema

+
+
+ +
+ +
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+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.StringdocAfter +
      Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
      +
      (package private) java.lang.ObjectdocChild +
      Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
      +
      (package private) java.lang.StringdocParent +
      Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
      +
      (package private) java.lang.BooleandocumentRoot +
      If true, indicates that the type is a valid at the document root.
      +
      (package private) java.lang.Objectextends_value +
      Indicates that this enum inherits symbols from a base enum.
      +
      (package private) java.lang.ObjectjsonldPredicate +
      Annotate this type with linked data context.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      SaladEnumSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.StringgetdocAfter() +
      This method returns the value of docAfter.
      +
      java.lang.ObjectgetdocChild() +
      This method returns the value of docChild.
      +
      java.lang.StringgetdocParent() +
      This method returns the value of docParent.
      +
      java.lang.BooleangetdocumentRoot() +
      This method returns the value of documentRoot.
      +
      java.lang.Objectgetextends() +
      This method returns the value of extends_value.
      +
      java.lang.ObjectgetjsonldPredicate() +
      This method returns the value of jsonldPredicate.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetdocAfter(java.lang.String value) +
      This method sets the value of docAfter.
      +
      voidsetdocChild(java.lang.String value) +
      This method sets the value of docChild.
      +
      voidsetdocChild(java.lang.String[] value) +
      This method sets the value of docChild.
      +
      voidsetdocParent(java.lang.String value) +
      This method sets the value of docParent.
      +
      voidsetdocumentRoot(java.lang.Boolean value) +
      This method sets the value of documentRoot.
      +
      voidsetextends(java.lang.String value) +
      This method sets the value of extends_value.
      +
      voidsetextends(java.lang.String[] value) +
      This method sets the value of extends_value.
      +
      voidsetjsonldPredicate(JsonldPredicate value) +
      This method sets the value of jsonldPredicate.
      +
      voidsetjsonldPredicate(java.lang.String value) +
      This method sets the value of jsonldPredicate.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
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    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        extends_value

        +
        java.lang.Object extends_value
        +
        Indicates that this enum inherits symbols from a base enum.
        +
        • +
      + + + +
        +
      • +

        documentRoot

        +
        java.lang.Boolean documentRoot
        +
        If true, indicates that the type is a valid at the document root. At least one type in a schema must be tagged with `documentRoot: true`.
        +
        • +
      + + + +
        +
      • +

        jsonldPredicate

        +
        java.lang.Object jsonldPredicate
        +
        Annotate this type with linked data context.
        +
        • +
      + + + +
        +
      • +

        docParent

        +
        java.lang.String docParent
        +
        Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        docAfter

        +
        java.lang.String docAfter
        +
        Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
        +
        • +
      + + + +
        +
      • +

        docChild

        +
        java.lang.Object docChild
        +
        Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SaladEnumSchema

        +
        public SaladEnumSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setextends

        +
        public void setextends(java.lang.String value)
        +
        This method sets the value of extends_value.
        +
        +
        Parameters:
        +
        value - will update extends_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setextends

        +
        public void setextends(java.lang.String[] value)
        +
        This method sets the value of extends_value.
        +
        +
        Parameters:
        +
        value - will update extends_value, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getextends

        +
        public java.lang.Object getextends()
        +
        This method returns the value of extends_value.
        +
        +
        Returns:
        +
        This method will return the value of extends_value, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocumentRoot

        +
        public void setdocumentRoot(java.lang.Boolean value)
        +
        This method sets the value of documentRoot.
        +
        +
        Specified by:
        +
        setdocumentRoot in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update documentRoot, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocumentRoot

        +
        public java.lang.Boolean getdocumentRoot()
        +
        This method returns the value of documentRoot.
        +
        +
        Specified by:
        +
        getdocumentRoot in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of documentRoot, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        public void setjsonldPredicate(java.lang.String value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Specified by:
        +
        setjsonldPredicate in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        public void setjsonldPredicate(JsonldPredicate value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Specified by:
        +
        setjsonldPredicate in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a JsonldPredicate type.
        +
        +
        • +
      + + + +
        +
      • +

        getjsonldPredicate

        +
        public java.lang.Object getjsonldPredicate()
        +
        This method returns the value of jsonldPredicate.
        +
        +
        Specified by:
        +
        getjsonldPredicate in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of jsonldPredicate, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocParent

        +
        public void setdocParent(java.lang.String value)
        +
        This method sets the value of docParent.
        +
        +
        Specified by:
        +
        setdocParent in interface DocType
        +
        Specified by:
        +
        setdocParent in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocParent

        +
        public java.lang.String getdocParent()
        +
        This method returns the value of docParent.
        +
        +
        Specified by:
        +
        getdocParent in interface DocType
        +
        Specified by:
        +
        getdocParent in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Specified by:
        +
        setdoc in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Specified by:
        +
        setdoc in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface DocType
        +
        Specified by:
        +
        getdoc in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocAfter

        +
        public void setdocAfter(java.lang.String value)
        +
        This method sets the value of docAfter.
        +
        +
        Specified by:
        +
        setdocAfter in interface DocType
        +
        Specified by:
        +
        setdocAfter in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocAfter

        +
        public java.lang.String getdocAfter()
        +
        This method returns the value of docAfter.
        +
        +
        Specified by:
        +
        getdocAfter in interface DocType
        +
        Specified by:
        +
        getdocAfter in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        public void setdocChild(java.lang.String value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Specified by:
        +
        setdocChild in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docChild, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        public void setdocChild(java.lang.String[] value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Specified by:
        +
        setdocChild in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docChild, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdocChild

        +
        public java.lang.Object getdocChild()
        +
        This method returns the value of docChild.
        +
        +
        Specified by:
        +
        getdocChild in interface DocType
        +
        Specified by:
        +
        getdocChild in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of docChild, which is a Object type.
        +
        +
        • +
      +
      • +
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+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SaladRecordField

+
+
+ +
+
    +
  • +
    +
    +
    public class SaladRecordField
+extends RecordField
    +
    A field of a record.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringdoc +
      A documentation string for this field
      +
      (package private) java.lang.ObjectjsonldPredicate +
      Annotate this type with linked data context.
      +
      (package private) java.lang.Stringname +
      The name of the field
      +
      (package private) java.lang.Objecttype +
      The field type
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      SaladRecordField() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetdoc() +
      This method returns the value of doc.
      +
      java.lang.ObjectgetjsonldPredicate() +
      This method returns the value of jsonldPredicate.
      +
      java.lang.Stringgetname() +
      This method returns the value of name.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetjsonldPredicate(JsonldPredicate value) +
      This method sets the value of jsonldPredicate.
      +
      voidsetjsonldPredicate(java.lang.String value) +
      This method sets the value of jsonldPredicate.
      +
      voidsetname(java.lang.String value) +
      This method sets the value of name.
      +
      voidsettype(ArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(ArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(EnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(EnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(PrimitiveType value) +
      This method sets the value of type.
      +
      voidsettype(PrimitiveType[] value) +
      This method sets the value of type.
      +
      voidsettype(RecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(RecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        jsonldPredicate

        +
        java.lang.Object jsonldPredicate
        +
        Annotate this type with linked data context.
        +
        • +
      + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The name of the field
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A documentation string for this field
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        The field type
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SaladRecordField

        +
        public SaladRecordField()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setjsonldPredicate

        +
        public void setjsonldPredicate(java.lang.String value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        public void setjsonldPredicate(JsonldPredicate value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a JsonldPredicate type.
        +
        +
        • +
      + + + +
        +
      • +

        getjsonldPredicate

        +
        public java.lang.Object getjsonldPredicate()
        +
        This method returns the value of jsonldPredicate.
        +
        +
        Returns:
        +
        This method will return the value of jsonldPredicate, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Overrides:
        +
        setname in class RecordField
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Overrides:
        +
        getname in class RecordField
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Overrides:
        +
        setdoc in class RecordField
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Overrides:
        +
        getdoc in class RecordField
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(RecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a RecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(PrimitiveType value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a PrimitiveType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(ArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a ArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(EnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Overrides:
        +
        settype in class RecordField
        +
        Parameters:
        +
        value - will update type, which is a EnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Overrides:
        +
        gettype in class RecordField
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SaladRecordSchema.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SaladRecordSchema.html new file mode 100644 index 00000000..7129723d --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SaladRecordSchema.html @@ -0,0 +1,983 @@ + + + + + +SaladRecordSchema + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SaladRecordSchema

+
+
+ +
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Booleanabstract_value +
      If true, this record is abstract and may be used as a base for other records, but is not valid on its own.
      +
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.StringdocAfter +
      Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
      +
      (package private) java.lang.ObjectdocChild +
      Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
      +
      (package private) java.lang.StringdocParent +
      Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
      +
      (package private) java.lang.BooleandocumentRoot +
      If true, indicates that the type is a valid at the document root.
      +
      (package private) java.lang.Objectextends_value +
      Indicates that this record inherits fields from one or more base records.
      +
      (package private) java.lang.ObjectjsonldPredicate +
      Annotate this type with linked data context.
      +
      (package private) java.lang.Stringname +
      The identifier for this type
      +
      (package private) SpecializeDef[]specialize +
      Only applies if `extends` is declared.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      SaladRecordSchema() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Booleangetabstract() +
      This method returns the value of abstract_value.
      +
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.StringgetdocAfter() +
      This method returns the value of docAfter.
      +
      java.lang.ObjectgetdocChild() +
      This method returns the value of docChild.
      +
      java.lang.StringgetdocParent() +
      This method returns the value of docParent.
      +
      java.lang.BooleangetdocumentRoot() +
      This method returns the value of documentRoot.
      +
      java.lang.Objectgetextends() +
      This method returns the value of extends_value.
      +
      java.lang.ObjectgetjsonldPredicate() +
      This method returns the value of jsonldPredicate.
      +
      java.lang.Stringgetname() +
      This method returns the value of name.
      +
      SpecializeDef[]getspecialize() +
      This method returns the value of specialize.
      +
      voidsetabstract(java.lang.Boolean value) +
      This method sets the value of abstract_value.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetdocAfter(java.lang.String value) +
      This method sets the value of docAfter.
      +
      voidsetdocChild(java.lang.String value) +
      This method sets the value of docChild.
      +
      voidsetdocChild(java.lang.String[] value) +
      This method sets the value of docChild.
      +
      voidsetdocParent(java.lang.String value) +
      This method sets the value of docParent.
      +
      voidsetdocumentRoot(java.lang.Boolean value) +
      This method sets the value of documentRoot.
      +
      voidsetextends(java.lang.String value) +
      This method sets the value of extends_value.
      +
      voidsetextends(java.lang.String[] value) +
      This method sets the value of extends_value.
      +
      voidsetjsonldPredicate(JsonldPredicate value) +
      This method sets the value of jsonldPredicate.
      +
      voidsetjsonldPredicate(java.lang.String value) +
      This method sets the value of jsonldPredicate.
      +
      voidsetname(java.lang.String value) +
      This method sets the value of name.
      +
      voidsetspecialize(SpecializeDef[] value) +
      This method sets the value of specialize.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        extends_value

        +
        java.lang.Object extends_value
        +
        Indicates that this record inherits fields from one or more base records.
        +
        • +
      + + + +
        +
      • +

        abstract_value

        +
        java.lang.Boolean abstract_value
        +
        If true, this record is abstract and may be used as a base for other records, but is not valid on its own.
        +
        • +
      + + + +
        +
      • +

        specialize

        +
        SpecializeDef[] specialize
        +
        Only applies if `extends` is declared. Apply type specialization using the base record as a template. For each field inherited from the base record, replace any instance of the type `specializeFrom` with `specializeTo`.
        +
        • +
      + + + +
        +
      • +

        name

        +
        java.lang.String name
        +
        The identifier for this type
        +
        • +
      + + + +
        +
      • +

        documentRoot

        +
        java.lang.Boolean documentRoot
        +
        If true, indicates that the type is a valid at the document root. At least one type in a schema must be tagged with `documentRoot: true`.
        +
        • +
      + + + +
        +
      • +

        jsonldPredicate

        +
        java.lang.Object jsonldPredicate
        +
        Annotate this type with linked data context.
        +
        • +
      + + + +
        +
      • +

        docParent

        +
        java.lang.String docParent
        +
        Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        docAfter

        +
        java.lang.String docAfter
        +
        Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
        +
        • +
      + + + +
        +
      • +

        docChild

        +
        java.lang.Object docChild
        +
        Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SaladRecordSchema

        +
        public SaladRecordSchema()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setextends

        +
        public void setextends(java.lang.String value)
        +
        This method sets the value of extends_value.
        +
        +
        Parameters:
        +
        value - will update extends_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setextends

        +
        public void setextends(java.lang.String[] value)
        +
        This method sets the value of extends_value.
        +
        +
        Parameters:
        +
        value - will update extends_value, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getextends

        +
        public java.lang.Object getextends()
        +
        This method returns the value of extends_value.
        +
        +
        Returns:
        +
        This method will return the value of extends_value, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setabstract

        +
        public void setabstract(java.lang.Boolean value)
        +
        This method sets the value of abstract_value.
        +
        +
        Parameters:
        +
        value - will update abstract_value, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getabstract

        +
        public java.lang.Boolean getabstract()
        +
        This method returns the value of abstract_value.
        +
        +
        Returns:
        +
        This method will return the value of abstract_value, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setspecialize

        +
        public void setspecialize(SpecializeDef[] value)
        +
        This method sets the value of specialize.
        +
        +
        Parameters:
        +
        value - will update specialize, which is a SpecializeDef array.
        +
        +
        • +
      + + + +
        +
      • +

        getspecialize

        +
        public SpecializeDef[] getspecialize()
        +
        This method returns the value of specialize.
        +
        +
        Returns:
        +
        This method will return the value of specialize, which is a SpecializeDef array.
        +
        +
        • +
      + + + +
        +
      • +

        setname

        +
        public void setname(java.lang.String value)
        +
        This method sets the value of name.
        +
        +
        Specified by:
        +
        setname in interface NamedType
        +
        Parameters:
        +
        value - will update name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getname

        +
        public java.lang.String getname()
        +
        This method returns the value of name.
        +
        +
        Specified by:
        +
        getname in interface NamedType
        +
        Returns:
        +
        This method will return the value of name, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocumentRoot

        +
        public void setdocumentRoot(java.lang.Boolean value)
        +
        This method sets the value of documentRoot.
        +
        +
        Specified by:
        +
        setdocumentRoot in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update documentRoot, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocumentRoot

        +
        public java.lang.Boolean getdocumentRoot()
        +
        This method returns the value of documentRoot.
        +
        +
        Specified by:
        +
        getdocumentRoot in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of documentRoot, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        public void setjsonldPredicate(java.lang.String value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Specified by:
        +
        setjsonldPredicate in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        public void setjsonldPredicate(JsonldPredicate value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Specified by:
        +
        setjsonldPredicate in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a JsonldPredicate type.
        +
        +
        • +
      + + + +
        +
      • +

        getjsonldPredicate

        +
        public java.lang.Object getjsonldPredicate()
        +
        This method returns the value of jsonldPredicate.
        +
        +
        Specified by:
        +
        getjsonldPredicate in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of jsonldPredicate, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocParent

        +
        public void setdocParent(java.lang.String value)
        +
        This method sets the value of docParent.
        +
        +
        Specified by:
        +
        setdocParent in interface DocType
        +
        Specified by:
        +
        setdocParent in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocParent

        +
        public java.lang.String getdocParent()
        +
        This method returns the value of docParent.
        +
        +
        Specified by:
        +
        getdocParent in interface DocType
        +
        Specified by:
        +
        getdocParent in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Specified by:
        +
        setdoc in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Specified by:
        +
        setdoc in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface DocType
        +
        Specified by:
        +
        getdoc in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocAfter

        +
        public void setdocAfter(java.lang.String value)
        +
        This method sets the value of docAfter.
        +
        +
        Specified by:
        +
        setdocAfter in interface DocType
        +
        Specified by:
        +
        setdocAfter in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocAfter

        +
        public java.lang.String getdocAfter()
        +
        This method returns the value of docAfter.
        +
        +
        Specified by:
        +
        getdocAfter in interface DocType
        +
        Specified by:
        +
        getdocAfter in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        public void setdocChild(java.lang.String value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Specified by:
        +
        setdocChild in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docChild, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        public void setdocChild(java.lang.String[] value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Specified by:
        +
        setdocChild in interface SchemaDefinedType
        +
        Parameters:
        +
        value - will update docChild, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdocChild

        +
        public java.lang.Object getdocChild()
        +
        This method returns the value of docChild.
        +
        +
        Specified by:
        +
        getdocChild in interface DocType
        +
        Specified by:
        +
        getdocChild in interface SchemaDefinedType
        +
        Returns:
        +
        This method will return the value of docChild, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ScatterFeatureRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ScatterFeatureRequirement.html new file mode 100644 index 00000000..6b8b7002 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ScatterFeatureRequirement.html @@ -0,0 +1,341 @@ + + + + + +ScatterFeatureRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class ScatterFeatureRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.ScatterFeatureRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class ScatterFeatureRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Indicates that the workflow platform must support the `scatter` and `scatterMethod` fields of [WorkflowStep](#WorkflowStep).
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'ScatterFeatureRequirement'
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'ScatterFeatureRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        ScatterFeatureRequirement

        +
        public ScatterFeatureRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ScatterMethod.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ScatterMethod.html new file mode 100644 index 00000000..88d0da42 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ScatterMethod.html @@ -0,0 +1,352 @@ + + + + + +ScatterMethod + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Enum ScatterMethod

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<ScatterMethod>
      • +
    • +
        +
      • org.commonwl.lang.ScatterMethod
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<ScatterMethod>
    +
    +
    +
    +
    public enum ScatterMethod
+extends java.lang.Enum<ScatterMethod>
    +
    The scatter method, as described in [workflow step scatter](#WorkflowStep).
    +
    • +
+
+
+
    +
  • + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Static Methods Concrete Methods 
      Modifier and TypeMethod and Description
      static ScatterMethodvalueOf(java.lang.String name) +
      Returns the enum constant of this type with the specified name.
      +
      static ScatterMethod[]values() +
      Returns an array containing the constants of this enum type, in +the order they are declared.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Enum

        +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
        • +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +getClass, notify, notifyAll, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Enum Constant Detail

      + + + +
        +
      • +

        dotproduct

        +
        public static final ScatterMethod dotproduct
        +
        • +
      + + + +
        +
      • +

        nested_crossproduct

        +
        public static final ScatterMethod nested_crossproduct
        +
        • +
      + + + +
        +
      • +

        flat_crossproduct

        +
        public static final ScatterMethod flat_crossproduct
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static ScatterMethod[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (ScatterMethod c : ScatterMethod.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static ScatterMethod valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SchemaBase.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SchemaBase.html new file mode 100644 index 00000000..99ad6bba --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SchemaBase.html @@ -0,0 +1,293 @@ + + + + + +SchemaBase + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface SchemaBase

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        label

        +
        static final java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlabel

        +
        void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SchemaDefRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SchemaDefRequirement.html new file mode 100644 index 00000000..83ca8426 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SchemaDefRequirement.html @@ -0,0 +1,437 @@ + + + + + +SchemaDefRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SchemaDefRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.SchemaDefRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class SchemaDefRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    This field consists of an array of type definitions which must be used when interpreting the `inputs` and `outputs` fields. When a `type` field contain a IRI, the implementation must check if the type is defined in `schemaDefs` and use that definition. If the type is not found in `schemaDefs`, it is an error. The entries in `schemaDefs` must be processed in the order listed such that later schema definitions may refer to earlier schema definitions.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'SchemaDefRequirement'
      +
      (package private) java.lang.Objecttypes +
      The list of type definitions.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      java.lang.Objectgettypes() +
      This method returns the value of types.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsettypes(InputArraySchema[] value) +
      This method sets the value of types.
      +
      voidsettypes(InputEnumSchema[] value) +
      This method sets the value of types.
      +
      voidsettypes(InputRecordSchema[] value) +
      This method sets the value of types.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        types

        +
        java.lang.Object types
        +
        The list of type definitions.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'SchemaDefRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SchemaDefRequirement

        +
        public SchemaDefRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        settypes

        +
        public void settypes(InputEnumSchema[] value)
        +
        This method sets the value of types.
        +
        +
        Parameters:
        +
        value - will update types, which is a InputEnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settypes

        +
        public void settypes(InputArraySchema[] value)
        +
        This method sets the value of types.
        +
        +
        Parameters:
        +
        value - will update types, which is a InputArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settypes

        +
        public void settypes(InputRecordSchema[] value)
        +
        This method sets the value of types.
        +
        +
        Parameters:
        +
        value - will update types, which is a InputRecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        gettypes

        +
        public java.lang.Object gettypes()
        +
        This method returns the value of types.
        +
        +
        Returns:
        +
        This method will return the value of types, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SchemaDefinedType.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SchemaDefinedType.html new file mode 100644 index 00000000..d6fa1180 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SchemaDefinedType.html @@ -0,0 +1,655 @@ + + + + + +SchemaDefinedType + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface SchemaDefinedType

+
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      static java.lang.StringdocAfter +
      Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
      +
      static java.lang.ObjectdocChild +
      Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
      +
      static java.lang.StringdocParent +
      Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
      +
      static java.lang.BooleandocumentRoot +
      If true, indicates that the type is a valid at the document root.
      +
      static java.lang.ObjectjsonldPredicate +
      Annotate this type with linked data context.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Abstract Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.StringgetdocAfter() +
      This method returns the value of docAfter.
      +
      java.lang.ObjectgetdocChild() +
      This method returns the value of docChild.
      +
      java.lang.StringgetdocParent() +
      This method returns the value of docParent.
      +
      java.lang.BooleangetdocumentRoot() +
      This method returns the value of documentRoot.
      +
      java.lang.ObjectgetjsonldPredicate() +
      This method returns the value of jsonldPredicate.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetdocAfter(java.lang.String value) +
      This method sets the value of docAfter.
      +
      voidsetdocChild(java.lang.String value) +
      This method sets the value of docChild.
      +
      voidsetdocChild(java.lang.String[] value) +
      This method sets the value of docChild.
      +
      voidsetdocParent(java.lang.String value) +
      This method sets the value of docParent.
      +
      voidsetdocumentRoot(java.lang.Boolean value) +
      This method sets the value of documentRoot.
      +
      voidsetjsonldPredicate(JsonldPredicate value) +
      This method sets the value of jsonldPredicate.
      +
      voidsetjsonldPredicate(java.lang.String value) +
      This method sets the value of jsonldPredicate.
      +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        documentRoot

        +
        static final java.lang.Boolean documentRoot
        +
        If true, indicates that the type is a valid at the document root. At least one type in a schema must be tagged with `documentRoot: true`.
        +
        • +
      + + + +
        +
      • +

        jsonldPredicate

        +
        static final java.lang.Object jsonldPredicate
        +
        Annotate this type with linked data context.
        +
        • +
      + + + +
        +
      • +

        docParent

        +
        static final java.lang.String docParent
        +
        Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        static final java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        docAfter

        +
        static final java.lang.String docAfter
        +
        Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level.
        +
        • +
      + + + +
        +
      • +

        docChild

        +
        static final java.lang.Object docChild
        +
        Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setdocumentRoot

        +
        void setdocumentRoot(java.lang.Boolean value)
        +
        This method sets the value of documentRoot.
        +
        +
        Parameters:
        +
        value - will update documentRoot, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocumentRoot

        +
        java.lang.Boolean getdocumentRoot()
        +
        This method returns the value of documentRoot.
        +
        +
        Returns:
        +
        This method will return the value of documentRoot, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        void setjsonldPredicate(java.lang.String value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setjsonldPredicate

        +
        void setjsonldPredicate(JsonldPredicate value)
        +
        This method sets the value of jsonldPredicate.
        +
        +
        Parameters:
        +
        value - will update jsonldPredicate, which is a JsonldPredicate type.
        +
        +
        • +
      + + + +
        +
      • +

        getjsonldPredicate

        +
        java.lang.Object getjsonldPredicate()
        +
        This method returns the value of jsonldPredicate.
        +
        +
        Returns:
        +
        This method will return the value of jsonldPredicate, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocParent

        +
        void setdocParent(java.lang.String value)
        +
        This method sets the value of docParent.
        +
        +
        Specified by:
        +
        setdocParent in interface DocType
        +
        Parameters:
        +
        value - will update docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocParent

        +
        java.lang.String getdocParent()
        +
        This method returns the value of docParent.
        +
        +
        Specified by:
        +
        getdocParent in interface DocType
        +
        Returns:
        +
        This method will return the value of docParent, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface DocType
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface DocType
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocAfter

        +
        void setdocAfter(java.lang.String value)
        +
        This method sets the value of docAfter.
        +
        +
        Specified by:
        +
        setdocAfter in interface DocType
        +
        Parameters:
        +
        value - will update docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdocAfter

        +
        java.lang.String getdocAfter()
        +
        This method returns the value of docAfter.
        +
        +
        Specified by:
        +
        getdocAfter in interface DocType
        +
        Returns:
        +
        This method will return the value of docAfter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        void setdocChild(java.lang.String value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Parameters:
        +
        value - will update docChild, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdocChild

        +
        void setdocChild(java.lang.String[] value)
        +
        This method sets the value of docChild.
        +
        +
        Specified by:
        +
        setdocChild in interface DocType
        +
        Parameters:
        +
        value - will update docChild, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdocChild

        +
        java.lang.Object getdocChild()
        +
        This method returns the value of docChild.
        +
        +
        Specified by:
        +
        getdocChild in interface DocType
        +
        Returns:
        +
        This method will return the value of docChild, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ShellCommandRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ShellCommandRequirement.html new file mode 100644 index 00000000..61423e28 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/ShellCommandRequirement.html @@ -0,0 +1,341 @@ + + + + + +ShellCommandRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class ShellCommandRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.ShellCommandRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class ShellCommandRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Modify the behavior of CommandLineTool to generate a single string containing a shell command line. Each item in the argument list must be joined into a string separated by single spaces and quoted to prevent intepretation by the shell, unless `CommandLineBinding` for that argument contains `shellQuote: false`. If `shellQuote: false` is specified, the argument is joined into the command string without quoting, which allows the use of shell metacharacters such as `|` for pipes.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'ShellCommandRequirement'
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'ShellCommandRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        ShellCommandRequirement

        +
        public ShellCommandRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Sink.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Sink.html new file mode 100644 index 00000000..bf77ff26 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Sink.html @@ -0,0 +1,365 @@ + + + + + +Sink + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + +
+
org.commonwl.lang
+

Interface Sink

+
+
+
+
    +
  • +
    +
    All Known Implementing Classes:
    +
    WorkflowStepInput
    +
    +
    +
    +
    public interface Sink
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      static LinkMergeMethodlinkMerge +
      The method to use to merge multiple inbound links into a single array.
      +
      static java.lang.Objectsource +
      Specifies one or more workflow parameters that will provide input to the underlying step parameter.
      +
      +
      • +
    + + +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        linkMerge

        +
        static final LinkMergeMethod linkMerge
        +
        The method to use to merge multiple inbound links into a single array. If not specified, the default method is merge_nested.
        +
        • +
      + + + +
        +
      • +

        source

        +
        static final java.lang.Object source
        +
        Specifies one or more workflow parameters that will provide input to the underlying step parameter.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlinkMerge

        +
        void setlinkMerge(LinkMergeMethod value)
        +
        This method sets the value of linkMerge.
        +
        +
        Parameters:
        +
        value - will update linkMerge, which is a LinkMergeMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        getlinkMerge

        +
        LinkMergeMethod getlinkMerge()
        +
        This method returns the value of linkMerge.
        +
        +
        Returns:
        +
        This method will return the value of linkMerge, which is a LinkMergeMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        setsource

        +
        void setsource(java.lang.String value)
        +
        This method sets the value of source.
        +
        +
        Parameters:
        +
        value - will update source, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsource

        +
        void setsource(java.lang.String[] value)
        +
        This method sets the value of source.
        +
        +
        Parameters:
        +
        value - will update source, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getsource

        +
        java.lang.Object getsource()
        +
        This method returns the value of source.
        +
        +
        Returns:
        +
        This method will return the value of source, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Field | 
    • +
  • Constr | 
    • +
  • Method
    • +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SoftwarePackage.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SoftwarePackage.html new file mode 100644 index 00000000..016d2cd3 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SoftwarePackage.html @@ -0,0 +1,447 @@ + + + + + +SoftwarePackage + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SoftwarePackage

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.SoftwarePackage
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class SoftwarePackage
+extends java.lang.Object
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringpackage_value +
      The common name of the software to be configured.
      +
      (package private) java.lang.Stringspecs +
      Must be one or more IRIs identifying resources for installing or enabling the software.
      +
      (package private) java.lang.Stringversion +
      The (optional) version of the software to configured.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      SoftwarePackage() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetpackage() +
      This method returns the value of package_value.
      +
      java.lang.Stringgetspecs() +
      This method returns the value of specs.
      +
      java.lang.Stringgetversion() +
      This method returns the value of version.
      +
      voidsetpackage(java.lang.String value) +
      This method sets the value of package_value.
      +
      voidsetspecs(java.lang.String value) +
      This method sets the value of specs.
      +
      voidsetversion(java.lang.String value) +
      This method sets the value of version.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        specs

        +
        java.lang.String specs
        +
        Must be one or more IRIs identifying resources for installing or enabling the software. Implementations may provide resolvers which map well-known software spec IRIs to some configuration action. For example, an IRI `https://packages.debian.org/jessie/bowtie` could be resolved with `apt-get install bowtie`. An IRI `https://anaconda.org/bioconda/bowtie` could be resolved with `conda install -c bioconda bowtie`. Tools may also provide IRIs to index entries such as [RRID](http://www.identifiers.org/rrid/), such as `http://identifiers.org/rrid/RRID:SCR_005476`
        +
        • +
      + + + +
        +
      • +

        package_value

        +
        java.lang.String package_value
        +
        The common name of the software to be configured.
        +
        • +
      + + + +
        +
      • +

        version

        +
        java.lang.String version
        +
        The (optional) version of the software to configured.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SoftwarePackage

        +
        public SoftwarePackage()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setspecs

        +
        public void setspecs(java.lang.String value)
        +
        This method sets the value of specs.
        +
        +
        Parameters:
        +
        value - will update specs, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getspecs

        +
        public java.lang.String getspecs()
        +
        This method returns the value of specs.
        +
        +
        Returns:
        +
        This method will return the value of specs, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setpackage

        +
        public void setpackage(java.lang.String value)
        +
        This method sets the value of package_value.
        +
        +
        Parameters:
        +
        value - will update package_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getpackage

        +
        public java.lang.String getpackage()
        +
        This method returns the value of package_value.
        +
        +
        Returns:
        +
        This method will return the value of package_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setversion

        +
        public void setversion(java.lang.String value)
        +
        This method sets the value of version.
        +
        +
        Parameters:
        +
        value - will update version, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getversion

        +
        public java.lang.String getversion()
        +
        This method returns the value of version.
        +
        +
        Returns:
        +
        This method will return the value of version, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SoftwareRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SoftwareRequirement.html new file mode 100644 index 00000000..9905c532 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SoftwareRequirement.html @@ -0,0 +1,397 @@ + + + + + +SoftwareRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SoftwareRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.SoftwareRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class SoftwareRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    A list of software packages that should be configured in the environment of the defined process.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'SoftwareRequirement'
      +
      (package private) SoftwarePackagepackages +
      The list of software to be configured.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      SoftwarePackagegetpackages() +
      This method returns the value of packages.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      voidsetpackages(SoftwarePackage value) +
      This method sets the value of packages.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        packages

        +
        SoftwarePackage packages
        +
        The list of software to be configured.
        +
        • +
      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'SoftwareRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SoftwareRequirement

        +
        public SoftwareRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setpackages

        +
        public void setpackages(SoftwarePackage value)
        +
        This method sets the value of packages.
        +
        +
        Parameters:
        +
        value - will update packages, which is a SoftwarePackage type.
        +
        +
        • +
      + + + +
        +
      • +

        getpackages

        +
        public SoftwarePackage getpackages()
        +
        This method returns the value of packages.
        +
        +
        Returns:
        +
        This method will return the value of packages, which is a SoftwarePackage type.
        +
        +
        • +
      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SpecializeDef.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SpecializeDef.html new file mode 100644 index 00000000..ded42823 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SpecializeDef.html @@ -0,0 +1,391 @@ + + + + + +SpecializeDef + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SpecializeDef

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.SpecializeDef
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class SpecializeDef
+extends java.lang.Object
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.StringspecializeFrom +
      The data type to be replaced
      +
      (package private) java.lang.StringspecializeTo +
      The new data type to replace with
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      SpecializeDef() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.StringgetspecializeFrom() +
      This method returns the value of specializeFrom.
      +
      java.lang.StringgetspecializeTo() +
      This method returns the value of specializeTo.
      +
      voidsetspecializeFrom(java.lang.String value) +
      This method sets the value of specializeFrom.
      +
      voidsetspecializeTo(java.lang.String value) +
      This method sets the value of specializeTo.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        specializeFrom

        +
        java.lang.String specializeFrom
        +
        The data type to be replaced
        +
        • +
      + + + +
        +
      • +

        specializeTo

        +
        java.lang.String specializeTo
        +
        The new data type to replace with
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SpecializeDef

        +
        public SpecializeDef()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setspecializeFrom

        +
        public void setspecializeFrom(java.lang.String value)
        +
        This method sets the value of specializeFrom.
        +
        +
        Parameters:
        +
        value - will update specializeFrom, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getspecializeFrom

        +
        public java.lang.String getspecializeFrom()
        +
        This method returns the value of specializeFrom.
        +
        +
        Returns:
        +
        This method will return the value of specializeFrom, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setspecializeTo

        +
        public void setspecializeTo(java.lang.String value)
        +
        This method sets the value of specializeTo.
        +
        +
        Parameters:
        +
        value - will update specializeTo, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getspecializeTo

        +
        public java.lang.String getspecializeTo()
        +
        This method returns the value of specializeTo.
        +
        +
        Returns:
        +
        This method will return the value of specializeTo, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/StepInputExpressionRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/StepInputExpressionRequirement.html new file mode 100644 index 00000000..5f18fb92 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/StepInputExpressionRequirement.html @@ -0,0 +1,341 @@ + + + + + +StepInputExpressionRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class StepInputExpressionRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.StepInputExpressionRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class StepInputExpressionRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Indicate that the workflow platform must support the `valueFrom` field of [WorkflowStepInput](#WorkflowStepInput).
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'StepInputExpressionRequirement'
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'StepInputExpressionRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        StepInputExpressionRequirement

        +
        public StepInputExpressionRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SubworkflowFeatureRequirement.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SubworkflowFeatureRequirement.html new file mode 100644 index 00000000..872ea6d6 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/SubworkflowFeatureRequirement.html @@ -0,0 +1,341 @@ + + + + + +SubworkflowFeatureRequirement + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class SubworkflowFeatureRequirement

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.SubworkflowFeatureRequirement
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    ProcessRequirement
    +
    +
    +
    +
    public class SubworkflowFeatureRequirement
+extends java.lang.Object
+implements ProcessRequirement
    +
    Indicates that the workflow platform must support nested workflows in the `run` field of [WorkflowStep](#WorkflowStep).
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringclass_value +
      Always 'SubworkflowFeatureRequirement'
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetclass() +
      This method returns the value of class_value.
      +
      voidsetclass(java.lang.String value) +
      This method sets the value of class_value.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        Always 'SubworkflowFeatureRequirement'
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SubworkflowFeatureRequirement

        +
        public SubworkflowFeatureRequirement()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Workflow.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Workflow.html new file mode 100644 index 00000000..fce0d399 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/Workflow.html @@ -0,0 +1,1138 @@ + + + + + +Workflow + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class Workflow

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.Workflow
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Process
    +
    +
    +
    +
    public class Workflow
+extends java.lang.Object
+implements Process
    +
    A workflow describes a set of **steps** and the **dependencies** between those steps. When a step produces output that will be consumed by a second step, the first step is a dependency of the second step.
    +
    • +
+
+
+ +
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        class_value

        +
        java.lang.String class_value
        +
        • +
      + + + +
        +
      • +

        steps

        +
        WorkflowStep[] steps
        +
        The individual steps that make up the workflow. Each step is executed when all of its input data links are fufilled. An implementation may choose to execute the steps in a different order than listed and/or execute steps concurrently, provided that dependencies between steps are met.
        +
        • +
      + + + +
        +
      • +

        outputs

        +
        WorkflowOutputParameter[] outputs
        +
        Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.
        +
        • +
      + + + +
        +
      • +

        requirements

        +
        java.lang.Object requirements
        +
        Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
        +
        • +
      + + + +
        +
      • +

        cwlVersion

        +
        CWLVersion cwlVersion
        +
        CWL document version. Always required at the document root. Not required for a Process embedded inside another Process.
        +
        • +
      + + + +
        +
      • +

        inputs

        +
        InputParameter[] inputs
        +
        Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object.
        +
        • +
      + + + +
        +
      • +

        hints

        +
        Any hints
        +
        Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A long, human-readable description of this process object.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this process object.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        Workflow

        +
        public Workflow()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setclass

        +
        public void setclass(java.lang.String value)
        +
        This method sets the value of class_value.
        +
        +
        Parameters:
        +
        value - will update class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getclass

        +
        public java.lang.String getclass()
        +
        This method returns the value of class_value.
        +
        +
        Returns:
        +
        This method will return the value of class_value, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsteps

        +
        public void setsteps(WorkflowStep[] value)
        +
        This method sets the value of steps.
        +
        +
        Parameters:
        +
        value - will update steps, which is a WorkflowStep array.
        +
        +
        • +
      + + + +
        +
      • +

        getsteps

        +
        public WorkflowStep[] getsteps()
        +
        This method returns the value of steps.
        +
        +
        Returns:
        +
        This method will return the value of steps, which is a WorkflowStep array.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputs

        +
        public void setoutputs(WorkflowOutputParameter[] value)
        +
        This method sets the value of outputs.
        +
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputs

        +
        public void setoutputs(OutputParameter[] value)
        +
        This is a dummy method which has no functionality, and is required + for implementing an interface method that was previously specialized.
        +
        +
        Specified by:
        +
        setoutputs in interface Process
        +
        Parameters:
        +
        value - will update outputs, which is a OutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputs

        +
        public WorkflowOutputParameter[] getoutputs()
        +
        This method returns the value of outputs.
        +
        +
        Specified by:
        +
        getoutputs in interface Process
        +
        Returns:
        +
        This method will return the value of outputs, which is a WorkflowOutputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(StepInputExpressionRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a StepInputExpressionRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(MultipleInputFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a MultipleInputFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SoftwareRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SoftwareRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SchemaDefRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SchemaDefRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InitialWorkDirRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a InitialWorkDirRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(EnvVarRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a EnvVarRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(DockerRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a DockerRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ResourceRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ResourceRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InlineJavascriptRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a InlineJavascriptRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ShellCommandRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ShellCommandRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ScatterFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a ScatterFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SubworkflowFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Specified by:
        +
        setrequirements in interface Process
        +
        Parameters:
        +
        value - will update requirements, which is a SubworkflowFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        getrequirements

        +
        public java.lang.Object getrequirements()
        +
        This method returns the value of requirements.
        +
        +
        Specified by:
        +
        getrequirements in interface Process
        +
        Returns:
        +
        This method will return the value of requirements, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setcwlVersion

        +
        public void setcwlVersion(CWLVersion value)
        +
        This method sets the value of cwlVersion.
        +
        +
        Specified by:
        +
        setcwlVersion in interface Process
        +
        Parameters:
        +
        value - will update cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        getcwlVersion

        +
        public CWLVersion getcwlVersion()
        +
        This method returns the value of cwlVersion.
        +
        +
        Specified by:
        +
        getcwlVersion in interface Process
        +
        Returns:
        +
        This method will return the value of cwlVersion, which is a CWLVersion type.
        +
        +
        • +
      + + + +
        +
      • +

        setinputs

        +
        public void setinputs(InputParameter[] value)
        +
        This method sets the value of inputs.
        +
        +
        Specified by:
        +
        setinputs in interface Process
        +
        Parameters:
        +
        value - will update inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        getinputs

        +
        public InputParameter[] getinputs()
        +
        This method returns the value of inputs.
        +
        +
        Specified by:
        +
        getinputs in interface Process
        +
        Returns:
        +
        This method will return the value of inputs, which is a InputParameter array.
        +
        +
        • +
      + + + +
        +
      • +

        sethints

        +
        public void sethints(Any value)
        +
        This method sets the value of hints.
        +
        +
        Specified by:
        +
        sethints in interface Process
        +
        Parameters:
        +
        value - will update hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        gethints

        +
        public Any gethints()
        +
        This method returns the value of hints.
        +
        +
        Specified by:
        +
        gethints in interface Process
        +
        Returns:
        +
        This method will return the value of hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Process
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Process
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Specified by:
        +
        setid in interface Process
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Specified by:
        +
        getid in interface Process
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Process
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Process
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
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+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/WorkflowOutputParameter.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/WorkflowOutputParameter.html new file mode 100644 index 00000000..387b41f9 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/WorkflowOutputParameter.html @@ -0,0 +1,1245 @@ + + + + + +WorkflowOutputParameter + + + + + + + + +
+ + +
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+ + + + +
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+ + +
+ + +
+
org.commonwl.lang
+

Class WorkflowOutputParameter

+
+
+ +
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Parameter, SchemaBase
    +
    +
    +
    +
    public class WorkflowOutputParameter
+extends OutputParameter
    +
    Describe an output parameter of a workflow. The parameter must be connected to one or more parameters defined in the workflow that will provide the value of the output parameter.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Objectdoc +
      A documentation string for this type, or an array of strings which should be concatenated.
      +
      (package private) java.lang.Objectformat +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this parameter object.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this object.
      +
      (package private) LinkMergeMethodlinkMerge +
      The method to use to merge multiple sources into a single array.
      +
      (package private) CommandOutputBindingoutputBinding +
      Describes how to handle the outputs of a process.
      +
      (package private) java.lang.ObjectoutputSource +
      Specifies one or more workflow parameters that supply the value of to the output parameter.
      +
      (package private) java.lang.ObjectsecondaryFiles +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Booleanstreamable +
      Only valid when `type: File` or is an array of `items: File`.
      +
      (package private) java.lang.Objecttype +
      Specify valid types of data that may be assigned to this parameter.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Objectgetdoc() +
      This method returns the value of doc.
      +
      java.lang.Objectgetformat() +
      This method returns the value of format.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      java.lang.Stringgetlabel() +
      This method returns the value of label.
      +
      LinkMergeMethodgetlinkMerge() +
      This method returns the value of linkMerge.
      +
      CommandOutputBindinggetoutputBinding() +
      This method returns the value of outputBinding.
      +
      java.lang.ObjectgetoutputSource() +
      This method returns the value of outputSource.
      +
      java.lang.ObjectgetsecondaryFiles() +
      This method returns the value of secondaryFiles.
      +
      java.lang.Booleangetstreamable() +
      This method returns the value of streamable.
      +
      java.lang.Objectgettype() +
      This method returns the value of type.
      +
      voidsetdoc(java.lang.String value) +
      This method sets the value of doc.
      +
      voidsetdoc(java.lang.String[] value) +
      This method sets the value of doc.
      +
      voidsetformat(Expression[] value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String value) +
      This method sets the value of format.
      +
      voidsetformat(java.lang.String[] value) +
      This method sets the value of format.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetlabel(java.lang.String value) +
      This method sets the value of label.
      +
      voidsetlinkMerge(LinkMergeMethod value) +
      This method sets the value of linkMerge.
      +
      voidsetoutputBinding(CommandOutputBinding value) +
      This method sets the value of outputBinding.
      +
      voidsetoutputSource(java.lang.String value) +
      This method sets the value of outputSource.
      +
      voidsetoutputSource(java.lang.String[] value) +
      This method sets the value of outputSource.
      +
      voidsetsecondaryFiles(Expression value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(Expression[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String value) +
      This method sets the value of secondaryFiles.
      +
      voidsetsecondaryFiles(java.lang.String[] value) +
      This method sets the value of secondaryFiles.
      +
      voidsetstreamable(java.lang.Boolean value) +
      This method sets the value of streamable.
      +
      voidsettype(CWLType value) +
      This method sets the value of type.
      +
      voidsettype(CWLType[] value) +
      This method sets the value of type.
      +
      voidsettype(OutputArraySchema value) +
      This method sets the value of type.
      +
      voidsettype(OutputArraySchema[] value) +
      This method sets the value of type.
      +
      voidsettype(OutputEnumSchema value) +
      This method sets the value of type.
      +
      voidsettype(OutputEnumSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(OutputRecordSchema value) +
      This method sets the value of type.
      +
      voidsettype(OutputRecordSchema[] value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String value) +
      This method sets the value of type.
      +
      voidsettype(java.lang.String[] value) +
      This method sets the value of type.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        linkMerge

        +
        LinkMergeMethod linkMerge
        +
        The method to use to merge multiple sources into a single array. If not specified, the default method is merge_nested.
        +
        • +
      + + + +
        +
      • +

        outputSource

        +
        java.lang.Object outputSource
        +
        Specifies one or more workflow parameters that supply the value of to the output parameter.
        +
        • +
      + + + +
        +
      • +

        type

        +
        java.lang.Object type
        +
        Specify valid types of data that may be assigned to this parameter.
        +
        • +
      + + + +
        +
      • +

        outputBinding

        +
        CommandOutputBinding outputBinding
        +
        Describes how to handle the outputs of a process.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this parameter object.
        +
        • +
      + + + +
        +
      • +

        streamable

        +
        java.lang.Boolean streamable
        +
        Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`.
        +
        • +
      + + + +
        +
      • +

        format

        +
        java.lang.Object format
        +
        Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.Object doc
        +
        A documentation string for this type, or an array of strings which should be concatenated.
        +
        • +
      + + + +
        +
      • +

        secondaryFiles

        +
        java.lang.Object secondaryFiles
        +
        Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        WorkflowOutputParameter

        +
        public WorkflowOutputParameter()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setlinkMerge

        +
        public void setlinkMerge(LinkMergeMethod value)
        +
        This method sets the value of linkMerge.
        +
        +
        Parameters:
        +
        value - will update linkMerge, which is a LinkMergeMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        getlinkMerge

        +
        public LinkMergeMethod getlinkMerge()
        +
        This method returns the value of linkMerge.
        +
        +
        Returns:
        +
        This method will return the value of linkMerge, which is a LinkMergeMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputSource

        +
        public void setoutputSource(java.lang.String value)
        +
        This method sets the value of outputSource.
        +
        +
        Parameters:
        +
        value - will update outputSource, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputSource

        +
        public void setoutputSource(java.lang.String[] value)
        +
        This method sets the value of outputSource.
        +
        +
        Parameters:
        +
        value - will update outputSource, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputSource

        +
        public java.lang.Object getoutputSource()
        +
        This method returns the value of outputSource.
        +
        +
        Returns:
        +
        This method will return the value of outputSource, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputRecordSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputRecordSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputEnumSchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputEnumSchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputRecordSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputRecordSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputEnumSchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputEnumSchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputArraySchema value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputArraySchema type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(OutputArraySchema[] value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a OutputArraySchema array.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(CWLType value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a CWLType type.
        +
        +
        • +
      + + + +
        +
      • +

        settype

        +
        public void settype(java.lang.String value)
        +
        This method sets the value of type.
        +
        +
        Parameters:
        +
        value - will update type, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        gettype

        +
        public java.lang.Object gettype()
        +
        This method returns the value of type.
        +
        +
        Returns:
        +
        This method will return the value of type, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setoutputBinding

        +
        public void setoutputBinding(CommandOutputBinding value)
        +
        This method sets the value of outputBinding.
        +
        +
        Overrides:
        +
        setoutputBinding in class OutputParameter
        +
        Parameters:
        +
        value - will update outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        getoutputBinding

        +
        public CommandOutputBinding getoutputBinding()
        +
        This method returns the value of outputBinding.
        +
        +
        Overrides:
        +
        getoutputBinding in class OutputParameter
        +
        Returns:
        +
        This method will return the value of outputBinding, which is a CommandOutputBinding type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Overrides:
        +
        setid in class OutputParameter
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Overrides:
        +
        getid in class OutputParameter
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setstreamable

        +
        public void setstreamable(java.lang.Boolean value)
        +
        This method sets the value of streamable.
        +
        +
        Specified by:
        +
        setstreamable in interface Parameter
        +
        Overrides:
        +
        setstreamable in class OutputParameter
        +
        Parameters:
        +
        value - will update streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        getstreamable

        +
        public java.lang.Boolean getstreamable()
        +
        This method returns the value of streamable.
        +
        +
        Specified by:
        +
        getstreamable in interface Parameter
        +
        Overrides:
        +
        getstreamable in class OutputParameter
        +
        Returns:
        +
        This method will return the value of streamable, which is a Boolean type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(Expression[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a Expression array.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setformat

        +
        public void setformat(java.lang.String[] value)
        +
        This method sets the value of format.
        +
        +
        Specified by:
        +
        setformat in interface Parameter
        +
        Overrides:
        +
        setformat in class OutputParameter
        +
        Parameters:
        +
        value - will update format, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getformat

        +
        public java.lang.Object getformat()
        +
        This method returns the value of format.
        +
        +
        Specified by:
        +
        getformat in interface Parameter
        +
        Overrides:
        +
        getformat in class OutputParameter
        +
        Returns:
        +
        This method will return the value of format, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class OutputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String[] value)
        +
        This method sets the value of doc.
        +
        +
        Specified by:
        +
        setdoc in interface Parameter
        +
        Overrides:
        +
        setdoc in class OutputParameter
        +
        Parameters:
        +
        value - will update doc, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.Object getdoc()
        +
        This method returns the value of doc.
        +
        +
        Specified by:
        +
        getdoc in interface Parameter
        +
        Overrides:
        +
        getdoc in class OutputParameter
        +
        Returns:
        +
        This method will return the value of doc, which is a Object type.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class OutputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsecondaryFiles

        +
        public void setsecondaryFiles(java.lang.String[] value)
        +
        This method sets the value of secondaryFiles.
        +
        +
        Specified by:
        +
        setsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        setsecondaryFiles in class OutputParameter
        +
        Parameters:
        +
        value - will update secondaryFiles, which is a String array.
        +
        +
        • +
      + + + + + + + +
        +
      • +

        getsecondaryFiles

        +
        public java.lang.Object getsecondaryFiles()
        +
        This method returns the value of secondaryFiles.
        +
        +
        Specified by:
        +
        getsecondaryFiles in interface Parameter
        +
        Overrides:
        +
        getsecondaryFiles in class OutputParameter
        +
        Returns:
        +
        This method will return the value of secondaryFiles, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Specified by:
        +
        setlabel in interface Parameter
        +
        Specified by:
        +
        setlabel in interface SchemaBase
        +
        Overrides:
        +
        setlabel in class OutputParameter
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Specified by:
        +
        getlabel in interface Parameter
        +
        Specified by:
        +
        getlabel in interface SchemaBase
        +
        Overrides:
        +
        getlabel in class OutputParameter
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
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+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/WorkflowStep.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/WorkflowStep.html new file mode 100644 index 00000000..d7689d4b --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/WorkflowStep.html @@ -0,0 +1,1157 @@ + + + + + +WorkflowStep + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class WorkflowStep

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.WorkflowStep
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class WorkflowStep
+extends java.lang.Object
    +
    A workflow step is an executable element of a workflow. It specifies the underlying process implementation (such as `CommandLineTool` or another `Workflow`) in the `run` field and connects the input and output parameters of the underlying process to workflow parameters.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringdoc +
      A long, human-readable description of this process object.
      +
      (package private) Anyhints +
      Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this workflow step.
      +
      (package private) java.lang.Stringid +
      The unique identifier for this workflow step.
      +
      (package private) WorkflowStepInputin +
      Defines the input parameters of the workflow step.
      +
      (package private) java.lang.Stringlabel +
      A short, human-readable label of this process object.
      +
      (package private) java.lang.Objectout +
      Defines the parameters representing the output of the process.
      +
      (package private) java.lang.Objectrequirements +
      Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this workflow step.
      +
      (package private) java.lang.Objectrun +
      Specifies the process to run.
      +
      (package private) java.lang.Objectscatter 
      (package private) ScatterMethodscatterMethod +
      Required if `scatter` is an array of more than one element.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      WorkflowStep() 
      +
      • +
    + + +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        requirements

        +
        java.lang.Object requirements
        +
        Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this workflow step. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
        +
        • +
      + + + +
        +
      • +

        in

        +
        WorkflowStepInput in
        +
        Defines the input parameters of the workflow step. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used build a user interface for constructing the input object.
        +
        • +
      + + + +
        +
      • +

        hints

        +
        Any hints
        +
        Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this workflow step. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning.
        +
        • +
      + + + +
        +
      • +

        scatter

        +
        java.lang.Object scatter
        +
        • +
      + + + +
        +
      • +

        scatterMethod

        +
        ScatterMethod scatterMethod
        +
        Required if `scatter` is an array of more than one element.
        +
        • +
      + + + +
        +
      • +

        doc

        +
        java.lang.String doc
        +
        A long, human-readable description of this process object.
        +
        • +
      + + + +
        +
      • +

        run

        +
        java.lang.Object run
        +
        Specifies the process to run.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        The unique identifier for this workflow step.
        +
        • +
      + + + +
        +
      • +

        label

        +
        java.lang.String label
        +
        A short, human-readable label of this process object.
        +
        • +
      + + + +
        +
      • +

        out

        +
        java.lang.Object out
        +
        Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        WorkflowStep

        +
        public WorkflowStep()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(StepInputExpressionRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a StepInputExpressionRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(MultipleInputFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a MultipleInputFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SoftwareRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a SoftwareRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SchemaDefRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a SchemaDefRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InitialWorkDirRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a InitialWorkDirRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(EnvVarRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a EnvVarRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(DockerRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a DockerRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ResourceRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a ResourceRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(InlineJavascriptRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a InlineJavascriptRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ShellCommandRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a ShellCommandRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(ScatterFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a ScatterFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        setrequirements

        +
        public void setrequirements(SubworkflowFeatureRequirement value)
        +
        This method sets the value of requirements.
        +
        +
        Parameters:
        +
        value - will update requirements, which is a SubworkflowFeatureRequirement type.
        +
        +
        • +
      + + + +
        +
      • +

        getrequirements

        +
        public java.lang.Object getrequirements()
        +
        This method returns the value of requirements.
        +
        +
        Returns:
        +
        This method will return the value of requirements, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setin

        +
        public void setin(WorkflowStepInput value)
        +
        This method sets the value of in.
        +
        +
        Parameters:
        +
        value - will update in, which is a WorkflowStepInput type.
        +
        +
        • +
      + + + +
        +
      • +

        getin

        +
        public WorkflowStepInput getin()
        +
        This method returns the value of in.
        +
        +
        Returns:
        +
        This method will return the value of in, which is a WorkflowStepInput type.
        +
        +
        • +
      + + + +
        +
      • +

        sethints

        +
        public void sethints(Any value)
        +
        This method sets the value of hints.
        +
        +
        Parameters:
        +
        value - will update hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        gethints

        +
        public Any gethints()
        +
        This method returns the value of hints.
        +
        +
        Returns:
        +
        This method will return the value of hints, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setscatter

        +
        public void setscatter(java.lang.String value)
        +
        This method sets the value of scatter.
        +
        +
        Parameters:
        +
        value - will update scatter, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setscatter

        +
        public void setscatter(java.lang.String[] value)
        +
        This method sets the value of scatter.
        +
        +
        Parameters:
        +
        value - will update scatter, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getscatter

        +
        public java.lang.Object getscatter()
        +
        This method returns the value of scatter.
        +
        +
        Returns:
        +
        This method will return the value of scatter, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setscatterMethod

        +
        public void setscatterMethod(ScatterMethod value)
        +
        This method sets the value of scatterMethod.
        +
        +
        Parameters:
        +
        value - will update scatterMethod, which is a ScatterMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        getscatterMethod

        +
        public ScatterMethod getscatterMethod()
        +
        This method returns the value of scatterMethod.
        +
        +
        Returns:
        +
        This method will return the value of scatterMethod, which is a ScatterMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        setdoc

        +
        public void setdoc(java.lang.String value)
        +
        This method sets the value of doc.
        +
        +
        Parameters:
        +
        value - will update doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getdoc

        +
        public java.lang.String getdoc()
        +
        This method returns the value of doc.
        +
        +
        Returns:
        +
        This method will return the value of doc, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setrun

        +
        public void setrun(CommandLineTool value)
        +
        This method sets the value of run.
        +
        +
        Parameters:
        +
        value - will update run, which is a CommandLineTool type.
        +
        +
        • +
      + + + +
        +
      • +

        setrun

        +
        public void setrun(java.lang.String value)
        +
        This method sets the value of run.
        +
        +
        Parameters:
        +
        value - will update run, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setrun

        +
        public void setrun(Workflow value)
        +
        This method sets the value of run.
        +
        +
        Parameters:
        +
        value - will update run, which is a Workflow type.
        +
        +
        • +
      + + + +
        +
      • +

        setrun

        +
        public void setrun(ExpressionTool value)
        +
        This method sets the value of run.
        +
        +
        Parameters:
        +
        value - will update run, which is a ExpressionTool type.
        +
        +
        • +
      + + + +
        +
      • +

        getrun

        +
        public java.lang.Object getrun()
        +
        This method returns the value of run.
        +
        +
        Returns:
        +
        This method will return the value of run, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setlabel

        +
        public void setlabel(java.lang.String value)
        +
        This method sets the value of label.
        +
        +
        Parameters:
        +
        value - will update label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getlabel

        +
        public java.lang.String getlabel()
        +
        This method returns the value of label.
        +
        +
        Returns:
        +
        This method will return the value of label, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setout

        +
        public void setout(WorkflowStepOutput[] value)
        +
        This method sets the value of out.
        +
        +
        Parameters:
        +
        value - will update out, which is a WorkflowStepOutput array.
        +
        +
        • +
      + + + +
        +
      • +

        setout

        +
        public void setout(java.lang.String[] value)
        +
        This method sets the value of out.
        +
        +
        Parameters:
        +
        value - will update out, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getout

        +
        public java.lang.Object getout()
        +
        This method returns the value of out.
        +
        +
        Returns:
        +
        This method will return the value of out, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/WorkflowStepInput.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/WorkflowStepInput.html new file mode 100644 index 00000000..a75bf66e --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/WorkflowStepInput.html @@ -0,0 +1,615 @@ + + + + + +WorkflowStepInput + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class WorkflowStepInput

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.WorkflowStepInput
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    Sink
    +
    +
    +
    +
    public class WorkflowStepInput
+extends java.lang.Object
+implements Sink
    +
    The input of a workflow step connects an upstream parameter (from the workflow inputs, or the outputs of other workflows steps) with the input parameters of the underlying step.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) Anydefault_value +
      The default value for this parameter if there is no `source` field.
      +
      (package private) java.lang.Stringid +
      A unique identifier for this workflow input parameter.
      +
      (package private) LinkMergeMethodlinkMerge +
      The method to use to merge multiple inbound links into a single array.
      +
      (package private) java.lang.Objectsource +
      Specifies one or more workflow parameters that will provide input to the underlying step parameter.
      +
      (package private) java.lang.ObjectvalueFrom +
      To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must be specified in the workflow or workflow step requirements.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      WorkflowStepInput() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      Anygetdefault() +
      This method returns the value of default_value.
      +
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      LinkMergeMethodgetlinkMerge() +
      This method returns the value of linkMerge.
      +
      java.lang.Objectgetsource() +
      This method returns the value of source.
      +
      java.lang.ObjectgetvalueFrom() +
      This method returns the value of valueFrom.
      +
      voidsetdefault(Any value) +
      This method sets the value of default_value.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      voidsetlinkMerge(LinkMergeMethod value) +
      This method sets the value of linkMerge.
      +
      voidsetsource(java.lang.String value) +
      This method sets the value of source.
      +
      voidsetsource(java.lang.String[] value) +
      This method sets the value of source.
      +
      voidsetvalueFrom(Expression value) +
      This method sets the value of valueFrom.
      +
      voidsetvalueFrom(java.lang.String value) +
      This method sets the value of valueFrom.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        default_value

        +
        Any default_value
        +
        The default value for this parameter if there is no `source` field.
        +
        • +
      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        A unique identifier for this workflow input parameter.
        +
        • +
      + + + +
        +
      • +

        valueFrom

        +
        java.lang.Object valueFrom
        +
        To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must be specified in the workflow or workflow step requirements. If `valueFrom` is a constant string value, use this as the value for this input parameter. If `valueFrom` is a parameter reference or expression, it must be evaluated to yield the actual value to be assiged to the input field. The `self` value of in the parameter reference or expression must be the value of the parameter(s) specified in the `source` field, or null if there is no `source` field. The value of `inputs` in the parameter reference or expression must be the input object to the workflow step after assigning the `source` values and then scattering. The order of evaluating `valueFrom` among step input parameters is undefined and the result of evaluating `valueFrom` on a parameter must not be visible to evaluation of `valueFrom` on other parameters.
        +
        • +
      + + + +
        +
      • +

        linkMerge

        +
        LinkMergeMethod linkMerge
        +
        The method to use to merge multiple inbound links into a single array. If not specified, the default method is merge_nested.
        +
        • +
      + + + +
        +
      • +

        source

        +
        java.lang.Object source
        +
        Specifies one or more workflow parameters that will provide input to the underlying step parameter.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        WorkflowStepInput

        +
        public WorkflowStepInput()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setdefault

        +
        public void setdefault(Any value)
        +
        This method sets the value of default_value.
        +
        +
        Parameters:
        +
        value - will update default_value, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        getdefault

        +
        public Any getdefault()
        +
        This method returns the value of default_value.
        +
        +
        Returns:
        +
        This method will return the value of default_value, which is a Any type.
        +
        +
        • +
      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setvalueFrom

        +
        public void setvalueFrom(java.lang.String value)
        +
        This method sets the value of valueFrom.
        +
        +
        Parameters:
        +
        value - will update valueFrom, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setvalueFrom

        +
        public void setvalueFrom(Expression value)
        +
        This method sets the value of valueFrom.
        +
        +
        Parameters:
        +
        value - will update valueFrom, which is a Expression type.
        +
        +
        • +
      + + + +
        +
      • +

        getvalueFrom

        +
        public java.lang.Object getvalueFrom()
        +
        This method returns the value of valueFrom.
        +
        +
        Returns:
        +
        This method will return the value of valueFrom, which is a Object type.
        +
        +
        • +
      + + + +
        +
      • +

        setlinkMerge

        +
        public void setlinkMerge(LinkMergeMethod value)
        +
        This method sets the value of linkMerge.
        +
        +
        Specified by:
        +
        setlinkMerge in interface Sink
        +
        Parameters:
        +
        value - will update linkMerge, which is a LinkMergeMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        getlinkMerge

        +
        public LinkMergeMethod getlinkMerge()
        +
        This method returns the value of linkMerge.
        +
        +
        Specified by:
        +
        getlinkMerge in interface Sink
        +
        Returns:
        +
        This method will return the value of linkMerge, which is a LinkMergeMethod type.
        +
        +
        • +
      + + + +
        +
      • +

        setsource

        +
        public void setsource(java.lang.String value)
        +
        This method sets the value of source.
        +
        +
        Specified by:
        +
        setsource in interface Sink
        +
        Parameters:
        +
        value - will update source, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        setsource

        +
        public void setsource(java.lang.String[] value)
        +
        This method sets the value of source.
        +
        +
        Specified by:
        +
        setsource in interface Sink
        +
        Parameters:
        +
        value - will update source, which is a String array.
        +
        +
        • +
      + + + +
        +
      • +

        getsource

        +
        public java.lang.Object getsource()
        +
        This method returns the value of source.
        +
        +
        Specified by:
        +
        getsource in interface Sink
        +
        Returns:
        +
        This method will return the value of source, which is a Object type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/WorkflowStepOutput.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/WorkflowStepOutput.html new file mode 100644 index 00000000..f97d266a --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/WorkflowStepOutput.html @@ -0,0 +1,336 @@ + + + + + +WorkflowStepOutput + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.lang
+

Class WorkflowStepOutput

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.lang.WorkflowStepOutput
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class WorkflowStepOutput
+extends java.lang.Object
    +
    Associate an output parameter of the underlying process with a workflow parameter. The workflow parameter (given in the `id` field) be may be used as a `source` to connect with input parameters of other workflow steps, or with an output parameter of the process.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.Stringid +
      A unique identifier for this workflow output parameter.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      WorkflowStepOutput() 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.Stringgetid() +
      This method returns the value of id.
      +
      voidsetid(java.lang.String value) +
      This method sets the value of id.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        id

        +
        java.lang.String id
        +
        A unique identifier for this workflow output parameter. This is the identifier to use in the `source` field of `WorkflowStepInput` to connect the output value to downstream parameters.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        WorkflowStepOutput

        +
        public WorkflowStepOutput()
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        setid

        +
        public void setid(java.lang.String value)
        +
        This method sets the value of id.
        +
        +
        Parameters:
        +
        value - will update id, which is a String type.
        +
        +
        • +
      + + + +
        +
      • +

        getid

        +
        public java.lang.String getid()
        +
        This method returns the value of id.
        +
        +
        Returns:
        +
        This method will return the value of id, which is a String type.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/package-frame.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/package-frame.html new file mode 100644 index 00000000..548b29cc --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/package-frame.html @@ -0,0 +1,103 @@ + + + + + +org.commonwl.lang + + + + + +

org.commonwl.lang

+
+

Interfaces

+ +

Classes

+ +

Enums

+ +
+ + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/package-summary.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/package-summary.html new file mode 100644 index 00000000..15a5562c --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/package-summary.html @@ -0,0 +1,558 @@ + + + + + +org.commonwl.lang + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+ + +
+ +
+

Package org.commonwl.lang

+
+
+ +
+ +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/package-tree.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/package-tree.html new file mode 100644 index 00000000..7b0ed3ae --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/package-tree.html @@ -0,0 +1,274 @@ + + + + + +org.commonwl.lang Class Hierarchy + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+ + +
+ +
+

Hierarchy For Package org.commonwl.lang

+Package Hierarchies: + +
+
+

Class Hierarchy

+ +

Interface Hierarchy

+ +

Enum Hierarchy

+ +
+ +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/stderr.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/stderr.html new file mode 100644 index 00000000..572bb34d --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/stderr.html @@ -0,0 +1,294 @@ + + + + + +stderr + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Enum stderr

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<stderr>
      • +
    • +
        +
      • org.commonwl.lang.stderr
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<stderr>
    +
    +
    +
    +
    public enum stderr
+extends java.lang.Enum<stderr>
    +
    Only valid as a `type` for a `CommandLineTool` output with no `outputBinding` set.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Static Methods Concrete Methods 
      Modifier and TypeMethod and Description
      static stderrvalueOf(java.lang.String name) +
      Returns the enum constant of this type with the specified name.
      +
      static stderr[]values() +
      Returns an array containing the constants of this enum type, in +the order they are declared.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Enum

        +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
        • +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +getClass, notify, notifyAll, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static stderr[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (stderr c : stderr.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static stderr valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/stdout.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/stdout.html new file mode 100644 index 00000000..c0caf5a9 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/lang/stdout.html @@ -0,0 +1,294 @@ + + + + + +stdout + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
+ + +
+ + +
+
org.commonwl.lang
+

Enum stdout

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • java.lang.Enum<stdout>
      • +
    • +
        +
      • org.commonwl.lang.stdout
        • +
      +
      • +
    +
    • +
+
+
    +
  • +
    +
    All Implemented Interfaces:
    +
    java.io.Serializable, java.lang.Comparable<stdout>
    +
    +
    +
    +
    public enum stdout
+extends java.lang.Enum<stdout>
    +
    Only valid as a `type` for a `CommandLineTool` output with no `outputBinding` set.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Static Methods Concrete Methods 
      Modifier and TypeMethod and Description
      static stdoutvalueOf(java.lang.String name) +
      Returns the enum constant of this type with the specified name.
      +
      static stdout[]values() +
      Returns an array containing the constants of this enum type, in +the order they are declared.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Enum

        +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
        • +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +getClass, notify, notifyAll, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        values

        +
        public static stdout[] values()
        +
        Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
        +for (stdout c : stdout.values())
+    System.out.println(c);
+
        +
        +
        Returns:
        +
        an array containing the constants of this enum type, in the order they are declared
        +
        +
        • +
      + + + +
        +
      • +

        valueOf

        +
        public static stdout valueOf(java.lang.String name)
        +
        Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
        +
        +
        Parameters:
        +
        name - the name of the enum constant to be returned.
        +
        Returns:
        +
        the enum constant with the specified name
        +
        Throws:
        +
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        +
        java.lang.NullPointerException - if the argument is null
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+
    +
  • Summary: 
    • +
  • Nested | 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
    +
  • Detail: 
    • +
  • Enum Constants | 
    • +
  • Field | 
    • +
  • Method
    • +
+
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/util/CWLJavaCodeGenerator.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/util/CWLJavaCodeGenerator.html new file mode 100644 index 00000000..391502f0 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/util/CWLJavaCodeGenerator.html @@ -0,0 +1,514 @@ + + + + + +CWLJavaCodeGenerator + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.util
+

Class CWLJavaCodeGenerator

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.util.CWLJavaCodeGenerator
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class CWLJavaCodeGenerator
+extends java.lang.Object
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.StringCWL_FILE +
      The String used for storing CWL filename.
      +
      (package private) java.lang.StringCWL_JAVA_CLASS_NAME +
      The String used for storing CWL Java code-generated class name.
      +
      (package private) java.lang.StringCWL_JAVA_FILE +
      The String used for storing CWL Java code-generated filename.
      +
      (package private) java.lang.StringCWL_OBJECT +
      The String used for storing CWL Java code-generated filename.
      +
      (package private) java.lang.StringTOOL_TYPE +
      The String used for storing if the CWL file is a CommandLineTool or Workflow.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      CWLJavaCodeGenerator(java.lang.String cwlFile) +
      The CommandOutputParameter used for storing outputs in the CWL file.
      +
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      private java.lang.StringaddIndentedNewline(java.lang.String text) +
      This method adds a newline character to a string of text.
      +
      private java.lang.StringaddNewline(java.lang.String text) +
      This method adds a newline character to a string of text.
      +
      (package private) java.lang.StringcleanStandardInput(java.lang.String reference) +
      Purpose: To remove the paranthesis "()" and dollar sign ($) + standard input.
      +
      (package private) java.lang.StringgetFirstElementOfArrayList(java.util.ArrayList arrayList) +
      Purpose: Returns the first element of an ArrayList as a String.
      +
      private voidprocessContents(java.util.Map contents) +
      This method processing of the contents of a CWL file for populating a CommandLineTool instance.
      +
      voidprocessFile() +
      This method starts the processing of the CWL file for populating the contents in a CommandLineTool.
      +
      (package private) java.lang.StringremoveBrackets(java.lang.String reference) +
      Purpose: To remove the brackets ([]) in a baseCommand.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        CWL_FILE

        +
        java.lang.String CWL_FILE
        +
        The String used for storing CWL filename.
        +
        • +
      + + + +
        +
      • +

        CWL_JAVA_CLASS_NAME

        +
        java.lang.String CWL_JAVA_CLASS_NAME
        +
        The String used for storing CWL Java code-generated class name.
        +
        • +
      + + + +
        +
      • +

        CWL_JAVA_FILE

        +
        java.lang.String CWL_JAVA_FILE
        +
        The String used for storing CWL Java code-generated filename.
        +
        • +
      + + + +
        +
      • +

        CWL_OBJECT

        +
        java.lang.String CWL_OBJECT
        +
        The String used for storing CWL Java code-generated filename.
        +
        • +
      + + + +
        +
      • +

        TOOL_TYPE

        +
        java.lang.String TOOL_TYPE
        +
        The String used for storing if the CWL file is a CommandLineTool or Workflow.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CWLJavaCodeGenerator

        +
        public CWLJavaCodeGenerator(java.lang.String cwlFile)
        +
        The CommandOutputParameter used for storing outputs in the CWL file.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        processFile

        +
        public void processFile()
+                 throws java.lang.Exception
        +
        This method starts the processing of the CWL file for populating the contents in a CommandLineTool.
        +
        +
        Throws:
        +
        java.lang.Exception - is thrown if there issues with reading the file.
        +
        +
        • +
      + + + +
        +
      • +

        addNewline

        +
        private java.lang.String addNewline(java.lang.String text)
        +
        This method adds a newline character to a string of text.
        +
        +
        Parameters:
        +
        text - is a String of text.
        +
        +
        • +
      + + + +
        +
      • +

        addIndentedNewline

        +
        private java.lang.String addIndentedNewline(java.lang.String text)
        +
        This method adds a newline character to a string of text.
        +
        +
        Parameters:
        +
        text - is a String of text.
        +
        +
        • +
      + + + +
        +
      • +

        processContents

        +
        private void processContents(java.util.Map contents)
+                      throws java.lang.Exception
        +
        This method processing of the contents of a CWL file for populating a CommandLineTool instance.
        +
        +
        Parameters:
        +
        contents - is a Map of the CWL YAML file.
        +
        Throws:
        +
        java.lang.Exception
        +
        +
        • +
      + + + +
        +
      • +

        removeBrackets

        +
        java.lang.String removeBrackets(java.lang.String reference)
        +
        Purpose: To remove the brackets ([]) in a baseCommand.
        +
        +
        Parameters:
        +
        reference - a String to be updated.
        +
        Returns:
        +
        an updated String.
        +
        +
        • +
      + + + +
        +
      • +

        cleanStandardInput

        +
        java.lang.String cleanStandardInput(java.lang.String reference)
        +
        Purpose: To remove the paranthesis "()" and dollar sign ($) + standard input.
        +
        +
        Parameters:
        +
        reference - a String to be updated.
        +
        Returns:
        +
        an updated String.
        +
        +
        • +
      + + + +
        +
      • +

        getFirstElementOfArrayList

        +
        java.lang.String getFirstElementOfArrayList(java.util.ArrayList arrayList)
        +
        Purpose: Returns the first element of an ArrayList as a String.
        +
        +
        Parameters:
        +
        arrayList - which is an ArrayList for retrieving its first element.
        +
        Returns:
        +
        an updated String.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/util/CWLReader.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/util/CWLReader.html new file mode 100644 index 00000000..20140dda --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/util/CWLReader.html @@ -0,0 +1,535 @@ + + + + + +CWLReader + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.util
+

Class CWLReader

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.util.CWLReader
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class CWLReader
+extends java.lang.Object
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) CommandLineToolCOMMAND_LINE_TOOL +
      The CommandLineTool used for storing class in the CWL file.
      +
      (package private) java.lang.StringCWL_FILE +
      The String used for storing CWL filename.
      +
      (package private) CommandInputParameter[]INPUTS +
      The CommandInputParameter used for storing inputs in the CWL file.
      +
      (package private) CommandOutputParameter[]OUTPUTS +
      The CommandOutputParameter used for storing outputs in the CWL file.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      CWLReader(java.lang.String cwlFile) 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      (package private) java.lang.StringcleanStandardInput(java.lang.String reference) +
      Purpose: To remove the paranthesis "()" and dollar sign ($) + standard input.
      +
      CommandLineToolgetCommandLineToolInstance() +
      Purpose: Returns the populated CommandLineTool instance.
      +
      (package private) java.lang.StringgetFirstElementOfArrayList(java.util.ArrayList arrayList) +
      Purpose: Returns the first element of an ArrayList as a String.
      +
      private voidprocessClass(java.lang.String classType) +
      This method processes the class in a CWL file, and updates the CommandLineTool contents.
      +
      private voidprocessContents(java.lang.String key, + java.lang.Object value) +
      This method processing of the contents of a CWL file for populating a CommandLineTool instance.
      +
      voidprocessFile() +
      This method starts the processing of the CWL file for populating the contents in a CommandLineTool.
      +
      private voidprocessInputs(java.util.Map inputs) +
      This method processes the intputs in a CWL file, and updates the CommandLineTool contents.
      +
      private voidprocessOutputs(java.util.Map outputs) +
      This method processes the outputs in a CWL file, and updates the CommandLineTool contents.
      +
      (package private) java.lang.StringremoveBrackets(java.lang.String reference) +
      Purpose: To remove the brackets ([]) in a baseCommand.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        CWL_FILE

        +
        java.lang.String CWL_FILE
        +
        The String used for storing CWL filename.
        +
        • +
      + + + +
        +
      • +

        COMMAND_LINE_TOOL

        +
        CommandLineTool COMMAND_LINE_TOOL
        +
        The CommandLineTool used for storing class in the CWL file.
        +
        • +
      + + + +
        +
      • +

        INPUTS

        +
        CommandInputParameter[] INPUTS
        +
        The CommandInputParameter used for storing inputs in the CWL file.
        +
        • +
      + + + +
        +
      • +

        OUTPUTS

        +
        CommandOutputParameter[] OUTPUTS
        +
        The CommandOutputParameter used for storing outputs in the CWL file.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        CWLReader

        +
        public CWLReader(java.lang.String cwlFile)
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        processFile

        +
        public void processFile()
+                 throws java.lang.Exception
        +
        This method starts the processing of the CWL file for populating the contents in a CommandLineTool.
        +
        +
        Throws:
        +
        java.lang.Exception - is thrown if there issues with reading the file.
        +
        +
        • +
      + + + +
        +
      • +

        processContents

        +
        private void processContents(java.lang.String key,
+                             java.lang.Object value)
        +
        This method processing of the contents of a CWL file for populating a CommandLineTool instance.
        +
        +
        Parameters:
        +
        key - is a String denoting the key of the element in the CWL file.
        +
        value - is an Object denoting the value of the element in the CWL file.
        +
        +
        • +
      + + + +
        +
      • +

        processClass

        +
        private void processClass(java.lang.String classType)
        +
        This method processes the class in a CWL file, and updates the CommandLineTool contents.
        +
        +
        Parameters:
        +
        classType - is a String of the type of the class (i.e. CommandLineTool).
        +
        +
        • +
      + + + +
        +
      • +

        processInputs

        +
        private void processInputs(java.util.Map inputs)
        +
        This method processes the intputs in a CWL file, and updates the CommandLineTool contents.
        +
        +
        Parameters:
        +
        inputs - is a key-value pair Map of the inputs.
        +
        +
        • +
      + + + +
        +
      • +

        processOutputs

        +
        private void processOutputs(java.util.Map outputs)
        +
        This method processes the outputs in a CWL file, and updates the CommandLineTool contents.
        +
        +
        Parameters:
        +
        outputs - is a key-value pair Map of the outputs.
        +
        +
        • +
      + + + +
        +
      • +

        removeBrackets

        +
        java.lang.String removeBrackets(java.lang.String reference)
        +
        Purpose: To remove the brackets ([]) in a baseCommand.
        +
        +
        Parameters:
        +
        reference - a String to be updated.
        +
        Returns:
        +
        an updated String.
        +
        +
        • +
      + + + +
        +
      • +

        cleanStandardInput

        +
        java.lang.String cleanStandardInput(java.lang.String reference)
        +
        Purpose: To remove the paranthesis "()" and dollar sign ($) + standard input.
        +
        +
        Parameters:
        +
        reference - a String to be updated.
        +
        Returns:
        +
        an updated String.
        +
        +
        • +
      + + + +
        +
      • +

        getFirstElementOfArrayList

        +
        java.lang.String getFirstElementOfArrayList(java.util.ArrayList arrayList)
        +
        Purpose: Returns the first element of an ArrayList as a String.
        +
        +
        Parameters:
        +
        arrayList - which is an ArrayList for retrieving its first element.
        +
        Returns:
        +
        an updated String.
        +
        +
        • +
      + + + +
        +
      • +

        getCommandLineToolInstance

        +
        public CommandLineTool getCommandLineToolInstance()
        +
        Purpose: Returns the populated CommandLineTool instance.
        +
        +
        Returns:
        +
        an CommandLineTool instance.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/util/JSONReader.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/util/JSONReader.html new file mode 100644 index 00000000..a2912712 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/util/JSONReader.html @@ -0,0 +1,371 @@ + + + + + +JSONReader + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.util
+

Class JSONReader

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.util.JSONReader
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class JSONReader
+extends java.lang.Object
    +
    This is used reading and processing a JSON file.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      (package private) java.lang.StringJSON_FILE +
      The String used for storing the JSON filename.
      +
      (package private) java.util.Map<java.lang.String,java.lang.String>jsonMap +
      The key-value pairs in a JSON file that sit underneath the root key in a JSON file.
      +
      (package private) java.lang.StringROOT_KEY +
      The String used for storing the key of the root of a JSON file's contents.
      +
      +
      • +
    + +
      +
    • + + +

      Constructor Summary

      + + + + + + + + +
      Constructors 
      Constructor and Description
      JSONReader(java.lang.String jsonFile) 
      +
      • +
    + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.StringgetValue(java.lang.String key) +
      This method is used to request the value using a key in the processed JSON file.
      +
      voidprocessFile() +
      This method will process a JSON file an store it's contents.
      +
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        JSON_FILE

        +
        java.lang.String JSON_FILE
        +
        The String used for storing the JSON filename.
        +
        • +
      + + + +
        +
      • +

        ROOT_KEY

        +
        java.lang.String ROOT_KEY
        +
        The String used for storing the key of the root of a JSON file's contents.
        +
        • +
      + + + +
        +
      • +

        jsonMap

        +
        java.util.Map<java.lang.String,java.lang.String> jsonMap
        +
        The key-value pairs in a JSON file that sit underneath the root key in a JSON file.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        JSONReader

        +
        public JSONReader(java.lang.String jsonFile)
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        processFile

        +
        public void processFile()
+                 throws java.lang.Exception
        +
        This method will process a JSON file an store it's contents.
        +
        +
        Throws:
        +
        java.lang.Exception - is thrown if there issues with reading the file.
        +
        +
        • +
      + + + +
        +
      • +

        getValue

        +
        public java.lang.String getValue(java.lang.String key)
        +
        This method is used to request the value using a key in the processed JSON file.
        +
        +
        Parameters:
        +
        key - is a particular key, which is a String.
        +
        Returns:
        +
        a String value for a particular key.
        +
        +
        • +
      +
      • +
    +
    • +
+
+
+ + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + + diff --git a/sdk-and-javadoc-generation/javadoc/org/commonwl/util/SystemCommandExecution.html b/sdk-and-javadoc-generation/javadoc/org/commonwl/util/SystemCommandExecution.html new file mode 100644 index 00000000..acc80cb1 --- /dev/null +++ b/sdk-and-javadoc-generation/javadoc/org/commonwl/util/SystemCommandExecution.html @@ -0,0 +1,566 @@ + + + + + +SystemCommandExecution + + + + + + + + +
+ + +
Skip navigation links
+ + + + +
+
+ + + +
+ +
+
+ + +
+ + +
+ + +
+
org.commonwl.util
+

Class SystemCommandExecution

+
+
+
    +
  • java.lang.Object
    • +
  • +
      +
    • org.commonwl.util.SystemCommandExecution
      • +
    +
    • +
+
+
    +
  • +
    +
    +
    public class SystemCommandExecution
+extends java.lang.Object
    +
    This is used for executing commands on the system.
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Summary

      + + + + + + + + + + + + + + + + + + + + + + +
      Fields 
      Modifier and TypeField and Description
      private java.lang.StringStandardError +
      The String used for storing the standard error.
      +
      private java.lang.StringStandardInput +
      The String used for storing the standard input.
      +
      private java.lang.StringStandardOutput +
      The String used for storing the standard output.
      +
      private java.lang.IntegerstatusCode +
      The Integer used for storing the return status code.
      +
      +
      • +
    + + + +
      +
    • + + +

      Method Summary

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      java.lang.StringcleanupClassName(java.lang.String className) +
      This method removes the "class" string from the class name, produced by the getClass() method.
      +
      java.lang.String[]executeCommand() +
      This method executes the command and returns a String array of the standard input, + standard output, and standard error.
      +
      voidextendExecutionCommand(java.lang.Object command) +
      This method is a helper method to process any object being requested to be run, such as + the ones returned by getbaseCommand() which are actually a String type.
      +
      voidextendExecutionCommand(java.lang.String command) +
      This method is a method to process a String command being requested to be run.
      +
      java.lang.StringgetStandardError() +
      This method returns the last value of the standard error.
      +
      java.lang.StringgetStandardInput() +
      This method returns the last value of the standard input.
      +
      java.lang.StringgetStandardOutput() +
      This method returns the last value of the standard output.
      +
      java.lang.IntegergetStatusCode() 
      voidnewExecutionCommand() +
      This method resets the standard input String.
      +
      voidsetStandardInput(java.lang.String inputText) +
      This method sets the standard input String.
      +
      voidsetStatusCode(java.lang.Integer statusCode) 
      +
        +
      • + + +

        Methods inherited from class java.lang.Object

        +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
        • +
      +
      • +
    +
    • +
+
+
+
    +
  • + +
      +
    • + + +

      Field Detail

      + + + +
        +
      • +

        StandardInput

        +
        private java.lang.String StandardInput
        +
        The String used for storing the standard input.
        +
        • +
      + + + +
        +
      • +

        StandardError

        +
        private java.lang.String StandardError
        +
        The String used for storing the standard error.
        +
        • +
      + + + +
        +
      • +

        StandardOutput

        +
        private java.lang.String StandardOutput
        +
        The String used for storing the standard output.
        +
        • +
      + + + +
        +
      • +

        statusCode

        +
        private java.lang.Integer statusCode
        +
        The Integer used for storing the return status code.
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Constructor Detail

      + + + +
        +
      • +

        SystemCommandExecution

        +
        public SystemCommandExecution()
        +
        • +
      + + + +
        +
      • +

        SystemCommandExecution

        +
        public SystemCommandExecution(java.lang.String StandardInput)
        +
        • +
      +
      • +
    + +
      +
    • + + +

      Method Detail

      + + + +
        +
      • +

        getStatusCode

        +
        public java.lang.Integer getStatusCode()
        +
        • +
      + + + +
        +
      • +

        setStatusCode

        +
        public void setStatusCode(java.lang.Integer statusCode)
        +
        • +
      + + + +
        +
      • +

        executeCommand

        +
        public java.lang.String[] executeCommand()
        +
        This method executes the command and returns a String array of the standard input, + standard output, and standard error.
        +
        +
        Returns:
        +
        a String array of the standard input, standard output, and standard error.
        +
        +
        • +
      + + + +
        +
      • +

        getStandardInput

        +
        public java.lang.String getStandardInput()
        +
        This method returns the last value of the standard input.
        +
        +
        Returns:
        +
        a String of the standard input.
        +
        +
        • +
      + + + +
        +
      • +

        getStandardError

        +
        public java.lang.String getStandardError()
        +
        This method returns the last value of the standard error.
        +
        +
        Returns:
        +
        a String of the standard error.
        +
        +
        • +
      + + + +
        +
      • +

        getStandardOutput

        +
        public java.lang.String getStandardOutput()
        +
        This method returns the last value of the standard output.
        +
        +
        Returns:
        +
        a String of the standard output.
        +
        +
        • +
      + + + +
        +
      • +

        cleanupClassName

        +
        public java.lang.String cleanupClassName(java.lang.String className)
        +
        This method removes the "class" string from the class name, produced by the getClass() method.
        +
        +
        Parameters:
        +
        className - a String of the class name.
        +
        Returns:
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+} +.deprecationComment, .emphasizedPhrase, .interfaceName { + font-style:italic; +} + +div.block div.block span.deprecationComment, div.block div.block span.emphasizedPhrase, +div.block div.block span.interfaceName { + font-style:normal; +} + +div.contentContainer ul.blockList li.blockList h2{ + padding-bottom:0px; +} diff --git a/sdk-and-javadoc-generation/lib/cwl.jar b/sdk-and-javadoc-generation/lib/cwl.jar new file mode 100644 index 00000000..6b8601e8 Binary files /dev/null and b/sdk-and-javadoc-generation/lib/cwl.jar differ diff --git a/sdk-and-javadoc-generation/lib/json-simple-1.1.1.jar b/sdk-and-javadoc-generation/lib/json-simple-1.1.1.jar new file mode 100755 index 00000000..66347a6c Binary files /dev/null and b/sdk-and-javadoc-generation/lib/json-simple-1.1.1.jar differ diff --git a/sdk-and-javadoc-generation/lib/snakeyaml-1.16.jar b/sdk-and-javadoc-generation/lib/snakeyaml-1.16.jar new file mode 100644 index 00000000..af144fa4 Binary files /dev/null and b/sdk-and-javadoc-generation/lib/snakeyaml-1.16.jar differ diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/Any.java b/sdk-and-javadoc-generation/org/commonwl/lang/Any.java new file mode 100644 index 00000000..90efb3a8 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/Any.java @@ -0,0 +1,75 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* The Any type validates for any non-null value. +* +*/ +public class Any extends Object { + + /***************************************************************************************************** + * + * This is the value of Any. + * + */ + Object value; + + public Any( Object objectInstance ) { + value = objectInstance; + } + + /***************************************************************************************************** + * + * This method sets the value of Any. + * + * @param objectInstance sets the value of Any, and is a Object type. + * + */ + public void set(Object objectInstance) { + value = objectInstance; + } + + /***************************************************************************************************** + * + * This method returns the value of Any. + * + * @return This method will return the value of Any, which is an Any type. + * + */ + public Object get() { + return (Object) value; + } + +} + diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/ArraySchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/ArraySchema.java new file mode 100644 index 00000000..7f061bf6 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/ArraySchema.java @@ -0,0 +1,38 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class ArraySchema { + + public ArraySchema() { super(); } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CWLType.java b/sdk-and-javadoc-generation/org/commonwl/lang/CWLType.java new file mode 100644 index 00000000..da9fff63 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CWLType.java @@ -0,0 +1,42 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + + /***************************************************************************************************** + * + * - Extends primitive types with the concept of a file and directory as a builtin type. - File: A File object - Directory: A Directory object + */ +public enum CWLType { + + File, Directory + +} diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CWLVersion.java b/sdk-and-javadoc-generation/org/commonwl/lang/CWLVersion.java new file mode 100644 index 00000000..6bc15f03 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CWLVersion.java @@ -0,0 +1,42 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + + /***************************************************************************************************** + * + * Version symbols for published CWL document versions. + */ +public enum CWLVersion { + + draft2, draft3_dev1, draft3_dev2, draft3_dev3, draft3_dev4, draft3_dev5, draft3, draft4_dev1, draft4_dev2, draft4_dev3, v1_0_dev4, v1_0 + +} diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputArraySchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputArraySchema.java new file mode 100644 index 00000000..3f8c454a --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputArraySchema.java @@ -0,0 +1,63 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class CommandInputArraySchema extends InputArraySchema { + + CommandLineBinding inputBinding = null; + + + public CommandInputArraySchema() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of inputBinding. + * + * @param value will update inputBinding, which is a CommandLineBinding type. + * + */ + public void setinputBinding( CommandLineBinding value ) { + inputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of inputBinding. + * + * @return This method will return the value of inputBinding, which is a CommandLineBinding type. + * + */ + public CommandLineBinding getinputBinding() { + return inputBinding; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputEnumSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputEnumSchema.java new file mode 100644 index 00000000..acb01155 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputEnumSchema.java @@ -0,0 +1,63 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class CommandInputEnumSchema extends InputEnumSchema { + + CommandLineBinding inputBinding = null; + + + public CommandInputEnumSchema() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of inputBinding. + * + * @param value will update inputBinding, which is a CommandLineBinding type. + * + */ + public void setinputBinding( CommandLineBinding value ) { + inputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of inputBinding. + * + * @return This method will return the value of inputBinding, which is a CommandLineBinding type. + * + */ + public CommandLineBinding getinputBinding() { + return inputBinding; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputParameter.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputParameter.java new file mode 100644 index 00000000..a89c18c4 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputParameter.java @@ -0,0 +1,462 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* An input parameter for a CommandLineTool. +*/ +public class CommandInputParameter extends InputParameter { + + /***************************************************************************************************** + * + * The default value for this parameter if not provided in the input object. + */ + Any default_value = null; + + /***************************************************************************************************** + * + * The unique identifier for this parameter object. + */ + String id = null; + + /***************************************************************************************************** + * + * Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters. + */ + CommandLineBinding inputBinding = null; + + /***************************************************************************************************** + * + * Specify valid types of data that may be assigned to this parameter. + */ + Object type = null; + + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. + */ + Boolean streamable = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter. + */ + Object format = null; + + /***************************************************************************************************** + * + * A documentation string for this type, or an array of strings which should be concatenated. + */ + Object doc = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path. + */ + Object secondaryFiles = null; + + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + public CommandInputParameter() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of default_value. + * + * @param value will update default_value, which is a Any type. + * + */ + public void setdefault( Any value ) { + default_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of default_value. + * + * @return This method will return the value of default_value, which is a Any type. + * + */ + public Any getdefault() { + return default_value; + } + + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ) { + id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid() { + return id; + } + + /***************************************************************************************************** + * + * This method sets the value of inputBinding. + * + * @param value will update inputBinding, which is a CommandLineBinding type. + * + */ + public void setinputBinding( CommandLineBinding value ) { + inputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of inputBinding. + * + * @return This method will return the value of inputBinding, which is a CommandLineBinding type. + * + */ + public CommandLineBinding getinputBinding() { + return inputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a InputEnumSchema array. + * + */ + public void settype( CommandInputEnumSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a InputEnumSchema type. + * + */ + public void settype( CommandInputEnumSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String array. + * + */ + public void settype( String [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a InputRecordSchema array. + * + */ + public void settype( CommandInputRecordSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a InputRecordSchema type. + * + */ + public void settype( CommandInputRecordSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CWLType array. + * + */ + public void settype( CWLType [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CWLType type. + * + */ + public void settype( CWLType value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String type. + * + */ + public void settype( String value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a InputArraySchema type. + * + */ + public void settype( CommandInputArraySchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a InputArraySchema array. + * + */ + public void settype( CommandInputArraySchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of type. + * + * @return This method will return the value of type, which is a Object type. + * + */ + public Object gettype() { + return type; + } + + /***************************************************************************************************** + * + * This method sets the value of streamable. + * + * @param value will update streamable, which is a Boolean type. + * + */ + public void setstreamable( Boolean value ) { + streamable = value; + } + + /***************************************************************************************************** + * + * This method returns the value of streamable. + * + * @return This method will return the value of streamable, which is a Boolean type. + * + */ + public Boolean getstreamable() { + return streamable; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a Expression array. + * + */ + public void setformat( Expression [] value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String type. + * + */ + public void setformat( String value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String array. + * + */ + public void setformat( String [] value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method returns the value of format. + * + * @return This method will return the value of format, which is a Object type. + * + */ + public Object getformat() { + return format; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String array. + * + */ + public void setdoc( String [] value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a Object type. + * + */ + public Object getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression array. + * + */ + public void setsecondaryFiles( Expression [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String type. + * + */ + public void setsecondaryFiles( String value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String array. + * + */ + public void setsecondaryFiles( String [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression type. + * + */ + public void setsecondaryFiles( Expression value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method returns the value of secondaryFiles. + * + * @return This method will return the value of secondaryFiles, which is a Object type. + * + */ + public Object getsecondaryFiles() { + return secondaryFiles; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputRecordField.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputRecordField.java new file mode 100644 index 00000000..5e19aed7 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputRecordField.java @@ -0,0 +1,275 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class CommandInputRecordField extends InputRecordField { + + /***************************************************************************************************** + * + * A short, human-readable label of this process object. + */ + String label = null; + + CommandLineBinding inputBinding = null; + + + /***************************************************************************************************** + * + * The name of the field + */ + String name = null; + + /***************************************************************************************************** + * + * A documentation string for this field + */ + String doc = null; + + /***************************************************************************************************** + * + * The field type + */ + Object type = null; + + + public CommandInputRecordField() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + + /***************************************************************************************************** + * + * This method sets the value of inputBinding. + * + * @param value will update inputBinding, which is a CommandLineBinding type. + * + */ + public void setinputBinding( CommandLineBinding value ) { + inputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of inputBinding. + * + * @return This method will return the value of inputBinding, which is a CommandLineBinding type. + * + */ + public CommandLineBinding getinputBinding() { + return inputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of name. + * + * @param value will update name, which is a String type. + * + */ + public void setname( String value ) { + name = value; + } + + /***************************************************************************************************** + * + * This method returns the value of name. + * + * @return This method will return the value of name, which is a String type. + * + */ + public String getname() { + return name; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a String type. + * + */ + public String getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a RecordSchema type. + * + */ + public void settype( RecordSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a EnumSchema type. + * + */ + public void settype( EnumSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a ArraySchema type. + * + */ + public void settype( ArraySchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String array. + * + */ + public void settype( String [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a PrimitiveType array. + * + */ + public void settype( PrimitiveType [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a RecordSchema array. + * + */ + public void settype( RecordSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a PrimitiveType type. + * + */ + public void settype( PrimitiveType value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a ArraySchema array. + * + */ + public void settype( ArraySchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String type. + * + */ + public void settype( String value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a EnumSchema array. + * + */ + public void settype( EnumSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of type. + * + * @return This method will return the value of type, which is a Object type. + * + */ + public Object gettype() { + return type; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputRecordSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputRecordSchema.java new file mode 100644 index 00000000..26efc658 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandInputRecordSchema.java @@ -0,0 +1,38 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class CommandInputRecordSchema extends InputRecordSchema { + + public CommandInputRecordSchema() { super(); } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandLineBinding.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandLineBinding.java new file mode 100644 index 00000000..736610dd --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandLineBinding.java @@ -0,0 +1,247 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class CommandLineBinding implements InputBinding { + + /***************************************************************************************************** + * + * If true (default), then the prefix and value must be added as separate command line arguments; if false, prefix and value must be concatenated into a single command line argument. + */ + Boolean separate = null; + + /***************************************************************************************************** + * + * Join the array elements into a single string with the elements separated by by `itemSeparator`. + */ + String itemSeparator = null; + + /***************************************************************************************************** + * + * Command line prefix to add before the value. + */ + String prefix = null; + + /***************************************************************************************************** + * + * If `ShellCommandRequirement` is in the requirements for the current command, this controls whether the value is quoted on the command line (default is true). Use `shellQuote: false` to inject metacharacters for operations such as pipes. + */ + Boolean shellQuote = null; + + /***************************************************************************************************** + * + * The sorting key. Default position is 0. + */ + Integer position = null; + + /***************************************************************************************************** + * + * If `valueFrom` is a constant string value, use this as the value and apply the binding rules above. If `valueFrom` is an expression, evaluate the expression to yield the actual value to use to build the command line and apply the binding rules above. If the inputBinding is associated with an input parameter, the value of `self` in the expression will be the value of the input parameter. When a binding is part of the `CommandLineTool.arguments` field, the `valueFrom` field is required. + */ + Object valueFrom = null; + + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. Read up to the first 64 KiB of text from the file and place it in the contents field of the file object for use by expressions. + */ + Boolean loadContents = null; + + + public CommandLineBinding() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of separate. + * + * @param value will update separate, which is a Boolean type. + * + */ + public void setseparate( Boolean value ) { + separate = value; + } + + /***************************************************************************************************** + * + * This method returns the value of separate. + * + * @return This method will return the value of separate, which is a Boolean type. + * + */ + public Boolean getseparate() { + return separate; + } + + /***************************************************************************************************** + * + * This method sets the value of itemSeparator. + * + * @param value will update itemSeparator, which is a String type. + * + */ + public void setitemSeparator( String value ) { + itemSeparator = value; + } + + /***************************************************************************************************** + * + * This method returns the value of itemSeparator. + * + * @return This method will return the value of itemSeparator, which is a String type. + * + */ + public String getitemSeparator() { + return itemSeparator; + } + + /***************************************************************************************************** + * + * This method sets the value of prefix. + * + * @param value will update prefix, which is a String type. + * + */ + public void setprefix( String value ) { + prefix = value; + } + + /***************************************************************************************************** + * + * This method returns the value of prefix. + * + * @return This method will return the value of prefix, which is a String type. + * + */ + public String getprefix() { + return prefix; + } + + /***************************************************************************************************** + * + * This method sets the value of shellQuote. + * + * @param value will update shellQuote, which is a Boolean type. + * + */ + public void setshellQuote( Boolean value ) { + shellQuote = value; + } + + /***************************************************************************************************** + * + * This method returns the value of shellQuote. + * + * @return This method will return the value of shellQuote, which is a Boolean type. + * + */ + public Boolean getshellQuote() { + return shellQuote; + } + + /***************************************************************************************************** + * + * This method sets the value of position. + * + * @param value will update position, which is a Integer type. + * + */ + public void setposition( Integer value ) { + position = value; + } + + /***************************************************************************************************** + * + * This method returns the value of position. + * + * @return This method will return the value of position, which is a Integer type. + * + */ + public Integer getposition() { + return position; + } + + /***************************************************************************************************** + * + * This method sets the value of valueFrom. + * + * @param value will update valueFrom, which is a String type. + * + */ + public void setvalueFrom( String value ) { + valueFrom = value; + } + + /***************************************************************************************************** + * + * This method sets the value of valueFrom. + * + * @param value will update valueFrom, which is a Expression type. + * + */ + public void setvalueFrom( Expression value ) { + valueFrom = value; + } + + /***************************************************************************************************** + * + * This method returns the value of valueFrom. + * + * @return This method will return the value of valueFrom, which is a Object type. + * + */ + public Object getvalueFrom() { + return valueFrom; + } + + /***************************************************************************************************** + * + * This method sets the value of loadContents. + * + * @param value will update loadContents, which is a Boolean type. + * + */ + public void setloadContents( Boolean value ) { + loadContents = value; + } + + /***************************************************************************************************** + * + * This method returns the value of loadContents. + * + * @return This method will return the value of loadContents, which is a Boolean type. + * + */ + public Boolean getloadContents() { + return loadContents; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandLineTool.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandLineTool.java new file mode 100644 index 00000000..958e7490 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandLineTool.java @@ -0,0 +1,725 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* This defines the schema of the CWL Command Line Tool Description document. +*/ +public class CommandLineTool implements Process { + + /***************************************************************************************************** + * + * A path to a file whose contents must be piped into the command's standard input stream. + */ + Object stdin = null; + + /***************************************************************************************************** + * + * Capture the command's standard output stream to a file written to the designated output directory. If `stdout` is a string, it specifies the file name to use. If `stdout` is an expression, the expression is evaluated and must return a string with the file name to use to capture stdout. If the return value is not a string, or the resulting path contains illegal characters (such as the path separator `/`) it is an error. + */ + Object stdout = null; + + /***************************************************************************************************** + * + * Exit codes that indicate the process completed successfully. + */ + Integer successCodes = null; + + /***************************************************************************************************** + * + * Exit codes that indicate the process failed due to a possibly temporary condition, where executing the process with the same runtime environment and inputs may produce different results. + */ + Integer temporaryFailCodes = null; + + /***************************************************************************************************** + * + * Specifies the program to execute. If an array, the first element of the array is the command to execute, and subsequent elements are mandatory command line arguments. The elements in `baseCommand` must appear before any command line bindings from `inputBinding` or `arguments`. If `baseCommand` is not provided or is an empty array, the first element of the command line produced after processing `inputBinding` or `arguments` must be used as the program to execute. If the program includes a path separator character it must be an absolute path, otherwise it is an error. If the program does not include a path separator, search the `$PATH` variable in the runtime environment of the workflow runner find the absolute path of the executable. + */ + Object baseCommand = null; + + /***************************************************************************************************** + * + * Command line bindings which are not directly associated with input parameters. + */ + Object arguments = null; + + /***************************************************************************************************** + * + * Capture the command's standard error stream to a file written to the designated output directory. If `stderr` is a string, it specifies the file name to use. If `stderr` is an expression, the expression is evaluated and must return a string with the file name to use to capture stderr. If the return value is not a string, or the resulting path contains illegal characters (such as the path separator `/`) it is an error. + */ + Object stderr = null; + + String class_value = null; + + /***************************************************************************************************** + * + * Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail. + */ + Integer permanentFailCodes = null; + + + /***************************************************************************************************** + * + * Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. + */ + CommandOutputParameter [] outputs = null; + + /***************************************************************************************************** + * + * Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option. + */ + Object requirements = null; + + /***************************************************************************************************** + * + * CWL document version. Always required at the document root. Not required for a Process embedded inside another Process. + */ + CWLVersion cwlVersion = null; + + /***************************************************************************************************** + * + * Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object. + */ + CommandInputParameter [] inputs = null; + + /***************************************************************************************************** + * + * Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning. + */ + Any hints = null; + + /***************************************************************************************************** + * + * A long, human-readable description of this process object. + */ + String doc = null; + + /***************************************************************************************************** + * + * The unique identifier for this process object. + */ + String id = null; + + /***************************************************************************************************** + * + * A short, human-readable label of this process object. + */ + String label = null; + + + public CommandLineTool() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of stdin. + * + * @param value will update stdin, which is a String type. + * + */ + public void setstdin( String value ) { + stdin = value; + } + + /***************************************************************************************************** + * + * This method sets the value of stdin. + * + * @param value will update stdin, which is a Expression type. + * + */ + public void setstdin( Expression value ) { + stdin = value; + } + + /***************************************************************************************************** + * + * This method returns the value of stdin. + * + * @return This method will return the value of stdin, which is a Object type. + * + */ + public Object getstdin() { + return stdin; + } + + /***************************************************************************************************** + * + * This method sets the value of stdout. + * + * @param value will update stdout, which is a String type. + * + */ + public void setstdout( String value ) { + stdout = value; + } + + /***************************************************************************************************** + * + * This method sets the value of stdout. + * + * @param value will update stdout, which is a Expression type. + * + */ + public void setstdout( Expression value ) { + stdout = value; + } + + /***************************************************************************************************** + * + * This method returns the value of stdout. + * + * @return This method will return the value of stdout, which is a Object type. + * + */ + public Object getstdout() { + return stdout; + } + + /***************************************************************************************************** + * + * This method sets the value of successCodes. + * + * @param value will update successCodes, which is a Integer type. + * + */ + public void setsuccessCodes( Integer value ) { + successCodes = value; + } + + /***************************************************************************************************** + * + * This method returns the value of successCodes. + * + * @return This method will return the value of successCodes, which is a Integer type. + * + */ + public Integer getsuccessCodes() { + return successCodes; + } + + /***************************************************************************************************** + * + * This method sets the value of temporaryFailCodes. + * + * @param value will update temporaryFailCodes, which is a Integer type. + * + */ + public void settemporaryFailCodes( Integer value ) { + temporaryFailCodes = value; + } + + /***************************************************************************************************** + * + * This method returns the value of temporaryFailCodes. + * + * @return This method will return the value of temporaryFailCodes, which is a Integer type. + * + */ + public Integer gettemporaryFailCodes() { + return temporaryFailCodes; + } + + /***************************************************************************************************** + * + * This method sets the value of baseCommand. + * + * @param value will update baseCommand, which is a String type. + * + */ + public void setbaseCommand( String value ) { + baseCommand = value; + } + + /***************************************************************************************************** + * + * This method sets the value of baseCommand. + * + * @param value will update baseCommand, which is a String array. + * + */ + public void setbaseCommand( String [] value ) { + baseCommand = value; + } + + /***************************************************************************************************** + * + * This method returns the value of baseCommand. + * + * @return This method will return the value of baseCommand, which is a Object type. + * + */ + public Object getbaseCommand() { + return baseCommand; + } + + /***************************************************************************************************** + * + * This method sets the value of arguments. + * + * @param value will update arguments, which is a Expression array. + * + */ + public void setarguments( Expression [] value ) { + arguments = value; + } + + /***************************************************************************************************** + * + * This method sets the value of arguments. + * + * @param value will update arguments, which is a CommandLineBinding array. + * + */ + public void setarguments( CommandLineBinding [] value ) { + arguments = value; + } + + /***************************************************************************************************** + * + * This method sets the value of arguments. + * + * @param value will update arguments, which is a String array. + * + */ + public void setarguments( String [] value ) { + arguments = value; + } + + /***************************************************************************************************** + * + * This method returns the value of arguments. + * + * @return This method will return the value of arguments, which is a Object type. + * + */ + public Object getarguments() { + return arguments; + } + + /***************************************************************************************************** + * + * This method sets the value of stderr. + * + * @param value will update stderr, which is a String type. + * + */ + public void setstderr( String value ) { + stderr = value; + } + + /***************************************************************************************************** + * + * This method sets the value of stderr. + * + * @param value will update stderr, which is a Expression type. + * + */ + public void setstderr( Expression value ) { + stderr = value; + } + + /***************************************************************************************************** + * + * This method returns the value of stderr. + * + * @return This method will return the value of stderr, which is a Object type. + * + */ + public Object getstderr() { + return stderr; + } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + + /***************************************************************************************************** + * + * This method sets the value of permanentFailCodes. + * + * @param value will update permanentFailCodes, which is a Integer type. + * + */ + public void setpermanentFailCodes( Integer value ) { + permanentFailCodes = value; + } + + /***************************************************************************************************** + * + * This method returns the value of permanentFailCodes. + * + * @return This method will return the value of permanentFailCodes, which is a Integer type. + * + */ + public Integer getpermanentFailCodes() { + return permanentFailCodes; + } + + /***************************************************************************************************** + * + * This method sets the value of outputs. + * + * @param value will update outputs, which is a OutputParameter array. + * + */ + public void setoutputs( CommandOutputParameter [] value ) { + outputs = value; + } + + /***************************************************************************************************** + * + * This is a dummy method which has no functionality, and is required + * for implementing an interface method that was previously specialized. + * + * + */ + public void setoutputs( OutputParameter [] value ) { + + } + + /***************************************************************************************************** + * + * This method returns the value of outputs. + * + * @return This method will return the value of outputs, which is a CommandOutputParameter array. + * + */ + public CommandOutputParameter [] getoutputs() { + return outputs; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a StepInputExpressionRequirement type. + * + */ + public void setrequirements( StepInputExpressionRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a MultipleInputFeatureRequirement type. + * + */ + public void setrequirements( MultipleInputFeatureRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SoftwareRequirement type. + * + */ + public void setrequirements( SoftwareRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SchemaDefRequirement type. + * + */ + public void setrequirements( SchemaDefRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a InitialWorkDirRequirement type. + * + */ + public void setrequirements( InitialWorkDirRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a EnvVarRequirement type. + * + */ + public void setrequirements( EnvVarRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a DockerRequirement type. + * + */ + public void setrequirements( DockerRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ResourceRequirement type. + * + */ + public void setrequirements( ResourceRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a InlineJavascriptRequirement type. + * + */ + public void setrequirements( InlineJavascriptRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ShellCommandRequirement type. + * + */ + public void setrequirements( ShellCommandRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ScatterFeatureRequirement type. + * + */ + public void setrequirements( ScatterFeatureRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SubworkflowFeatureRequirement type. + * + */ + public void setrequirements( SubworkflowFeatureRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method returns the value of requirements. + * + * @return This method will return the value of requirements, which is a Object type. + * + */ + public Object getrequirements() { + return requirements; + } + + /***************************************************************************************************** + * + * This method sets the value of cwlVersion. + * + * @param value will update cwlVersion, which is a CWLVersion type. + * + */ + public void setcwlVersion( CWLVersion value ) { + cwlVersion = value; + } + + /***************************************************************************************************** + * + * This method returns the value of cwlVersion. + * + * @return This method will return the value of cwlVersion, which is a CWLVersion type. + * + */ + public CWLVersion getcwlVersion() { + return cwlVersion; + } + + /***************************************************************************************************** + * + * This method sets the value of inputs. + * + * @param value will update inputs, which is a InputParameter array. + * + */ + public void setinputs( CommandInputParameter [] value ) { + inputs = value; + } + + /***************************************************************************************************** + * + * This is a dummy method which has no functionality, and is required + * for implementing an interface method that was previously specialized. + * + * + */ + public void setinputs( InputParameter [] value ) { + + } + + /***************************************************************************************************** + * + * This method returns the value of inputs. + * + * @return This method will return the value of inputs, which is a CommandInputParameter array. + * + */ + public CommandInputParameter [] getinputs() { + return inputs; + } + + /***************************************************************************************************** + * + * This method sets the value of hints. + * + * @param value will update hints, which is a Any type. + * + */ + public void sethints( Any value ) { + hints = value; + } + + /***************************************************************************************************** + * + * This method returns the value of hints. + * + * @return This method will return the value of hints, which is a Any type. + * + */ + public Any gethints() { + return hints; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a String type. + * + */ + public String getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ) { + id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid() { + return id; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputArraySchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputArraySchema.java new file mode 100644 index 00000000..495aa0da --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputArraySchema.java @@ -0,0 +1,63 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class CommandOutputArraySchema extends OutputArraySchema { + + CommandOutputBinding outputBinding = null; + + + public CommandOutputArraySchema() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of outputBinding. + * + * @param value will update outputBinding, which is a CommandOutputBinding type. + * + */ + public void setoutputBinding( CommandOutputBinding value ) { + outputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outputBinding. + * + * @return This method will return the value of outputBinding, which is a CommandOutputBinding type. + * + */ + public CommandOutputBinding getoutputBinding() { + return outputBinding; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputBinding.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputBinding.java new file mode 100644 index 00000000..7d2e236e --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputBinding.java @@ -0,0 +1,160 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Describes how to generate an output parameter based on the files produced by a CommandLineTool. +*/ +public class CommandOutputBinding implements OutputBinding { + + /***************************************************************************************************** + * + * For each file matched in `glob`, read up to the first 64 KiB of text from the file and place it in the `contents` field of the file object for manipulation by `outputEval`. + */ + Boolean loadContents = null; + + /***************************************************************************************************** + * + * Evaluate an expression to generate the output value. If `glob` was specified, the value of `self` must be an array containing file objects that were matched. If no files were matched, `self` must be a zero length array; if a single file was matched, the value of `self` is an array of a single element. Additionally, if `loadContents` is `true`, the File objects must include up to the first 64 KiB of file contents in the `contents` field. + */ + Object outputEval = null; + + /***************************************************************************************************** + * + * Find files relative to the output directory, using POSIX glob(3) pathname matching. If an array is provided, find files that match any pattern in the array. If an expression is provided, the expression must return a string or an array of strings, which will then be evaluated as one or more glob patterns. Must only match and return files which actually exist. + */ + Object glob = null; + + + public CommandOutputBinding() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of loadContents. + * + * @param value will update loadContents, which is a Boolean type. + * + */ + public void setloadContents( Boolean value ) { + loadContents = value; + } + + /***************************************************************************************************** + * + * This method returns the value of loadContents. + * + * @return This method will return the value of loadContents, which is a Boolean type. + * + */ + public Boolean getloadContents() { + return loadContents; + } + + /***************************************************************************************************** + * + * This method sets the value of outputEval. + * + * @param value will update outputEval, which is a String type. + * + */ + public void setoutputEval( String value ) { + outputEval = value; + } + + /***************************************************************************************************** + * + * This method sets the value of outputEval. + * + * @param value will update outputEval, which is a Expression type. + * + */ + public void setoutputEval( Expression value ) { + outputEval = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outputEval. + * + * @return This method will return the value of outputEval, which is a Object type. + * + */ + public Object getoutputEval() { + return outputEval; + } + + /***************************************************************************************************** + * + * This method sets the value of glob. + * + * @param value will update glob, which is a String type. + * + */ + public void setglob( String value ) { + glob = value; + } + + /***************************************************************************************************** + * + * This method sets the value of glob. + * + * @param value will update glob, which is a String array. + * + */ + public void setglob( String [] value ) { + glob = value; + } + + /***************************************************************************************************** + * + * This method sets the value of glob. + * + * @param value will update glob, which is a Expression type. + * + */ + public void setglob( Expression value ) { + glob = value; + } + + /***************************************************************************************************** + * + * This method returns the value of glob. + * + * @return This method will return the value of glob, which is a Object type. + * + */ + public Object getglob() { + return glob; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputEnumSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputEnumSchema.java new file mode 100644 index 00000000..df558931 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputEnumSchema.java @@ -0,0 +1,63 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class CommandOutputEnumSchema extends OutputEnumSchema { + + CommandOutputBinding outputBinding = null; + + + public CommandOutputEnumSchema() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of outputBinding. + * + * @param value will update outputBinding, which is a CommandOutputBinding type. + * + */ + public void setoutputBinding( CommandOutputBinding value ) { + outputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outputBinding. + * + * @return This method will return the value of outputBinding, which is a CommandOutputBinding type. + * + */ + public CommandOutputBinding getoutputBinding() { + return outputBinding; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputParameter.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputParameter.java new file mode 100644 index 00000000..5ab682b6 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputParameter.java @@ -0,0 +1,457 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* An output parameter for a CommandLineTool. +*/ +public class CommandOutputParameter extends OutputParameter { + + /***************************************************************************************************** + * + * Specify valid types of data that may be assigned to this parameter. + */ + Object type = null; + + + /***************************************************************************************************** + * + * Describes how to handle the outputs of a process. + */ + CommandOutputBinding outputBinding = null; + + /***************************************************************************************************** + * + * The unique identifier for this parameter object. + */ + String id = null; + + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. + */ + Boolean streamable = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter. + */ + Object format = null; + + /***************************************************************************************************** + * + * A documentation string for this type, or an array of strings which should be concatenated. + */ + Object doc = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path. + */ + Object secondaryFiles = null; + + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + public CommandOutputParameter() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CommandOutputArraySchema type. + * + */ + public void settype( CommandOutputArraySchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a stderr type. + * + */ + public void settype( stderr value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String array. + * + */ + public void settype( String [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CommandOutputArraySchema array. + * + */ + public void settype( CommandOutputArraySchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CWLType array. + * + */ + public void settype( CWLType [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CommandOutputRecordSchema array. + * + */ + public void settype( CommandOutputRecordSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CWLType type. + * + */ + public void settype( CWLType value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a stdout type. + * + */ + public void settype( stdout value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CommandOutputEnumSchema type. + * + */ + public void settype( CommandOutputEnumSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String type. + * + */ + public void settype( String value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CommandOutputRecordSchema type. + * + */ + public void settype( CommandOutputRecordSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CommandOutputEnumSchema array. + * + */ + public void settype( CommandOutputEnumSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of type. + * + * @return This method will return the value of type, which is a Object type. + * + */ + public Object gettype() { + return type; + } + + /***************************************************************************************************** + * + * This method sets the value of outputBinding. + * + * @param value will update outputBinding, which is a CommandOutputBinding type. + * + */ + public void setoutputBinding( CommandOutputBinding value ) { + outputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outputBinding. + * + * @return This method will return the value of outputBinding, which is a CommandOutputBinding type. + * + */ + public CommandOutputBinding getoutputBinding() { + return outputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ) { + id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid() { + return id; + } + + /***************************************************************************************************** + * + * This method sets the value of streamable. + * + * @param value will update streamable, which is a Boolean type. + * + */ + public void setstreamable( Boolean value ) { + streamable = value; + } + + /***************************************************************************************************** + * + * This method returns the value of streamable. + * + * @return This method will return the value of streamable, which is a Boolean type. + * + */ + public Boolean getstreamable() { + return streamable; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a Expression array. + * + */ + public void setformat( Expression [] value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String type. + * + */ + public void setformat( String value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String array. + * + */ + public void setformat( String [] value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method returns the value of format. + * + * @return This method will return the value of format, which is a Object type. + * + */ + public Object getformat() { + return format; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String array. + * + */ + public void setdoc( String [] value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a Object type. + * + */ + public Object getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression array. + * + */ + public void setsecondaryFiles( Expression [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String type. + * + */ + public void setsecondaryFiles( String value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String array. + * + */ + public void setsecondaryFiles( String [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression type. + * + */ + public void setsecondaryFiles( Expression value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method returns the value of secondaryFiles. + * + * @return This method will return the value of secondaryFiles, which is a Object type. + * + */ + public Object getsecondaryFiles() { + return secondaryFiles; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputRecordField.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputRecordField.java new file mode 100644 index 00000000..cd89c311 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputRecordField.java @@ -0,0 +1,247 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class CommandOutputRecordField extends OutputRecordField { + + CommandOutputBinding outputBinding = null; + + + /***************************************************************************************************** + * + * The name of the field + */ + String name = null; + + /***************************************************************************************************** + * + * A documentation string for this field + */ + String doc = null; + + /***************************************************************************************************** + * + * The field type + */ + Object type = null; + + + public CommandOutputRecordField() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of outputBinding. + * + * @param value will update outputBinding, which is a CommandOutputBinding type. + * + */ + public void setoutputBinding( CommandOutputBinding value ) { + outputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outputBinding. + * + * @return This method will return the value of outputBinding, which is a CommandOutputBinding type. + * + */ + public CommandOutputBinding getoutputBinding() { + return outputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of name. + * + * @param value will update name, which is a String type. + * + */ + public void setname( String value ) { + name = value; + } + + /***************************************************************************************************** + * + * This method returns the value of name. + * + * @return This method will return the value of name, which is a String type. + * + */ + public String getname() { + return name; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a String type. + * + */ + public String getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a RecordSchema type. + * + */ + public void settype( RecordSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a EnumSchema type. + * + */ + public void settype( EnumSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a ArraySchema type. + * + */ + public void settype( ArraySchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String array. + * + */ + public void settype( String [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a PrimitiveType array. + * + */ + public void settype( PrimitiveType [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a RecordSchema array. + * + */ + public void settype( RecordSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a PrimitiveType type. + * + */ + public void settype( PrimitiveType value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a ArraySchema array. + * + */ + public void settype( ArraySchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String type. + * + */ + public void settype( String value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a EnumSchema array. + * + */ + public void settype( EnumSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of type. + * + * @return This method will return the value of type, which is a Object type. + * + */ + public Object gettype() { + return type; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputRecordSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputRecordSchema.java new file mode 100644 index 00000000..c8c5cd6c --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/CommandOutputRecordSchema.java @@ -0,0 +1,38 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class CommandOutputRecordSchema extends OutputRecordSchema { + + public CommandOutputRecordSchema() { super(); } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/Directory.java b/sdk-and-javadoc-generation/org/commonwl/lang/Directory.java new file mode 100644 index 00000000..9b8ca5e6 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/Directory.java @@ -0,0 +1,194 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Represents a directory to present to a command line tool. +*/ +public class Directory { + + /***************************************************************************************************** + * + * The local path where the Directory is made available prior to executing a CommandLineTool. This must be set by the implementation. This field must not be used in any other context. The command line tool being executed must be able to to access the directory at `path` using the POSIX `opendir(2)` syscall. If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) (`|`,`{@literal &}`, `;`, `(`, `)`, `(`,`)`, `$`,`` ` ``, `\`, ``, `'`, `(space)`, `(tab)`, and `(newline)`) or characters [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) then implementations may terminate the process with a `permanentFailure`. + */ + String path = null; + + /***************************************************************************************************** + * + * The base name of the directory, that is, the name of the file without any leading directory path. The base name must not contain a slash `/`. If not provided, the implementation must set this field based on the `location` field by taking the final path component after parsing `location` as an IRI. If `basename` is provided, it is not required to match the value from `location`. When this file is made available to a CommandLineTool, it must be named with `basename`, i.e. the final component of the `path` field must match `basename`. + */ + String basename = null; + + /***************************************************************************************************** + * + * An IRI that identifies the directory resource. This may be a relative reference, in which case it must be resolved using the base IRI of the document. The location may refer to a local or remote resource. If the `listing` field is not set, the implementation must use the location IRI to retrieve directory listing. If an implementation is unable to retrieve the directory listing stored at a remote resource (due to unsupported protocol, access denied, or other issue) it must signal an error. If the `location` field is not provided, the `listing` field must be provided. The implementation must assign a unique identifier for the `location` field. If the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, then follow the rules above. + */ + String location = null; + + /***************************************************************************************************** + * + * List of files or subdirectories contained in this directory. The name of each file or subdirectory is determined by the `basename` field of each `File` or `Directory` object. It is an error if a `File` shares a `basename` with any other entry in `listing`. If two or more `Directory` object share the same `basename`, this must be treated as equivalent to a single subdirectory with the listings recursively merged. + */ + Object listing = null; + + /***************************************************************************************************** + * + * Must be `Directory` to indicate this object describes a Directory. + */ + Directory class_value = null; + + + public Directory() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of path. + * + * @param value will update path, which is a String type. + * + */ + public void setpath( String value ) { + path = value; + } + + /***************************************************************************************************** + * + * This method returns the value of path. + * + * @return This method will return the value of path, which is a String type. + * + */ + public String getpath() { + return path; + } + + /***************************************************************************************************** + * + * This method sets the value of basename. + * + * @param value will update basename, which is a String type. + * + */ + public void setbasename( String value ) { + basename = value; + } + + /***************************************************************************************************** + * + * This method returns the value of basename. + * + * @return This method will return the value of basename, which is a String type. + * + */ + public String getbasename() { + return basename; + } + + /***************************************************************************************************** + * + * This method sets the value of location. + * + * @param value will update location, which is a String type. + * + */ + public void setlocation( String value ) { + location = value; + } + + /***************************************************************************************************** + * + * This method returns the value of location. + * + * @return This method will return the value of location, which is a String type. + * + */ + public String getlocation() { + return location; + } + + /***************************************************************************************************** + * + * This method sets the value of listing. + * + * @param value will update listing, which is a File array. + * + */ + public void setlisting( File [] value ) { + listing = value; + } + + /***************************************************************************************************** + * + * This method sets the value of listing. + * + * @param value will update listing, which is a Directory array. + * + */ + public void setlisting( Directory [] value ) { + listing = value; + } + + /***************************************************************************************************** + * + * This method returns the value of listing. + * + * @return This method will return the value of listing, which is a Object type. + * + */ + public Object getlisting() { + return listing; + } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a Directory type. + * + */ + public void setclass( Directory value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a Directory type. + * + */ + public Directory getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/Dirent.java b/sdk-and-javadoc-generation/org/commonwl/lang/Dirent.java new file mode 100644 index 00000000..b7d216f3 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/Dirent.java @@ -0,0 +1,149 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Define a file or subdirectory that must be placed in the designated output directory prior to executing the command line tool. May be the result of executing an expression, such as building a configuration file from a template. +*/ +public class Dirent { + + /***************************************************************************************************** + * + * If the value is a string literal or an expression which evaluates to a string, a new file must be created with the string as the file contents. If the value is an expression that evaluates to a `File` object, this indicates the referenced file should be added to the designated output directory prior to executing the tool. If the value is an expression that evaluates to a `Dirent` object, this indicates that the File or Directory in `entry` should be added to the designated output directory with the name in `entryname`. If `writable` is false, the file may be made available using a bind mount or file system link to avoid unnecessary copying of the input file. + */ + Object entry = null; + + /***************************************************************************************************** + * + * The name of the file or subdirectory to create in the output directory. If `entry` is a File or Directory, this overrides `basename`. Optional. + */ + Object entryname = null; + + /***************************************************************************************************** + * + * If true, the file or directory must be writable by the tool. Changes to the file or directory must be isolated and not visible by any other CommandLineTool process. This may be implemented by making a copy of the original file or directory. Default false (files and directories read-only by default). + */ + Boolean writable = null; + + + public Dirent() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of entry. + * + * @param value will update entry, which is a String type. + * + */ + public void setentry( String value ) { + entry = value; + } + + /***************************************************************************************************** + * + * This method sets the value of entry. + * + * @param value will update entry, which is a Expression type. + * + */ + public void setentry( Expression value ) { + entry = value; + } + + /***************************************************************************************************** + * + * This method returns the value of entry. + * + * @return This method will return the value of entry, which is a Object type. + * + */ + public Object getentry() { + return entry; + } + + /***************************************************************************************************** + * + * This method sets the value of entryname. + * + * @param value will update entryname, which is a String type. + * + */ + public void setentryname( String value ) { + entryname = value; + } + + /***************************************************************************************************** + * + * This method sets the value of entryname. + * + * @param value will update entryname, which is a Expression type. + * + */ + public void setentryname( Expression value ) { + entryname = value; + } + + /***************************************************************************************************** + * + * This method returns the value of entryname. + * + * @return This method will return the value of entryname, which is a Object type. + * + */ + public Object getentryname() { + return entryname; + } + + /***************************************************************************************************** + * + * This method sets the value of writable. + * + * @param value will update writable, which is a Boolean type. + * + */ + public void setwritable( Boolean value ) { + writable = value; + } + + /***************************************************************************************************** + * + * This method returns the value of writable. + * + * @return This method will return the value of writable, which is a Boolean type. + * + */ + public Boolean getwritable() { + return writable; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/DocType.java b/sdk-and-javadoc-generation/org/commonwl/lang/DocType.java new file mode 100644 index 00000000..bee4914c --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/DocType.java @@ -0,0 +1,147 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public interface DocType { + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`. + */ + String docParent = null; + + /***************************************************************************************************** + * + * A documentation string for this type, or an array of strings which should be concatenated. + */ + Object doc = null; + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level. + */ + String docAfter = null; + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type. + */ + Object docChild = null; + + + /***************************************************************************************************** + * + * This method sets the value of docParent. + * + * @param value will update docParent, which is a String type. + * + */ + public void setdocParent( String value ); + + /***************************************************************************************************** + * + * This method returns the value of docParent. + * + * @return This method will return the value of docParent, which is a String type. + * + */ + public String getdocParent(); + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ); + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String array. + * + */ + public void setdoc( String [] value ); + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a Object type. + * + */ + public Object getdoc(); + /***************************************************************************************************** + * + * This method sets the value of docAfter. + * + * @param value will update docAfter, which is a String type. + * + */ + public void setdocAfter( String value ); + + /***************************************************************************************************** + * + * This method returns the value of docAfter. + * + * @return This method will return the value of docAfter, which is a String type. + * + */ + public String getdocAfter(); + /***************************************************************************************************** + * + * This method sets the value of docChild. + * + * @param value will update docChild, which is a String type. + * + */ + public void setdocChild( String value ); + + /***************************************************************************************************** + * + * This method sets the value of docChild. + * + * @param value will update docChild, which is a String array. + * + */ + public void setdocChild( String [] value ); + + /***************************************************************************************************** + * + * This method returns the value of docChild. + * + * @return This method will return the value of docChild, which is a Object type. + * + */ + public Object getdocChild(); +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/DockerRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/DockerRequirement.java new file mode 100644 index 00000000..4b51aadf --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/DockerRequirement.java @@ -0,0 +1,239 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Indicates that a workflow component should be run in a [Docker](http://docker.com) container, and specifies how to fetch or build the image. +*/ +public class DockerRequirement implements ProcessRequirement { + + /***************************************************************************************************** + * + * Supply the contents of a Dockerfile which will be built using `docker build`. + */ + String dockerFile = null; + + /***************************************************************************************************** + * + * Specify a Docker image to retrieve using `docker pull`. + */ + String dockerPull = null; + + /***************************************************************************************************** + * + * Provide HTTP URL to download and gunzip a Docker images using `docker import. + */ + String dockerImport = null; + + /***************************************************************************************************** + * + * Set the designated output directory to a specific location inside the Docker container. + */ + String dockerOutputDirectory = null; + + /***************************************************************************************************** + * + * Specify a HTTP URL from which to download a Docker image using `docker load`. + */ + String dockerLoad = null; + + /***************************************************************************************************** + * + * The image id that will be used for `docker run`. May be a human-readable image name or the image identifier hash. May be skipped if `dockerPull` is specified, in which case the `dockerPull` image id must be used. + */ + String dockerImageId = null; + + /***************************************************************************************************** + * + * Always 'DockerRequirement' + */ + String class_value = null; + + + public DockerRequirement() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of dockerFile. + * + * @param value will update dockerFile, which is a String type. + * + */ + public void setdockerFile( String value ) { + dockerFile = value; + } + + /***************************************************************************************************** + * + * This method returns the value of dockerFile. + * + * @return This method will return the value of dockerFile, which is a String type. + * + */ + public String getdockerFile() { + return dockerFile; + } + + /***************************************************************************************************** + * + * This method sets the value of dockerPull. + * + * @param value will update dockerPull, which is a String type. + * + */ + public void setdockerPull( String value ) { + dockerPull = value; + } + + /***************************************************************************************************** + * + * This method returns the value of dockerPull. + * + * @return This method will return the value of dockerPull, which is a String type. + * + */ + public String getdockerPull() { + return dockerPull; + } + + /***************************************************************************************************** + * + * This method sets the value of dockerImport. + * + * @param value will update dockerImport, which is a String type. + * + */ + public void setdockerImport( String value ) { + dockerImport = value; + } + + /***************************************************************************************************** + * + * This method returns the value of dockerImport. + * + * @return This method will return the value of dockerImport, which is a String type. + * + */ + public String getdockerImport() { + return dockerImport; + } + + /***************************************************************************************************** + * + * This method sets the value of dockerOutputDirectory. + * + * @param value will update dockerOutputDirectory, which is a String type. + * + */ + public void setdockerOutputDirectory( String value ) { + dockerOutputDirectory = value; + } + + /***************************************************************************************************** + * + * This method returns the value of dockerOutputDirectory. + * + * @return This method will return the value of dockerOutputDirectory, which is a String type. + * + */ + public String getdockerOutputDirectory() { + return dockerOutputDirectory; + } + + /***************************************************************************************************** + * + * This method sets the value of dockerLoad. + * + * @param value will update dockerLoad, which is a String type. + * + */ + public void setdockerLoad( String value ) { + dockerLoad = value; + } + + /***************************************************************************************************** + * + * This method returns the value of dockerLoad. + * + * @return This method will return the value of dockerLoad, which is a String type. + * + */ + public String getdockerLoad() { + return dockerLoad; + } + + /***************************************************************************************************** + * + * This method sets the value of dockerImageId. + * + * @param value will update dockerImageId, which is a String type. + * + */ + public void setdockerImageId( String value ) { + dockerImageId = value; + } + + /***************************************************************************************************** + * + * This method returns the value of dockerImageId. + * + * @return This method will return the value of dockerImageId, which is a String type. + * + */ + public String getdockerImageId() { + return dockerImageId; + } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/Documentation.java b/sdk-and-javadoc-generation/org/commonwl/lang/Documentation.java new file mode 100644 index 00000000..d3f45d6e --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/Documentation.java @@ -0,0 +1,235 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* A documentation section. This type exists to facilitate self-documenting schemas but has no role in formal validation. +*/ +public class Documentation implements NamedType, DocType { + + /***************************************************************************************************** + * + * Must be `documentation` + */ + Object type = null; + + + /***************************************************************************************************** + * + * The identifier for this type + */ + String name = null; + + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`. + */ + String docParent = null; + + /***************************************************************************************************** + * + * A documentation string for this type, or an array of strings which should be concatenated. + */ + Object doc = null; + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level. + */ + String docAfter = null; + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type. + */ + Object docChild = null; + + + public Documentation() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a Object type. + * + */ + public void settype( Object value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of type. + * + * @return This method will return the value of type, which is a Object type. + * + */ + public Object gettype() { + return type; + } + + /***************************************************************************************************** + * + * This method sets the value of name. + * + * @param value will update name, which is a String type. + * + */ + public void setname( String value ) { + name = value; + } + + /***************************************************************************************************** + * + * This method returns the value of name. + * + * @return This method will return the value of name, which is a String type. + * + */ + public String getname() { + return name; + } + + /***************************************************************************************************** + * + * This method sets the value of docParent. + * + * @param value will update docParent, which is a String type. + * + */ + public void setdocParent( String value ) { + docParent = value; + } + + /***************************************************************************************************** + * + * This method returns the value of docParent. + * + * @return This method will return the value of docParent, which is a String type. + * + */ + public String getdocParent() { + return docParent; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String array. + * + */ + public void setdoc( String [] value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a Object type. + * + */ + public Object getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of docAfter. + * + * @param value will update docAfter, which is a String type. + * + */ + public void setdocAfter( String value ) { + docAfter = value; + } + + /***************************************************************************************************** + * + * This method returns the value of docAfter. + * + * @return This method will return the value of docAfter, which is a String type. + * + */ + public String getdocAfter() { + return docAfter; + } + + /***************************************************************************************************** + * + * This method sets the value of docChild. + * + * @param value will update docChild, which is a String type. + * + */ + public void setdocChild( String value ) { + docChild = value; + } + + /***************************************************************************************************** + * + * This method sets the value of docChild. + * + * @param value will update docChild, which is a String array. + * + */ + public void setdocChild( String [] value ) { + docChild = value; + } + + /***************************************************************************************************** + * + * This method returns the value of docChild. + * + * @return This method will return the value of docChild, which is a Object type. + * + */ + public Object getdocChild() { + return docChild; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/EnumSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/EnumSchema.java new file mode 100644 index 00000000..20baac75 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/EnumSchema.java @@ -0,0 +1,42 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Define an enumerated type. +*/ +public class EnumSchema { + + public EnumSchema() { super(); } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/EnvVarRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/EnvVarRequirement.java new file mode 100644 index 00000000..dd95d941 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/EnvVarRequirement.java @@ -0,0 +1,99 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Define a list of environment variables which will be set in the execution environment of the tool. See `EnvironmentDef` for details. +*/ +public class EnvVarRequirement implements ProcessRequirement { + + /***************************************************************************************************** + * + * The list of environment variables. + */ + EnvironmentDef envDef = null; + + /***************************************************************************************************** + * + * Always 'EnvVarRequirement' + */ + String class_value = null; + + + public EnvVarRequirement() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of envDef. + * + * @param value will update envDef, which is a EnvironmentDef type. + * + */ + public void setenvDef( EnvironmentDef value ) { + envDef = value; + } + + /***************************************************************************************************** + * + * This method returns the value of envDef. + * + * @return This method will return the value of envDef, which is a EnvironmentDef type. + * + */ + public EnvironmentDef getenvDef() { + return envDef; + } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/EnvironmentDef.java b/sdk-and-javadoc-generation/org/commonwl/lang/EnvironmentDef.java new file mode 100644 index 00000000..db8bacb3 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/EnvironmentDef.java @@ -0,0 +1,110 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Define an environment variable that will be set in the runtime environment by the workflow platform when executing the command line tool. May be the result of executing an expression, such as getting a parameter from input. +*/ +public class EnvironmentDef { + + /***************************************************************************************************** + * + * The environment variable name + */ + String envName = null; + + /***************************************************************************************************** + * + * The environment variable value + */ + Object envValue = null; + + + public EnvironmentDef() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of envName. + * + * @param value will update envName, which is a String type. + * + */ + public void setenvName( String value ) { + envName = value; + } + + /***************************************************************************************************** + * + * This method returns the value of envName. + * + * @return This method will return the value of envName, which is a String type. + * + */ + public String getenvName() { + return envName; + } + + /***************************************************************************************************** + * + * This method sets the value of envValue. + * + * @param value will update envValue, which is a String type. + * + */ + public void setenvValue( String value ) { + envValue = value; + } + + /***************************************************************************************************** + * + * This method sets the value of envValue. + * + * @param value will update envValue, which is a Expression type. + * + */ + public void setenvValue( Expression value ) { + envValue = value; + } + + /***************************************************************************************************** + * + * This method returns the value of envValue. + * + * @return This method will return the value of envValue, which is a Object type. + * + */ + public Object getenvValue() { + return envValue; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/Expression.java b/sdk-and-javadoc-generation/org/commonwl/lang/Expression.java new file mode 100644 index 00000000..50066b5f --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/Expression.java @@ -0,0 +1,42 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + + /***************************************************************************************************** + * + * 'Expression' is not a real type. It indicates that a field must allow runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement) is declared and supported by the platform, the field must also allow Javascript expressions. + */ +public enum Expression { + + ExpressionPlaceholder + +} diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/ExpressionTool.java b/sdk-and-javadoc-generation/org/commonwl/lang/ExpressionTool.java new file mode 100644 index 00000000..717fd14b --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/ExpressionTool.java @@ -0,0 +1,463 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Execute an expression as a Workflow step. +*/ +public class ExpressionTool implements Process { + + /***************************************************************************************************** + * + * The expression to execute. The expression must return a JSON object which matches the output parameters of the ExpressionTool. + */ + Object expression = null; + + String class_value = null; + + + /***************************************************************************************************** + * + * Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. + */ + ExpressionToolOutputParameter [] outputs = null; + + /***************************************************************************************************** + * + * Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option. + */ + Object requirements = null; + + /***************************************************************************************************** + * + * CWL document version. Always required at the document root. Not required for a Process embedded inside another Process. + */ + CWLVersion cwlVersion = null; + + /***************************************************************************************************** + * + * Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object. + */ + InputParameter [] inputs = null; + + /***************************************************************************************************** + * + * Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning. + */ + Any hints = null; + + /***************************************************************************************************** + * + * A long, human-readable description of this process object. + */ + String doc = null; + + /***************************************************************************************************** + * + * The unique identifier for this process object. + */ + String id = null; + + /***************************************************************************************************** + * + * A short, human-readable label of this process object. + */ + String label = null; + + + public ExpressionTool() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of expression. + * + * @param value will update expression, which is a String type. + * + */ + public void setexpression( String value ) { + expression = value; + } + + /***************************************************************************************************** + * + * This method sets the value of expression. + * + * @param value will update expression, which is a Expression type. + * + */ + public void setexpression( Expression value ) { + expression = value; + } + + /***************************************************************************************************** + * + * This method returns the value of expression. + * + * @return This method will return the value of expression, which is a Object type. + * + */ + public Object getexpression() { + return expression; + } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + + /***************************************************************************************************** + * + * This method sets the value of outputs. + * + * @param value will update outputs, which is a OutputParameter array. + * + */ + public void setoutputs( ExpressionToolOutputParameter [] value ) { + outputs = value; + } + + /***************************************************************************************************** + * + * This is a dummy method which has no functionality, and is required + * for implementing an interface method that was previously specialized. + * + * + */ + public void setoutputs( OutputParameter [] value ) { + + } + + /***************************************************************************************************** + * + * This method returns the value of outputs. + * + * @return This method will return the value of outputs, which is a ExpressionToolOutputParameter array. + * + */ + public ExpressionToolOutputParameter [] getoutputs() { + return outputs; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a StepInputExpressionRequirement type. + * + */ + public void setrequirements( StepInputExpressionRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a MultipleInputFeatureRequirement type. + * + */ + public void setrequirements( MultipleInputFeatureRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SoftwareRequirement type. + * + */ + public void setrequirements( SoftwareRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SchemaDefRequirement type. + * + */ + public void setrequirements( SchemaDefRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a InitialWorkDirRequirement type. + * + */ + public void setrequirements( InitialWorkDirRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a EnvVarRequirement type. + * + */ + public void setrequirements( EnvVarRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a DockerRequirement type. + * + */ + public void setrequirements( DockerRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ResourceRequirement type. + * + */ + public void setrequirements( ResourceRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a InlineJavascriptRequirement type. + * + */ + public void setrequirements( InlineJavascriptRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ShellCommandRequirement type. + * + */ + public void setrequirements( ShellCommandRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ScatterFeatureRequirement type. + * + */ + public void setrequirements( ScatterFeatureRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SubworkflowFeatureRequirement type. + * + */ + public void setrequirements( SubworkflowFeatureRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method returns the value of requirements. + * + * @return This method will return the value of requirements, which is a Object type. + * + */ + public Object getrequirements() { + return requirements; + } + + /***************************************************************************************************** + * + * This method sets the value of cwlVersion. + * + * @param value will update cwlVersion, which is a CWLVersion type. + * + */ + public void setcwlVersion( CWLVersion value ) { + cwlVersion = value; + } + + /***************************************************************************************************** + * + * This method returns the value of cwlVersion. + * + * @return This method will return the value of cwlVersion, which is a CWLVersion type. + * + */ + public CWLVersion getcwlVersion() { + return cwlVersion; + } + + /***************************************************************************************************** + * + * This method sets the value of inputs. + * + * @param value will update inputs, which is a InputParameter array. + * + */ + public void setinputs( InputParameter [] value ) { + inputs = value; + } + + /***************************************************************************************************** + * + * This method returns the value of inputs. + * + * @return This method will return the value of inputs, which is a InputParameter array. + * + */ + public InputParameter [] getinputs() { + return inputs; + } + + /***************************************************************************************************** + * + * This method sets the value of hints. + * + * @param value will update hints, which is a Any type. + * + */ + public void sethints( Any value ) { + hints = value; + } + + /***************************************************************************************************** + * + * This method returns the value of hints. + * + * @return This method will return the value of hints, which is a Any type. + * + */ + public Any gethints() { + return hints; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a String type. + * + */ + public String getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ) { + id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid() { + return id; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/ExpressionToolOutputParameter.java b/sdk-and-javadoc-generation/org/commonwl/lang/ExpressionToolOutputParameter.java new file mode 100644 index 00000000..4e7799b5 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/ExpressionToolOutputParameter.java @@ -0,0 +1,431 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class ExpressionToolOutputParameter extends OutputParameter { + + /***************************************************************************************************** + * + * Specify valid types of data that may be assigned to this parameter. + */ + Object type = null; + + + /***************************************************************************************************** + * + * Describes how to handle the outputs of a process. + */ + CommandOutputBinding outputBinding = null; + + /***************************************************************************************************** + * + * The unique identifier for this parameter object. + */ + String id = null; + + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. + */ + Boolean streamable = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter. + */ + Object format = null; + + /***************************************************************************************************** + * + * A documentation string for this type, or an array of strings which should be concatenated. + */ + Object doc = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path. + */ + Object secondaryFiles = null; + + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + public ExpressionToolOutputParameter() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a OutputRecordSchema array. + * + */ + public void settype( OutputRecordSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a OutputEnumSchema array. + * + */ + public void settype( OutputEnumSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String array. + * + */ + public void settype( String [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a OutputRecordSchema type. + * + */ + public void settype( OutputRecordSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a OutputEnumSchema type. + * + */ + public void settype( OutputEnumSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CWLType array. + * + */ + public void settype( CWLType [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a OutputArraySchema type. + * + */ + public void settype( OutputArraySchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a OutputArraySchema array. + * + */ + public void settype( OutputArraySchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CWLType type. + * + */ + public void settype( CWLType value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String type. + * + */ + public void settype( String value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of type. + * + * @return This method will return the value of type, which is a Object type. + * + */ + public Object gettype() { + return type; + } + + /***************************************************************************************************** + * + * This method sets the value of outputBinding. + * + * @param value will update outputBinding, which is a CommandOutputBinding type. + * + */ + public void setoutputBinding( CommandOutputBinding value ) { + outputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outputBinding. + * + * @return This method will return the value of outputBinding, which is a CommandOutputBinding type. + * + */ + public CommandOutputBinding getoutputBinding() { + return outputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ) { + id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid() { + return id; + } + + /***************************************************************************************************** + * + * This method sets the value of streamable. + * + * @param value will update streamable, which is a Boolean type. + * + */ + public void setstreamable( Boolean value ) { + streamable = value; + } + + /***************************************************************************************************** + * + * This method returns the value of streamable. + * + * @return This method will return the value of streamable, which is a Boolean type. + * + */ + public Boolean getstreamable() { + return streamable; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a Expression array. + * + */ + public void setformat( Expression [] value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String type. + * + */ + public void setformat( String value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String array. + * + */ + public void setformat( String [] value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method returns the value of format. + * + * @return This method will return the value of format, which is a Object type. + * + */ + public Object getformat() { + return format; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String array. + * + */ + public void setdoc( String [] value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a Object type. + * + */ + public Object getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression array. + * + */ + public void setsecondaryFiles( Expression [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String type. + * + */ + public void setsecondaryFiles( String value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String array. + * + */ + public void setsecondaryFiles( String [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression type. + * + */ + public void setsecondaryFiles( Expression value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method returns the value of secondaryFiles. + * + * @return This method will return the value of secondaryFiles, which is a Object type. + * + */ + public Object getsecondaryFiles() { + return secondaryFiles; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/File.java b/sdk-and-javadoc-generation/org/commonwl/lang/File.java new file mode 100644 index 00000000..0b9cf405 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/File.java @@ -0,0 +1,390 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Represents a file (or group of files if `secondaryFiles` is specified) that must be accessible by tools using standard POSIX file system call API such as open(2) and read(2). +*/ +public class File { + + /***************************************************************************************************** + * + * The local host path where the File is available when a CommandLineTool is executed. This field must be set by the implementation. The final path component must match the value of `basename`. This field must not be used in any other context. The command line tool being executed must be able to to access the file at `path` using the POSIX `open(2)` syscall. As a special case, if the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, and remove the `path` field. If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) (`|`,`{@literal &}`, `;`, `(`, `)`, `(`,`)`, `$`,`` ` ``, `\`, ``, `'`, `(space)`, `(tab)`, and `(newline)`) or characters [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) then implementations may terminate the process with a `permanentFailure`. + */ + String path = null; + + /***************************************************************************************************** + * + * The base name of the file, that is, the name of the file without any leading directory path. The base name must not contain a slash `/`. If not provided, the implementation must set this field based on the `location` field by taking the final path component after parsing `location` as an IRI. If `basename` is provided, it is not required to match the value from `location`. When this file is made available to a CommandLineTool, it must be named with `basename`, i.e. the final component of the `path` field must match `basename`. + */ + String basename = null; + + /***************************************************************************************************** + * + * The basename extension such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period. Leading periods on the basename are ignored; a basename of `.cshrc` will have an empty `nameext`. The implementation must set this field automatically based on the value of `basename` prior to evaluating parameter references or expressions. + */ + String nameext = null; + + /***************************************************************************************************** + * + * Optional file size + */ + Long size = null; + + /***************************************************************************************************** + * + * File contents literal. Maximum of 64 KiB. If neither `location` nor `path` is provided, `contents` must be non-null. The implementation must assign a unique identifier for the `location` field. When the file is staged as input to CommandLineTool, the value of `contents` must be written to a file. If `loadContents` of `inputBinding` or `outputBinding` is true and `location` is valid, the implementation must read up to the first 64 KiB of text from the file and place it in the contents field. + */ + String contents = null; + + /***************************************************************************************************** + * + * Optional hash code for validating file integrity. Currently must be in the form sha1$ + hexadecimal string using the SHA-1 algorithm. + */ + String checksum = null; + + /***************************************************************************************************** + * + * The format of the file: this must be an IRI of a concept node that represents the file format, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. Reasoning about format compatability must be done by checking that an input file format is the same, `owl:equivalentClass` or `rdfs:subClassOf` the format required by the input parameter. `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if `(B) owl:equivalentClass (C)` and `(B) owl:subclassOf (A)` then infer `(C) owl:subclassOf (A)`. File format ontologies may be provided in the $schema metadata at the root of the document. If no ontologies are specified in `$schema`, the runtime may perform exact file format matches. + */ + String format = null; + + /***************************************************************************************************** + * + * An IRI that identifies the file resource. This may be a relative reference, in which case it must be resolved using the base IRI of the document. The location may refer to a local or remote resource; the implementation must use the IRI to retrieve file content. If an implementation is unable to retrieve the file content stored at a remote resource (due to unsupported protocol, access denied, or other issue) it must signal an error. If the `location` field is not provided, the `contents` field must be provided. The implementation must assign a unique identifier for the `location` field. If the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, then follow the rules above. + */ + String location = null; + + /***************************************************************************************************** + * + * A list of additional files that are associated with the primary file and must be transferred alongside the primary file. Examples include indexes of the primary file, or external references which must be included when loading primary document. A file object listed in `secondaryFiles` may itself include `secondaryFiles` for which the same rules apply. + */ + Object secondaryFiles = null; + + /***************************************************************************************************** + * + * Must be `File` to indicate this object describes a file. + */ + File class_value = null; + + /***************************************************************************************************** + * + * The name of the directory containing file, that is, the path leading up to the final slash in the path such that `dirname + '/' + basename == path`. The implementation must set this field based on the value of `path` prior to evaluating parameter references or expressions in a CommandLineTool document. This field must not be used in any other context. + */ + String dirname = null; + + /***************************************************************************************************** + * + * The basename root such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period. For the purposess of path splitting leading periods on the basename are ignored; a basename of `.cshrc` will have a nameroot of `.cshrc`. The implementation must set this field automatically based on the value of `basename` prior to evaluating parameter references or expressions. + */ + String nameroot = null; + + + public File() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of path. + * + * @param value will update path, which is a String type. + * + */ + public void setpath( String value ) { + path = value; + } + + /***************************************************************************************************** + * + * This method returns the value of path. + * + * @return This method will return the value of path, which is a String type. + * + */ + public String getpath() { + return path; + } + + /***************************************************************************************************** + * + * This method sets the value of basename. + * + * @param value will update basename, which is a String type. + * + */ + public void setbasename( String value ) { + basename = value; + } + + /***************************************************************************************************** + * + * This method returns the value of basename. + * + * @return This method will return the value of basename, which is a String type. + * + */ + public String getbasename() { + return basename; + } + + /***************************************************************************************************** + * + * This method sets the value of nameext. + * + * @param value will update nameext, which is a String type. + * + */ + public void setnameext( String value ) { + nameext = value; + } + + /***************************************************************************************************** + * + * This method returns the value of nameext. + * + * @return This method will return the value of nameext, which is a String type. + * + */ + public String getnameext() { + return nameext; + } + + /***************************************************************************************************** + * + * This method sets the value of size. + * + * @param value will update size, which is a Long type. + * + */ + public void setsize( Long value ) { + size = value; + } + + /***************************************************************************************************** + * + * This method returns the value of size. + * + * @return This method will return the value of size, which is a Long type. + * + */ + public Long getsize() { + return size; + } + + /***************************************************************************************************** + * + * This method sets the value of contents. + * + * @param value will update contents, which is a String type. + * + */ + public void setcontents( String value ) { + contents = value; + } + + /***************************************************************************************************** + * + * This method returns the value of contents. + * + * @return This method will return the value of contents, which is a String type. + * + */ + public String getcontents() { + return contents; + } + + /***************************************************************************************************** + * + * This method sets the value of checksum. + * + * @param value will update checksum, which is a String type. + * + */ + public void setchecksum( String value ) { + checksum = value; + } + + /***************************************************************************************************** + * + * This method returns the value of checksum. + * + * @return This method will return the value of checksum, which is a String type. + * + */ + public String getchecksum() { + return checksum; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String type. + * + */ + public void setformat( String value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method returns the value of format. + * + * @return This method will return the value of format, which is a String type. + * + */ + public String getformat() { + return format; + } + + /***************************************************************************************************** + * + * This method sets the value of location. + * + * @param value will update location, which is a String type. + * + */ + public void setlocation( String value ) { + location = value; + } + + /***************************************************************************************************** + * + * This method returns the value of location. + * + * @return This method will return the value of location, which is a String type. + * + */ + public String getlocation() { + return location; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a File array. + * + */ + public void setsecondaryFiles( File [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Directory array. + * + */ + public void setsecondaryFiles( Directory [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method returns the value of secondaryFiles. + * + * @return This method will return the value of secondaryFiles, which is a Object type. + * + */ + public Object getsecondaryFiles() { + return secondaryFiles; + } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a File type. + * + */ + public void setclass( File value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a File type. + * + */ + public File getclass() { + return class_value; + } + + /***************************************************************************************************** + * + * This method sets the value of dirname. + * + * @param value will update dirname, which is a String type. + * + */ + public void setdirname( String value ) { + dirname = value; + } + + /***************************************************************************************************** + * + * This method returns the value of dirname. + * + * @return This method will return the value of dirname, which is a String type. + * + */ + public String getdirname() { + return dirname; + } + + /***************************************************************************************************** + * + * This method sets the value of nameroot. + * + * @param value will update nameroot, which is a String type. + * + */ + public void setnameroot( String value ) { + nameroot = value; + } + + /***************************************************************************************************** + * + * This method returns the value of nameroot. + * + * @return This method will return the value of nameroot, which is a String type. + * + */ + public String getnameroot() { + return nameroot; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/InitialWorkDirRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/InitialWorkDirRequirement.java new file mode 100644 index 00000000..032f5f81 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/InitialWorkDirRequirement.java @@ -0,0 +1,143 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Define a list of files and subdirectories that must be created by the workflow platform in the designated output directory prior to executing the command line tool. +*/ +public class InitialWorkDirRequirement implements ProcessRequirement { + + /***************************************************************************************************** + * + * The list of files or subdirectories that must be placed in the designated output directory prior to executing the command line tool. May be an expression. If so, the expression return value must validate as `{type: array, items: [File, Directory]}`. + */ + Object listing = null; + + /***************************************************************************************************** + * + * InitialWorkDirRequirement + */ + String class_value = null; + + + public InitialWorkDirRequirement() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of listing. + * + * @param value will update listing, which is a Dirent array. + * + */ + public void setlisting( Dirent [] value ) { + listing = value; + } + + /***************************************************************************************************** + * + * This method sets the value of listing. + * + * @param value will update listing, which is a File array. + * + */ + public void setlisting( File [] value ) { + listing = value; + } + + /***************************************************************************************************** + * + * This method sets the value of listing. + * + * @param value will update listing, which is a Directory array. + * + */ + public void setlisting( Directory [] value ) { + listing = value; + } + + /***************************************************************************************************** + * + * This method sets the value of listing. + * + * @param value will update listing, which is a Expression array. + * + */ + public void setlisting( Expression [] value ) { + listing = value; + } + + /***************************************************************************************************** + * + * This method sets the value of listing. + * + * @param value will update listing, which is a String array. + * + */ + public void setlisting( String [] value ) { + listing = value; + } + + /***************************************************************************************************** + * + * This method returns the value of listing. + * + * @return This method will return the value of listing, which is a Object type. + * + */ + public Object getlisting() { + return listing; + } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/InlineJavascriptRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/InlineJavascriptRequirement.java new file mode 100644 index 00000000..ff5cbbdf --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/InlineJavascriptRequirement.java @@ -0,0 +1,99 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Indicates that the workflow platform must support inline Javascript expressions. If this requirement is not present, the workflow platform must not perform expression interpolatation. +*/ +public class InlineJavascriptRequirement implements ProcessRequirement { + + /***************************************************************************************************** + * + * Additional code fragments that will also be inserted before executing the expression code. Allows for function definitions that may be called from CWL expressions. + */ + String expressionLib = null; + + /***************************************************************************************************** + * + * Always 'InlineJavascriptRequirement' + */ + String class_value = null; + + + public InlineJavascriptRequirement() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of expressionLib. + * + * @param value will update expressionLib, which is a String type. + * + */ + public void setexpressionLib( String value ) { + expressionLib = value; + } + + /***************************************************************************************************** + * + * This method returns the value of expressionLib. + * + * @return This method will return the value of expressionLib, which is a String type. + * + */ + public String getexpressionLib() { + return expressionLib; + } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/InputArraySchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/InputArraySchema.java new file mode 100644 index 00000000..404cd99c --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/InputArraySchema.java @@ -0,0 +1,92 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class InputArraySchema extends ArraySchema implements InputSchema { + + CommandLineBinding inputBinding = null; + + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + public InputArraySchema() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of inputBinding. + * + * @param value will update inputBinding, which is a CommandLineBinding type. + * + */ + public void setinputBinding( CommandLineBinding value ) { + inputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of inputBinding. + * + * @return This method will return the value of inputBinding, which is a CommandLineBinding type. + * + */ + public CommandLineBinding getinputBinding() { + return inputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/InputBinding.java b/sdk-and-javadoc-generation/org/commonwl/lang/InputBinding.java new file mode 100644 index 00000000..aeffa36b --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/InputBinding.java @@ -0,0 +1,60 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public interface InputBinding { + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. Read up to the first 64 KiB of text from the file and place it in the contents field of the file object for use by expressions. + */ + Boolean loadContents = null; + + + /***************************************************************************************************** + * + * This method sets the value of loadContents. + * + * @param value will update loadContents, which is a Boolean type. + * + */ + public void setloadContents( Boolean value ); + + /***************************************************************************************************** + * + * This method returns the value of loadContents. + * + * @return This method will return the value of loadContents, which is a Boolean type. + * + */ + public Boolean getloadContents(); +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/InputEnumSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/InputEnumSchema.java new file mode 100644 index 00000000..9d4b0551 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/InputEnumSchema.java @@ -0,0 +1,92 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class InputEnumSchema extends EnumSchema implements InputSchema { + + CommandLineBinding inputBinding = null; + + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + public InputEnumSchema() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of inputBinding. + * + * @param value will update inputBinding, which is a CommandLineBinding type. + * + */ + public void setinputBinding( CommandLineBinding value ) { + inputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of inputBinding. + * + * @return This method will return the value of inputBinding, which is a CommandLineBinding type. + * + */ + public CommandLineBinding getinputBinding() { + return inputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/InputParameter.java b/sdk-and-javadoc-generation/org/commonwl/lang/InputParameter.java new file mode 100644 index 00000000..9ef48a39 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/InputParameter.java @@ -0,0 +1,458 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class InputParameter implements Parameter { + + /***************************************************************************************************** + * + * The default value for this parameter if not provided in the input object. + */ + Any default_value = null; + + /***************************************************************************************************** + * + * The unique identifier for this parameter object. + */ + String id = null; + + /***************************************************************************************************** + * + * Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters. + */ + CommandLineBinding inputBinding = null; + + /***************************************************************************************************** + * + * Specify valid types of data that may be assigned to this parameter. + */ + Object type = null; + + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. + */ + Boolean streamable = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter. + */ + Object format = null; + + /***************************************************************************************************** + * + * A documentation string for this type, or an array of strings which should be concatenated. + */ + Object doc = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path. + */ + Object secondaryFiles = null; + + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + public InputParameter() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of default_value. + * + * @param value will update default_value, which is a Any type. + * + */ + public void setdefault( Any value ) { + default_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of default_value. + * + * @return This method will return the value of default_value, which is a Any type. + * + */ + public Any getdefault() { + return default_value; + } + + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ) { + id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid() { + return id; + } + + /***************************************************************************************************** + * + * This method sets the value of inputBinding. + * + * @param value will update inputBinding, which is a CommandLineBinding type. + * + */ + public void setinputBinding( CommandLineBinding value ) { + inputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of inputBinding. + * + * @return This method will return the value of inputBinding, which is a CommandLineBinding type. + * + */ + public CommandLineBinding getinputBinding() { + return inputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a InputEnumSchema array. + * + */ + public void settype( InputEnumSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a InputEnumSchema type. + * + */ + public void settype( InputEnumSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String array. + * + */ + public void settype( String [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a InputRecordSchema array. + * + */ + public void settype( InputRecordSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a InputRecordSchema type. + * + */ + public void settype( InputRecordSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CWLType array. + * + */ + public void settype( CWLType [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CWLType type. + * + */ + public void settype( CWLType value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String type. + * + */ + public void settype( String value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a InputArraySchema type. + * + */ + public void settype( InputArraySchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a InputArraySchema array. + * + */ + public void settype( InputArraySchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of type. + * + * @return This method will return the value of type, which is a Object type. + * + */ + public Object gettype() { + return type; + } + + /***************************************************************************************************** + * + * This method sets the value of streamable. + * + * @param value will update streamable, which is a Boolean type. + * + */ + public void setstreamable( Boolean value ) { + streamable = value; + } + + /***************************************************************************************************** + * + * This method returns the value of streamable. + * + * @return This method will return the value of streamable, which is a Boolean type. + * + */ + public Boolean getstreamable() { + return streamable; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a Expression array. + * + */ + public void setformat( Expression [] value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String type. + * + */ + public void setformat( String value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String array. + * + */ + public void setformat( String [] value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method returns the value of format. + * + * @return This method will return the value of format, which is a Object type. + * + */ + public Object getformat() { + return format; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String array. + * + */ + public void setdoc( String [] value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a Object type. + * + */ + public Object getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression array. + * + */ + public void setsecondaryFiles( Expression [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String type. + * + */ + public void setsecondaryFiles( String value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String array. + * + */ + public void setsecondaryFiles( String [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression type. + * + */ + public void setsecondaryFiles( Expression value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method returns the value of secondaryFiles. + * + * @return This method will return the value of secondaryFiles, which is a Object type. + * + */ + public Object getsecondaryFiles() { + return secondaryFiles; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/InputRecordField.java b/sdk-and-javadoc-generation/org/commonwl/lang/InputRecordField.java new file mode 100644 index 00000000..109a326d --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/InputRecordField.java @@ -0,0 +1,275 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class InputRecordField extends RecordField { + + /***************************************************************************************************** + * + * A short, human-readable label of this process object. + */ + String label = null; + + CommandLineBinding inputBinding = null; + + + /***************************************************************************************************** + * + * The name of the field + */ + String name = null; + + /***************************************************************************************************** + * + * A documentation string for this field + */ + String doc = null; + + /***************************************************************************************************** + * + * The field type + */ + Object type = null; + + + public InputRecordField() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + + /***************************************************************************************************** + * + * This method sets the value of inputBinding. + * + * @param value will update inputBinding, which is a CommandLineBinding type. + * + */ + public void setinputBinding( CommandLineBinding value ) { + inputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of inputBinding. + * + * @return This method will return the value of inputBinding, which is a CommandLineBinding type. + * + */ + public CommandLineBinding getinputBinding() { + return inputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of name. + * + * @param value will update name, which is a String type. + * + */ + public void setname( String value ) { + name = value; + } + + /***************************************************************************************************** + * + * This method returns the value of name. + * + * @return This method will return the value of name, which is a String type. + * + */ + public String getname() { + return name; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a String type. + * + */ + public String getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a RecordSchema type. + * + */ + public void settype( InputRecordSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a EnumSchema type. + * + */ + public void settype( InputEnumSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a ArraySchema type. + * + */ + public void settype( InputArraySchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String array. + * + */ + public void settype( String [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a PrimitiveType array. + * + */ + public void settype( CWLType [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a RecordSchema array. + * + */ + public void settype( InputRecordSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a PrimitiveType type. + * + */ + public void settype( CWLType value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a ArraySchema array. + * + */ + public void settype( InputArraySchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String type. + * + */ + public void settype( String value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a EnumSchema array. + * + */ + public void settype( InputEnumSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of type. + * + * @return This method will return the value of type, which is a Object type. + * + */ + public Object gettype() { + return type; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/InputRecordSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/InputRecordSchema.java new file mode 100644 index 00000000..ad586dfd --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/InputRecordSchema.java @@ -0,0 +1,67 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class InputRecordSchema extends RecordSchema implements InputSchema { + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + public InputRecordSchema() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/InputSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/InputSchema.java new file mode 100644 index 00000000..21621edf --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/InputSchema.java @@ -0,0 +1,60 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public interface InputSchema extends SchemaBase { + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ); + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel(); +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/JsonldPredicate.java b/sdk-and-javadoc-generation/org/commonwl/lang/JsonldPredicate.java new file mode 100644 index 00000000..54fbe6cc --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/JsonldPredicate.java @@ -0,0 +1,295 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Attached to a record field to define how the parent record field is handled for URI resolution and JSON-LD context generation. +*/ +public class JsonldPredicate { + + /***************************************************************************************************** + * + * Structure hint, corresponds to JSON-LD `@container` directive. + */ + String _container = null; + + /***************************************************************************************************** + * + * If true, this indicates that link validation traversal must stop at this field. This field (it is is a URI) or any fields under it (if it is an object or array) are not subject to link checking. + */ + Boolean noLinkCheck = null; + + /***************************************************************************************************** + * + * Field must be expanded based on the the Schema Salad type DSL. + */ + Boolean typeDSL = null; + + /***************************************************************************************************** + * + * If true and `_type` is `@id` this indicates that the parent field must be resolved according to identity resolution rules instead of link resolution rules. In addition, the field value is considered an assertion that the linked value exists; absence of an object in the loaded document with the URI is not an error. + */ + Boolean identity = null; + + /***************************************************************************************************** + * + * The context type hint, corresponds to JSON-LD `@type` directive. * If the value of this field is `@id` and `identity` is false or unspecified, the parent field must be resolved using the link resolution rules. If `identity` is true, the parent field must be resolved using the identifier expansion rules. * If the value of this field is `@vocab`, the parent field must be resolved using the vocabulary resolution rules. + */ + String _type = null; + + /***************************************************************************************************** + * + * If the field contains a relative reference, it must be resolved by searching for valid document references in each successive parent scope in the document fragment. For example, a reference of `foo` in the context `#foo/bar/baz` will first check for the existence of `#foo/bar/baz/foo`, followed by `#foo/bar/foo`, then `#foo/foo` and then finally `#foo`. The first valid URI in the search order shall be used as the fully resolved value of the identifier. The value of the refScope field is the specified number of levels from the containing identifer scope before starting the search, so if `refScope: 2` then baz and bar must be stripped to get the base `#foo` and search `#foo/foo` and the `#foo`. The last scope searched must be the top level scope before determining if the identifier cannot be resolved. + */ + Integer refScope = null; + + /***************************************************************************************************** + * + * If the value of the field is a JSON object, it must be transformed into an array of JSON objects, where each key-value pair from the source JSON object is a list item, the list items must be JSON objects, and the key is assigned to the field specified by `mapSubject`. + */ + String mapSubject = null; + + /***************************************************************************************************** + * + * The predicate URI that this field corresponds to. Corresponds to JSON-LD `@id` directive. + */ + String _id = null; + + /***************************************************************************************************** + * + * Only applies if `mapSubject` is also provided. If the value of the field is a JSON object, it is transformed as described in `mapSubject`, with the addition that when the value of a map item is not an object, the item is transformed to a JSON object with the key assigned to the field specified by `mapSubject` and the value assigned to the field specified by `mapPredicate`. + */ + String mapPredicate = null; + + + public JsonldPredicate() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of _container. + * + * @param value will update _container, which is a String type. + * + */ + public void set_container( String value ) { + _container = value; + } + + /***************************************************************************************************** + * + * This method returns the value of _container. + * + * @return This method will return the value of _container, which is a String type. + * + */ + public String get_container() { + return _container; + } + + /***************************************************************************************************** + * + * This method sets the value of noLinkCheck. + * + * @param value will update noLinkCheck, which is a Boolean type. + * + */ + public void setnoLinkCheck( Boolean value ) { + noLinkCheck = value; + } + + /***************************************************************************************************** + * + * This method returns the value of noLinkCheck. + * + * @return This method will return the value of noLinkCheck, which is a Boolean type. + * + */ + public Boolean getnoLinkCheck() { + return noLinkCheck; + } + + /***************************************************************************************************** + * + * This method sets the value of typeDSL. + * + * @param value will update typeDSL, which is a Boolean type. + * + */ + public void settypeDSL( Boolean value ) { + typeDSL = value; + } + + /***************************************************************************************************** + * + * This method returns the value of typeDSL. + * + * @return This method will return the value of typeDSL, which is a Boolean type. + * + */ + public Boolean gettypeDSL() { + return typeDSL; + } + + /***************************************************************************************************** + * + * This method sets the value of identity. + * + * @param value will update identity, which is a Boolean type. + * + */ + public void setidentity( Boolean value ) { + identity = value; + } + + /***************************************************************************************************** + * + * This method returns the value of identity. + * + * @return This method will return the value of identity, which is a Boolean type. + * + */ + public Boolean getidentity() { + return identity; + } + + /***************************************************************************************************** + * + * This method sets the value of _type. + * + * @param value will update _type, which is a String type. + * + */ + public void set_type( String value ) { + _type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of _type. + * + * @return This method will return the value of _type, which is a String type. + * + */ + public String get_type() { + return _type; + } + + /***************************************************************************************************** + * + * This method sets the value of refScope. + * + * @param value will update refScope, which is a Integer type. + * + */ + public void setrefScope( Integer value ) { + refScope = value; + } + + /***************************************************************************************************** + * + * This method returns the value of refScope. + * + * @return This method will return the value of refScope, which is a Integer type. + * + */ + public Integer getrefScope() { + return refScope; + } + + /***************************************************************************************************** + * + * This method sets the value of mapSubject. + * + * @param value will update mapSubject, which is a String type. + * + */ + public void setmapSubject( String value ) { + mapSubject = value; + } + + /***************************************************************************************************** + * + * This method returns the value of mapSubject. + * + * @return This method will return the value of mapSubject, which is a String type. + * + */ + public String getmapSubject() { + return mapSubject; + } + + /***************************************************************************************************** + * + * This method sets the value of _id. + * + * @param value will update _id, which is a String type. + * + */ + public void set_id( String value ) { + _id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of _id. + * + * @return This method will return the value of _id, which is a String type. + * + */ + public String get_id() { + return _id; + } + + /***************************************************************************************************** + * + * This method sets the value of mapPredicate. + * + * @param value will update mapPredicate, which is a String type. + * + */ + public void setmapPredicate( String value ) { + mapPredicate = value; + } + + /***************************************************************************************************** + * + * This method returns the value of mapPredicate. + * + * @return This method will return the value of mapPredicate, which is a String type. + * + */ + public String getmapPredicate() { + return mapPredicate; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/LinkMergeMethod.java b/sdk-and-javadoc-generation/org/commonwl/lang/LinkMergeMethod.java new file mode 100644 index 00000000..f6468ef1 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/LinkMergeMethod.java @@ -0,0 +1,42 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + + /***************************************************************************************************** + * + * The input link merge method, described in [WorkflowStepInput](#WorkflowStepInput). + */ +public enum LinkMergeMethod { + + merge_nested, merge_flattened + +} diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/MultipleInputFeatureRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/MultipleInputFeatureRequirement.java new file mode 100644 index 00000000..12f1062b --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/MultipleInputFeatureRequirement.java @@ -0,0 +1,71 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Indicates that the workflow platform must support multiple inbound data links listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput). +*/ +public class MultipleInputFeatureRequirement implements ProcessRequirement { + + /***************************************************************************************************** + * + * Always 'MultipleInputFeatureRequirement' + */ + String class_value = null; + + + public MultipleInputFeatureRequirement() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/NamedType.java b/sdk-and-javadoc-generation/org/commonwl/lang/NamedType.java new file mode 100644 index 00000000..7598230f --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/NamedType.java @@ -0,0 +1,60 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public interface NamedType { + + /***************************************************************************************************** + * + * The identifier for this type + */ + String name = null; + + + /***************************************************************************************************** + * + * This method sets the value of name. + * + * @param value will update name, which is a String type. + * + */ + public void setname( String value ); + + /***************************************************************************************************** + * + * This method returns the value of name. + * + * @return This method will return the value of name, which is a String type. + * + */ + public String getname(); +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/OutputArraySchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/OutputArraySchema.java new file mode 100644 index 00000000..74412017 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/OutputArraySchema.java @@ -0,0 +1,92 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class OutputArraySchema extends ArraySchema implements OutputSchema { + + CommandOutputBinding outputBinding = null; + + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + public OutputArraySchema() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of outputBinding. + * + * @param value will update outputBinding, which is a CommandOutputBinding type. + * + */ + public void setoutputBinding( CommandOutputBinding value ) { + outputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outputBinding. + * + * @return This method will return the value of outputBinding, which is a CommandOutputBinding type. + * + */ + public CommandOutputBinding getoutputBinding() { + return outputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/OutputBinding.java b/sdk-and-javadoc-generation/org/commonwl/lang/OutputBinding.java new file mode 100644 index 00000000..8bbb218d --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/OutputBinding.java @@ -0,0 +1,36 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public interface OutputBinding { + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/OutputEnumSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/OutputEnumSchema.java new file mode 100644 index 00000000..a21c0cbe --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/OutputEnumSchema.java @@ -0,0 +1,92 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class OutputEnumSchema extends EnumSchema implements OutputSchema { + + CommandOutputBinding outputBinding = null; + + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + public OutputEnumSchema() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of outputBinding. + * + * @param value will update outputBinding, which is a CommandOutputBinding type. + * + */ + public void setoutputBinding( CommandOutputBinding value ) { + outputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outputBinding. + * + * @return This method will return the value of outputBinding, which is a CommandOutputBinding type. + * + */ + public CommandOutputBinding getoutputBinding() { + return outputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/OutputParameter.java b/sdk-and-javadoc-generation/org/commonwl/lang/OutputParameter.java new file mode 100644 index 00000000..411cfb34 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/OutputParameter.java @@ -0,0 +1,303 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class OutputParameter implements Parameter { + + /***************************************************************************************************** + * + * Describes how to handle the outputs of a process. + */ + CommandOutputBinding outputBinding = null; + + /***************************************************************************************************** + * + * The unique identifier for this parameter object. + */ + String id = null; + + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. + */ + Boolean streamable = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter. + */ + Object format = null; + + /***************************************************************************************************** + * + * A documentation string for this type, or an array of strings which should be concatenated. + */ + Object doc = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path. + */ + Object secondaryFiles = null; + + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + public OutputParameter() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of outputBinding. + * + * @param value will update outputBinding, which is a CommandOutputBinding type. + * + */ + public void setoutputBinding( CommandOutputBinding value ) { + outputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outputBinding. + * + * @return This method will return the value of outputBinding, which is a CommandOutputBinding type. + * + */ + public CommandOutputBinding getoutputBinding() { + return outputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ) { + id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid() { + return id; + } + + /***************************************************************************************************** + * + * This method sets the value of streamable. + * + * @param value will update streamable, which is a Boolean type. + * + */ + public void setstreamable( Boolean value ) { + streamable = value; + } + + /***************************************************************************************************** + * + * This method returns the value of streamable. + * + * @return This method will return the value of streamable, which is a Boolean type. + * + */ + public Boolean getstreamable() { + return streamable; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a Expression array. + * + */ + public void setformat( Expression [] value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String type. + * + */ + public void setformat( String value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String array. + * + */ + public void setformat( String [] value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method returns the value of format. + * + * @return This method will return the value of format, which is a Object type. + * + */ + public Object getformat() { + return format; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String array. + * + */ + public void setdoc( String [] value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a Object type. + * + */ + public Object getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression array. + * + */ + public void setsecondaryFiles( Expression [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String type. + * + */ + public void setsecondaryFiles( String value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String array. + * + */ + public void setsecondaryFiles( String [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression type. + * + */ + public void setsecondaryFiles( Expression value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method returns the value of secondaryFiles. + * + * @return This method will return the value of secondaryFiles, which is a Object type. + * + */ + public Object getsecondaryFiles() { + return secondaryFiles; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/OutputRecordField.java b/sdk-and-javadoc-generation/org/commonwl/lang/OutputRecordField.java new file mode 100644 index 00000000..ddeb7da4 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/OutputRecordField.java @@ -0,0 +1,247 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class OutputRecordField extends RecordField { + + CommandOutputBinding outputBinding = null; + + + /***************************************************************************************************** + * + * The name of the field + */ + String name = null; + + /***************************************************************************************************** + * + * A documentation string for this field + */ + String doc = null; + + /***************************************************************************************************** + * + * The field type + */ + Object type = null; + + + public OutputRecordField() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of outputBinding. + * + * @param value will update outputBinding, which is a CommandOutputBinding type. + * + */ + public void setoutputBinding( CommandOutputBinding value ) { + outputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outputBinding. + * + * @return This method will return the value of outputBinding, which is a CommandOutputBinding type. + * + */ + public CommandOutputBinding getoutputBinding() { + return outputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of name. + * + * @param value will update name, which is a String type. + * + */ + public void setname( String value ) { + name = value; + } + + /***************************************************************************************************** + * + * This method returns the value of name. + * + * @return This method will return the value of name, which is a String type. + * + */ + public String getname() { + return name; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a String type. + * + */ + public String getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a RecordSchema type. + * + */ + public void settype( OutputRecordSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a EnumSchema type. + * + */ + public void settype( OutputEnumSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a ArraySchema type. + * + */ + public void settype( OutputArraySchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String array. + * + */ + public void settype( String [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a PrimitiveType array. + * + */ + public void settype( CWLType [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a RecordSchema array. + * + */ + public void settype( OutputRecordSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a PrimitiveType type. + * + */ + public void settype( CWLType value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a ArraySchema array. + * + */ + public void settype( OutputArraySchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String type. + * + */ + public void settype( String value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a EnumSchema array. + * + */ + public void settype( OutputEnumSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of type. + * + * @return This method will return the value of type, which is a Object type. + * + */ + public Object gettype() { + return type; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/OutputRecordSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/OutputRecordSchema.java new file mode 100644 index 00000000..5c679c18 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/OutputRecordSchema.java @@ -0,0 +1,67 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class OutputRecordSchema extends RecordSchema implements OutputSchema { + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + public OutputRecordSchema() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/OutputSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/OutputSchema.java new file mode 100644 index 00000000..a7e66709 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/OutputSchema.java @@ -0,0 +1,60 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public interface OutputSchema extends SchemaBase { + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ); + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel(); +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/Parameter.java b/sdk-and-javadoc-generation/org/commonwl/lang/Parameter.java new file mode 100644 index 00000000..30ecd2d6 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/Parameter.java @@ -0,0 +1,211 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Define an input or output parameter to a process. +*/ +public interface Parameter extends SchemaBase { + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. + */ + Boolean streamable = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter. + */ + Object format = null; + + /***************************************************************************************************** + * + * A documentation string for this type, or an array of strings which should be concatenated. + */ + Object doc = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path. + */ + Object secondaryFiles = null; + + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + /***************************************************************************************************** + * + * This method sets the value of streamable. + * + * @param value will update streamable, which is a Boolean type. + * + */ + public void setstreamable( Boolean value ); + + /***************************************************************************************************** + * + * This method returns the value of streamable. + * + * @return This method will return the value of streamable, which is a Boolean type. + * + */ + public Boolean getstreamable(); + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a Expression array. + * + */ + public void setformat( Expression [] value ); + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String type. + * + */ + public void setformat( String value ); + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String array. + * + */ + public void setformat( String [] value ); + + /***************************************************************************************************** + * + * This method returns the value of format. + * + * @return This method will return the value of format, which is a Object type. + * + */ + public Object getformat(); + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ); + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String array. + * + */ + public void setdoc( String [] value ); + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a Object type. + * + */ + public Object getdoc(); + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression array. + * + */ + public void setsecondaryFiles( Expression [] value ); + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String type. + * + */ + public void setsecondaryFiles( String value ); + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String array. + * + */ + public void setsecondaryFiles( String [] value ); + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression type. + * + */ + public void setsecondaryFiles( Expression value ); + + /***************************************************************************************************** + * + * This method returns the value of secondaryFiles. + * + * @return This method will return the value of secondaryFiles, which is a Object type. + * + */ + public Object getsecondaryFiles(); + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ); + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel(); +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/PrimitiveType.java b/sdk-and-javadoc-generation/org/commonwl/lang/PrimitiveType.java new file mode 100644 index 00000000..44ca67d8 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/PrimitiveType.java @@ -0,0 +1,134 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Salad data types are based on Avro schema declarations. Refer to the +* [Avro schema declaration documentation](https://avro.apache.org/docs/current/spec.html#schemas) for +* detailed information. +* The types are: 1) null: no value, +* 2) boolean: a binary value, +* 3) int: 32-bit signed integer, +* 4) long: 64-bit signed integer, +* 5) float: single precision (32-bit) IEEE 754 floating-point number, +* 6) double: double precision (64-bit) IEEE 754 floating-point number, and +* 7) string: Unicode character sequence. +* +*/ +public class PrimitiveType extends Object { + + Object value; + + public PrimitiveType( Object objectInstance ) { + value = objectInstance; + } + + /***************************************************************************************************** + * + * This method sets the value of PrimitiveType. + * + * @param objectInstance sets the value of PrimitiveType, and is a Boolean type. + * + */ + public void set(Boolean objectInstance) { + value = objectInstance; + } + + /***************************************************************************************************** + * + * This method sets the value of PrimitiveType. + * + * @param objectInstance sets the value of PrimitiveType, and is a Integer type. + * + */ + public void set(Integer objectInstance) { + value = objectInstance; + } + + /***************************************************************************************************** + * + * This method sets the value of PrimitiveType. + * + * @param objectInstance sets the value of PrimitiveType, and is a Long type. + * + */ + public void set(Long objectInstance) { + value = objectInstance; + } + + /***************************************************************************************************** + * + * This method sets the value of PrimitiveType. + * + * @param objectInstance sets the value of PrimitiveType, and is a Float type. + * + */ + public void set(Float objectInstance) { + value = objectInstance; + } + + /***************************************************************************************************** + * + * This method sets the value of PrimitiveType. + * + * @param objectInstance sets the value of PrimitiveType, and is a Double type. + * + */ + public void set(Double objectInstance) { + value = objectInstance; + } + + /***************************************************************************************************** + * + * This method sets the value of PrimitiveType. + * + * @param objectInstance sets the value of PrimitiveType, and is a String type. + * + */ + public void set(String objectInstance) { + value = objectInstance; + } + + /***************************************************************************************************** + * + * This method returns the value of PrimitiveType. + * + * @return This method will return the value of PrimitiveType, which is an Object type. + * + */ + public Object get() { + return (Object) value; + } + +} + diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/Process.java b/sdk-and-javadoc-generation/org/commonwl/lang/Process.java new file mode 100644 index 00000000..34168806 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/Process.java @@ -0,0 +1,320 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public interface Process { + + /***************************************************************************************************** + * + * Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. + */ + OutputParameter [] outputs = null; + + /***************************************************************************************************** + * + * Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option. + */ + Object requirements = null; + + /***************************************************************************************************** + * + * CWL document version. Always required at the document root. Not required for a Process embedded inside another Process. + */ + CWLVersion cwlVersion = null; + + /***************************************************************************************************** + * + * Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object. + */ + InputParameter [] inputs = null; + + /***************************************************************************************************** + * + * Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning. + */ + Any hints = null; + + /***************************************************************************************************** + * + * A long, human-readable description of this process object. + */ + String doc = null; + + /***************************************************************************************************** + * + * The unique identifier for this process object. + */ + String id = null; + + /***************************************************************************************************** + * + * A short, human-readable label of this process object. + */ + String label = null; + + + /***************************************************************************************************** + * + * This method sets the value of outputs. + * + * @param value will update outputs, which is a OutputParameter array. + * + */ + public void setoutputs( OutputParameter [] value ); + + /***************************************************************************************************** + * + * This method returns the value of outputs. + * + * @return This method will return the value of outputs, which is a OutputParameter array. + * + */ + public OutputParameter [] getoutputs(); + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a StepInputExpressionRequirement type. + * + */ + public void setrequirements( StepInputExpressionRequirement value ); + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a MultipleInputFeatureRequirement type. + * + */ + public void setrequirements( MultipleInputFeatureRequirement value ); + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SoftwareRequirement type. + * + */ + public void setrequirements( SoftwareRequirement value ); + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SchemaDefRequirement type. + * + */ + public void setrequirements( SchemaDefRequirement value ); + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a InitialWorkDirRequirement type. + * + */ + public void setrequirements( InitialWorkDirRequirement value ); + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a EnvVarRequirement type. + * + */ + public void setrequirements( EnvVarRequirement value ); + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a DockerRequirement type. + * + */ + public void setrequirements( DockerRequirement value ); + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ResourceRequirement type. + * + */ + public void setrequirements( ResourceRequirement value ); + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a InlineJavascriptRequirement type. + * + */ + public void setrequirements( InlineJavascriptRequirement value ); + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ShellCommandRequirement type. + * + */ + public void setrequirements( ShellCommandRequirement value ); + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ScatterFeatureRequirement type. + * + */ + public void setrequirements( ScatterFeatureRequirement value ); + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SubworkflowFeatureRequirement type. + * + */ + public void setrequirements( SubworkflowFeatureRequirement value ); + + /***************************************************************************************************** + * + * This method returns the value of requirements. + * + * @return This method will return the value of requirements, which is a Object type. + * + */ + public Object getrequirements(); + /***************************************************************************************************** + * + * This method sets the value of cwlVersion. + * + * @param value will update cwlVersion, which is a CWLVersion type. + * + */ + public void setcwlVersion( CWLVersion value ); + + /***************************************************************************************************** + * + * This method returns the value of cwlVersion. + * + * @return This method will return the value of cwlVersion, which is a CWLVersion type. + * + */ + public CWLVersion getcwlVersion(); + /***************************************************************************************************** + * + * This method sets the value of inputs. + * + * @param value will update inputs, which is a InputParameter array. + * + */ + public void setinputs( InputParameter [] value ); + + /***************************************************************************************************** + * + * This method returns the value of inputs. + * + * @return This method will return the value of inputs, which is a InputParameter array. + * + */ + public InputParameter [] getinputs(); + /***************************************************************************************************** + * + * This method sets the value of hints. + * + * @param value will update hints, which is a Any type. + * + */ + public void sethints( Any value ); + + /***************************************************************************************************** + * + * This method returns the value of hints. + * + * @return This method will return the value of hints, which is a Any type. + * + */ + public Any gethints(); + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ); + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a String type. + * + */ + public String getdoc(); + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ); + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid(); + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ); + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel(); +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/ProcessRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/ProcessRequirement.java new file mode 100644 index 00000000..36b3ceee --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/ProcessRequirement.java @@ -0,0 +1,40 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* A process requirement declares a prerequisite that may or must be fulfilled before executing a process. See [`Process.hints`](#process) and [`Process.requirements`](#process). +*/ +public interface ProcessRequirement { + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/RecordField.java b/sdk-and-javadoc-generation/org/commonwl/lang/RecordField.java new file mode 100644 index 00000000..a9b022f8 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/RecordField.java @@ -0,0 +1,226 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* A field of a record. +*/ +public class RecordField { + + /***************************************************************************************************** + * + * The name of the field + */ + String name = null; + + /***************************************************************************************************** + * + * A documentation string for this field + */ + String doc = null; + + /***************************************************************************************************** + * + * The field type + */ + Object type = null; + + + public RecordField() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of name. + * + * @param value will update name, which is a String type. + * + */ + public void setname( String value ) { + name = value; + } + + /***************************************************************************************************** + * + * This method returns the value of name. + * + * @return This method will return the value of name, which is a String type. + * + */ + public String getname() { + return name; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a String type. + * + */ + public String getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a RecordSchema type. + * + */ + public void settype( RecordSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a EnumSchema type. + * + */ + public void settype( EnumSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a ArraySchema type. + * + */ + public void settype( ArraySchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String array. + * + */ + public void settype( String [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a PrimitiveType array. + * + */ + public void settype( PrimitiveType [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a RecordSchema array. + * + */ + public void settype( RecordSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a PrimitiveType type. + * + */ + public void settype( PrimitiveType value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a ArraySchema array. + * + */ + public void settype( ArraySchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String type. + * + */ + public void settype( String value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a EnumSchema array. + * + */ + public void settype( EnumSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of type. + * + * @return This method will return the value of type, which is a Object type. + * + */ + public Object gettype() { + return type; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/RecordSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/RecordSchema.java new file mode 100644 index 00000000..7944e740 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/RecordSchema.java @@ -0,0 +1,38 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class RecordSchema { + + public RecordSchema() { super(); } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/ResourceRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/ResourceRequirement.java new file mode 100644 index 00000000..93dfedd9 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/ResourceRequirement.java @@ -0,0 +1,471 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Specify basic hardware resource requirements. +*/ +public class ResourceRequirement implements ProcessRequirement { + + /***************************************************************************************************** + * + * Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) + */ + Object tmpdirMin = null; + + /***************************************************************************************************** + * + * Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) + */ + Object tmpdirMax = null; + + /***************************************************************************************************** + * + * Maximum reserved RAM in mebibytes (2**20) + */ + Object ramMax = null; + + /***************************************************************************************************** + * + * Maximum reserved number of CPU cores + */ + Object coresMax = null; + + /***************************************************************************************************** + * + * Minimum reserved RAM in mebibytes (2**20) + */ + Object ramMin = null; + + /***************************************************************************************************** + * + * Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) + */ + Object outdirMin = null; + + /***************************************************************************************************** + * + * Minimum reserved number of CPU cores + */ + Object coresMin = null; + + /***************************************************************************************************** + * + * Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) + */ + Object outdirMax = null; + + /***************************************************************************************************** + * + * Always 'ResourceRequirement' + */ + String class_value = null; + + + public ResourceRequirement() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of tmpdirMin. + * + * @param value will update tmpdirMin, which is a Expression type. + * + */ + public void settmpdirMin( Expression value ) { + tmpdirMin = value; + } + + /***************************************************************************************************** + * + * This method sets the value of tmpdirMin. + * + * @param value will update tmpdirMin, which is a String type. + * + */ + public void settmpdirMin( String value ) { + tmpdirMin = value; + } + + /***************************************************************************************************** + * + * This method sets the value of tmpdirMin. + * + * @param value will update tmpdirMin, which is a Long type. + * + */ + public void settmpdirMin( Long value ) { + tmpdirMin = value; + } + + /***************************************************************************************************** + * + * This method returns the value of tmpdirMin. + * + * @return This method will return the value of tmpdirMin, which is a Object type. + * + */ + public Object gettmpdirMin() { + return tmpdirMin; + } + + /***************************************************************************************************** + * + * This method sets the value of tmpdirMax. + * + * @param value will update tmpdirMax, which is a Expression type. + * + */ + public void settmpdirMax( Expression value ) { + tmpdirMax = value; + } + + /***************************************************************************************************** + * + * This method sets the value of tmpdirMax. + * + * @param value will update tmpdirMax, which is a String type. + * + */ + public void settmpdirMax( String value ) { + tmpdirMax = value; + } + + /***************************************************************************************************** + * + * This method sets the value of tmpdirMax. + * + * @param value will update tmpdirMax, which is a Long type. + * + */ + public void settmpdirMax( Long value ) { + tmpdirMax = value; + } + + /***************************************************************************************************** + * + * This method returns the value of tmpdirMax. + * + * @return This method will return the value of tmpdirMax, which is a Object type. + * + */ + public Object gettmpdirMax() { + return tmpdirMax; + } + + /***************************************************************************************************** + * + * This method sets the value of ramMax. + * + * @param value will update ramMax, which is a Expression type. + * + */ + public void setramMax( Expression value ) { + ramMax = value; + } + + /***************************************************************************************************** + * + * This method sets the value of ramMax. + * + * @param value will update ramMax, which is a String type. + * + */ + public void setramMax( String value ) { + ramMax = value; + } + + /***************************************************************************************************** + * + * This method sets the value of ramMax. + * + * @param value will update ramMax, which is a Long type. + * + */ + public void setramMax( Long value ) { + ramMax = value; + } + + /***************************************************************************************************** + * + * This method returns the value of ramMax. + * + * @return This method will return the value of ramMax, which is a Object type. + * + */ + public Object getramMax() { + return ramMax; + } + + /***************************************************************************************************** + * + * This method sets the value of coresMax. + * + * @param value will update coresMax, which is a Expression type. + * + */ + public void setcoresMax( Expression value ) { + coresMax = value; + } + + /***************************************************************************************************** + * + * This method sets the value of coresMax. + * + * @param value will update coresMax, which is a String type. + * + */ + public void setcoresMax( String value ) { + coresMax = value; + } + + /***************************************************************************************************** + * + * This method sets the value of coresMax. + * + * @param value will update coresMax, which is a Integer type. + * + */ + public void setcoresMax( Integer value ) { + coresMax = value; + } + + /***************************************************************************************************** + * + * This method returns the value of coresMax. + * + * @return This method will return the value of coresMax, which is a Object type. + * + */ + public Object getcoresMax() { + return coresMax; + } + + /***************************************************************************************************** + * + * This method sets the value of ramMin. + * + * @param value will update ramMin, which is a Expression type. + * + */ + public void setramMin( Expression value ) { + ramMin = value; + } + + /***************************************************************************************************** + * + * This method sets the value of ramMin. + * + * @param value will update ramMin, which is a String type. + * + */ + public void setramMin( String value ) { + ramMin = value; + } + + /***************************************************************************************************** + * + * This method sets the value of ramMin. + * + * @param value will update ramMin, which is a Long type. + * + */ + public void setramMin( Long value ) { + ramMin = value; + } + + /***************************************************************************************************** + * + * This method returns the value of ramMin. + * + * @return This method will return the value of ramMin, which is a Object type. + * + */ + public Object getramMin() { + return ramMin; + } + + /***************************************************************************************************** + * + * This method sets the value of outdirMin. + * + * @param value will update outdirMin, which is a Expression type. + * + */ + public void setoutdirMin( Expression value ) { + outdirMin = value; + } + + /***************************************************************************************************** + * + * This method sets the value of outdirMin. + * + * @param value will update outdirMin, which is a String type. + * + */ + public void setoutdirMin( String value ) { + outdirMin = value; + } + + /***************************************************************************************************** + * + * This method sets the value of outdirMin. + * + * @param value will update outdirMin, which is a Long type. + * + */ + public void setoutdirMin( Long value ) { + outdirMin = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outdirMin. + * + * @return This method will return the value of outdirMin, which is a Object type. + * + */ + public Object getoutdirMin() { + return outdirMin; + } + + /***************************************************************************************************** + * + * This method sets the value of coresMin. + * + * @param value will update coresMin, which is a Expression type. + * + */ + public void setcoresMin( Expression value ) { + coresMin = value; + } + + /***************************************************************************************************** + * + * This method sets the value of coresMin. + * + * @param value will update coresMin, which is a String type. + * + */ + public void setcoresMin( String value ) { + coresMin = value; + } + + /***************************************************************************************************** + * + * This method sets the value of coresMin. + * + * @param value will update coresMin, which is a Long type. + * + */ + public void setcoresMin( Long value ) { + coresMin = value; + } + + /***************************************************************************************************** + * + * This method returns the value of coresMin. + * + * @return This method will return the value of coresMin, which is a Object type. + * + */ + public Object getcoresMin() { + return coresMin; + } + + /***************************************************************************************************** + * + * This method sets the value of outdirMax. + * + * @param value will update outdirMax, which is a Expression type. + * + */ + public void setoutdirMax( Expression value ) { + outdirMax = value; + } + + /***************************************************************************************************** + * + * This method sets the value of outdirMax. + * + * @param value will update outdirMax, which is a String type. + * + */ + public void setoutdirMax( String value ) { + outdirMax = value; + } + + /***************************************************************************************************** + * + * This method sets the value of outdirMax. + * + * @param value will update outdirMax, which is a Long type. + * + */ + public void setoutdirMax( Long value ) { + outdirMax = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outdirMax. + * + * @return This method will return the value of outdirMax, which is a Object type. + * + */ + public Object getoutdirMax() { + return outdirMax; + } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/SaladEnumSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/SaladEnumSchema.java new file mode 100644 index 00000000..2741bc3d --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/SaladEnumSchema.java @@ -0,0 +1,285 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Define an enumerated type. +*/ +public class SaladEnumSchema extends EnumSchema implements SchemaDefinedType { + + /***************************************************************************************************** + * + * Indicates that this enum inherits symbols from a base enum. + */ + Object extends_value = null; + + + /***************************************************************************************************** + * + * If true, indicates that the type is a valid at the document root. At least one type in a schema must be tagged with `documentRoot: true`. + */ + Boolean documentRoot = null; + + /***************************************************************************************************** + * + * Annotate this type with linked data context. + */ + Object jsonldPredicate = null; + + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`. + */ + String docParent = null; + + /***************************************************************************************************** + * + * A documentation string for this type, or an array of strings which should be concatenated. + */ + Object doc = null; + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level. + */ + String docAfter = null; + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type. + */ + Object docChild = null; + + + public SaladEnumSchema() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of extends_value. + * + * @param value will update extends_value, which is a String type. + * + */ + public void setextends( String value ) { + extends_value = value; + } + + /***************************************************************************************************** + * + * This method sets the value of extends_value. + * + * @param value will update extends_value, which is a String array. + * + */ + public void setextends( String [] value ) { + extends_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of extends_value. + * + * @return This method will return the value of extends_value, which is a Object type. + * + */ + public Object getextends() { + return extends_value; + } + + /***************************************************************************************************** + * + * This method sets the value of documentRoot. + * + * @param value will update documentRoot, which is a Boolean type. + * + */ + public void setdocumentRoot( Boolean value ) { + documentRoot = value; + } + + /***************************************************************************************************** + * + * This method returns the value of documentRoot. + * + * @return This method will return the value of documentRoot, which is a Boolean type. + * + */ + public Boolean getdocumentRoot() { + return documentRoot; + } + + /***************************************************************************************************** + * + * This method sets the value of jsonldPredicate. + * + * @param value will update jsonldPredicate, which is a String type. + * + */ + public void setjsonldPredicate( String value ) { + jsonldPredicate = value; + } + + /***************************************************************************************************** + * + * This method sets the value of jsonldPredicate. + * + * @param value will update jsonldPredicate, which is a JsonldPredicate type. + * + */ + public void setjsonldPredicate( JsonldPredicate value ) { + jsonldPredicate = value; + } + + /***************************************************************************************************** + * + * This method returns the value of jsonldPredicate. + * + * @return This method will return the value of jsonldPredicate, which is a Object type. + * + */ + public Object getjsonldPredicate() { + return jsonldPredicate; + } + + /***************************************************************************************************** + * + * This method sets the value of docParent. + * + * @param value will update docParent, which is a String type. + * + */ + public void setdocParent( String value ) { + docParent = value; + } + + /***************************************************************************************************** + * + * This method returns the value of docParent. + * + * @return This method will return the value of docParent, which is a String type. + * + */ + public String getdocParent() { + return docParent; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String array. + * + */ + public void setdoc( String [] value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a Object type. + * + */ + public Object getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of docAfter. + * + * @param value will update docAfter, which is a String type. + * + */ + public void setdocAfter( String value ) { + docAfter = value; + } + + /***************************************************************************************************** + * + * This method returns the value of docAfter. + * + * @return This method will return the value of docAfter, which is a String type. + * + */ + public String getdocAfter() { + return docAfter; + } + + /***************************************************************************************************** + * + * This method sets the value of docChild. + * + * @param value will update docChild, which is a String type. + * + */ + public void setdocChild( String value ) { + docChild = value; + } + + /***************************************************************************************************** + * + * This method sets the value of docChild. + * + * @param value will update docChild, which is a String array. + * + */ + public void setdocChild( String [] value ) { + docChild = value; + } + + /***************************************************************************************************** + * + * This method returns the value of docChild. + * + * @return This method will return the value of docChild, which is a Object type. + * + */ + public Object getdocChild() { + return docChild; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/SaladRecordField.java b/sdk-and-javadoc-generation/org/commonwl/lang/SaladRecordField.java new file mode 100644 index 00000000..1ae8ac27 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/SaladRecordField.java @@ -0,0 +1,266 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* A field of a record. +*/ +public class SaladRecordField extends RecordField { + + /***************************************************************************************************** + * + * Annotate this type with linked data context. + */ + Object jsonldPredicate = null; + + + /***************************************************************************************************** + * + * The name of the field + */ + String name = null; + + /***************************************************************************************************** + * + * A documentation string for this field + */ + String doc = null; + + /***************************************************************************************************** + * + * The field type + */ + Object type = null; + + + public SaladRecordField() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of jsonldPredicate. + * + * @param value will update jsonldPredicate, which is a String type. + * + */ + public void setjsonldPredicate( String value ) { + jsonldPredicate = value; + } + + /***************************************************************************************************** + * + * This method sets the value of jsonldPredicate. + * + * @param value will update jsonldPredicate, which is a JsonldPredicate type. + * + */ + public void setjsonldPredicate( JsonldPredicate value ) { + jsonldPredicate = value; + } + + /***************************************************************************************************** + * + * This method returns the value of jsonldPredicate. + * + * @return This method will return the value of jsonldPredicate, which is a Object type. + * + */ + public Object getjsonldPredicate() { + return jsonldPredicate; + } + + /***************************************************************************************************** + * + * This method sets the value of name. + * + * @param value will update name, which is a String type. + * + */ + public void setname( String value ) { + name = value; + } + + /***************************************************************************************************** + * + * This method returns the value of name. + * + * @return This method will return the value of name, which is a String type. + * + */ + public String getname() { + return name; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a String type. + * + */ + public String getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a RecordSchema type. + * + */ + public void settype( RecordSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a EnumSchema type. + * + */ + public void settype( EnumSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a ArraySchema type. + * + */ + public void settype( ArraySchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String array. + * + */ + public void settype( String [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a PrimitiveType array. + * + */ + public void settype( PrimitiveType [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a RecordSchema array. + * + */ + public void settype( RecordSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a PrimitiveType type. + * + */ + public void settype( PrimitiveType value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a ArraySchema array. + * + */ + public void settype( ArraySchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String type. + * + */ + public void settype( String value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a EnumSchema array. + * + */ + public void settype( EnumSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of type. + * + * @return This method will return the value of type, which is a Object type. + * + */ + public Object gettype() { + return type; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/SaladRecordSchema.java b/sdk-and-javadoc-generation/org/commonwl/lang/SaladRecordSchema.java new file mode 100644 index 00000000..28566904 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/SaladRecordSchema.java @@ -0,0 +1,366 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class SaladRecordSchema extends RecordSchema implements NamedType, SchemaDefinedType { + + /***************************************************************************************************** + * + * Indicates that this record inherits fields from one or more base records. + */ + Object extends_value = null; + + /***************************************************************************************************** + * + * If true, this record is abstract and may be used as a base for other records, but is not valid on its own. + */ + Boolean abstract_value = null; + + /***************************************************************************************************** + * + * Only applies if `extends` is declared. Apply type specialization using the base record as a template. For each field inherited from the base record, replace any instance of the type `specializeFrom` with `specializeTo`. + */ + SpecializeDef [] specialize = null; + + + /***************************************************************************************************** + * + * The identifier for this type + */ + String name = null; + + + /***************************************************************************************************** + * + * If true, indicates that the type is a valid at the document root. At least one type in a schema must be tagged with `documentRoot: true`. + */ + Boolean documentRoot = null; + + /***************************************************************************************************** + * + * Annotate this type with linked data context. + */ + Object jsonldPredicate = null; + + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`. + */ + String docParent = null; + + /***************************************************************************************************** + * + * A documentation string for this type, or an array of strings which should be concatenated. + */ + Object doc = null; + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level. + */ + String docAfter = null; + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type. + */ + Object docChild = null; + + + public SaladRecordSchema() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of extends_value. + * + * @param value will update extends_value, which is a String type. + * + */ + public void setextends( String value ) { + extends_value = value; + } + + /***************************************************************************************************** + * + * This method sets the value of extends_value. + * + * @param value will update extends_value, which is a String array. + * + */ + public void setextends( String [] value ) { + extends_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of extends_value. + * + * @return This method will return the value of extends_value, which is a Object type. + * + */ + public Object getextends() { + return extends_value; + } + + /***************************************************************************************************** + * + * This method sets the value of abstract_value. + * + * @param value will update abstract_value, which is a Boolean type. + * + */ + public void setabstract( Boolean value ) { + abstract_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of abstract_value. + * + * @return This method will return the value of abstract_value, which is a Boolean type. + * + */ + public Boolean getabstract() { + return abstract_value; + } + + /***************************************************************************************************** + * + * This method sets the value of specialize. + * + * @param value will update specialize, which is a SpecializeDef array. + * + */ + public void setspecialize( SpecializeDef [] value ) { + specialize = value; + } + + /***************************************************************************************************** + * + * This method returns the value of specialize. + * + * @return This method will return the value of specialize, which is a SpecializeDef array. + * + */ + public SpecializeDef [] getspecialize() { + return specialize; + } + + /***************************************************************************************************** + * + * This method sets the value of name. + * + * @param value will update name, which is a String type. + * + */ + public void setname( String value ) { + name = value; + } + + /***************************************************************************************************** + * + * This method returns the value of name. + * + * @return This method will return the value of name, which is a String type. + * + */ + public String getname() { + return name; + } + + /***************************************************************************************************** + * + * This method sets the value of documentRoot. + * + * @param value will update documentRoot, which is a Boolean type. + * + */ + public void setdocumentRoot( Boolean value ) { + documentRoot = value; + } + + /***************************************************************************************************** + * + * This method returns the value of documentRoot. + * + * @return This method will return the value of documentRoot, which is a Boolean type. + * + */ + public Boolean getdocumentRoot() { + return documentRoot; + } + + /***************************************************************************************************** + * + * This method sets the value of jsonldPredicate. + * + * @param value will update jsonldPredicate, which is a String type. + * + */ + public void setjsonldPredicate( String value ) { + jsonldPredicate = value; + } + + /***************************************************************************************************** + * + * This method sets the value of jsonldPredicate. + * + * @param value will update jsonldPredicate, which is a JsonldPredicate type. + * + */ + public void setjsonldPredicate( JsonldPredicate value ) { + jsonldPredicate = value; + } + + /***************************************************************************************************** + * + * This method returns the value of jsonldPredicate. + * + * @return This method will return the value of jsonldPredicate, which is a Object type. + * + */ + public Object getjsonldPredicate() { + return jsonldPredicate; + } + + /***************************************************************************************************** + * + * This method sets the value of docParent. + * + * @param value will update docParent, which is a String type. + * + */ + public void setdocParent( String value ) { + docParent = value; + } + + /***************************************************************************************************** + * + * This method returns the value of docParent. + * + * @return This method will return the value of docParent, which is a String type. + * + */ + public String getdocParent() { + return docParent; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String array. + * + */ + public void setdoc( String [] value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a Object type. + * + */ + public Object getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of docAfter. + * + * @param value will update docAfter, which is a String type. + * + */ + public void setdocAfter( String value ) { + docAfter = value; + } + + /***************************************************************************************************** + * + * This method returns the value of docAfter. + * + * @return This method will return the value of docAfter, which is a String type. + * + */ + public String getdocAfter() { + return docAfter; + } + + /***************************************************************************************************** + * + * This method sets the value of docChild. + * + * @param value will update docChild, which is a String type. + * + */ + public void setdocChild( String value ) { + docChild = value; + } + + /***************************************************************************************************** + * + * This method sets the value of docChild. + * + * @param value will update docChild, which is a String array. + * + */ + public void setdocChild( String [] value ) { + docChild = value; + } + + /***************************************************************************************************** + * + * This method returns the value of docChild. + * + * @return This method will return the value of docChild, which is a Object type. + * + */ + public Object getdocChild() { + return docChild; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/ScatterFeatureRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/ScatterFeatureRequirement.java new file mode 100644 index 00000000..e455d025 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/ScatterFeatureRequirement.java @@ -0,0 +1,71 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Indicates that the workflow platform must support the `scatter` and `scatterMethod` fields of [WorkflowStep](#WorkflowStep). +*/ +public class ScatterFeatureRequirement implements ProcessRequirement { + + /***************************************************************************************************** + * + * Always 'ScatterFeatureRequirement' + */ + String class_value = null; + + + public ScatterFeatureRequirement() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/ScatterMethod.java b/sdk-and-javadoc-generation/org/commonwl/lang/ScatterMethod.java new file mode 100644 index 00000000..5437038e --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/ScatterMethod.java @@ -0,0 +1,42 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + + /***************************************************************************************************** + * + * The scatter method, as described in [workflow step scatter](#WorkflowStep). + */ +public enum ScatterMethod { + + dotproduct, nested_crossproduct, flat_crossproduct + +} diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/SchemaBase.java b/sdk-and-javadoc-generation/org/commonwl/lang/SchemaBase.java new file mode 100644 index 00000000..bbd7843e --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/SchemaBase.java @@ -0,0 +1,60 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public interface SchemaBase { + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ); + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel(); +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/SchemaDefRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/SchemaDefRequirement.java new file mode 100644 index 00000000..74760320 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/SchemaDefRequirement.java @@ -0,0 +1,121 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* This field consists of an array of type definitions which must be used when interpreting the `inputs` and `outputs` fields. When a `type` field contain a IRI, the implementation must check if the type is defined in `schemaDefs` and use that definition. If the type is not found in `schemaDefs`, it is an error. The entries in `schemaDefs` must be processed in the order listed such that later schema definitions may refer to earlier schema definitions. +*/ +public class SchemaDefRequirement implements ProcessRequirement { + + /***************************************************************************************************** + * + * The list of type definitions. + */ + Object types = null; + + /***************************************************************************************************** + * + * Always 'SchemaDefRequirement' + */ + String class_value = null; + + + public SchemaDefRequirement() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of types. + * + * @param value will update types, which is a InputEnumSchema array. + * + */ + public void settypes( InputEnumSchema [] value ) { + types = value; + } + + /***************************************************************************************************** + * + * This method sets the value of types. + * + * @param value will update types, which is a InputArraySchema array. + * + */ + public void settypes( InputArraySchema [] value ) { + types = value; + } + + /***************************************************************************************************** + * + * This method sets the value of types. + * + * @param value will update types, which is a InputRecordSchema array. + * + */ + public void settypes( InputRecordSchema [] value ) { + types = value; + } + + /***************************************************************************************************** + * + * This method returns the value of types. + * + * @return This method will return the value of types, which is a Object type. + * + */ + public Object gettypes() { + return types; + } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/SchemaDefinedType.java b/sdk-and-javadoc-generation/org/commonwl/lang/SchemaDefinedType.java new file mode 100644 index 00000000..4c5db024 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/SchemaDefinedType.java @@ -0,0 +1,207 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Abstract base for schema-defined types. +*/ +public interface SchemaDefinedType extends DocType { + + /***************************************************************************************************** + * + * If true, indicates that the type is a valid at the document root. At least one type in a schema must be tagged with `documentRoot: true`. + */ + Boolean documentRoot = null; + + /***************************************************************************************************** + * + * Annotate this type with linked data context. + */ + Object jsonldPredicate = null; + + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for this type should appear in a subsection under `docParent`. + */ + String docParent = null; + + /***************************************************************************************************** + * + * A documentation string for this type, or an array of strings which should be concatenated. + */ + Object doc = null; + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for this type should appear after the `docAfter` section at the same level. + */ + String docAfter = null; + + /***************************************************************************************************** + * + * Hint to indicate that during documentation generation, documentation for `docChild` should appear in a subsection under this type. + */ + Object docChild = null; + + + /***************************************************************************************************** + * + * This method sets the value of documentRoot. + * + * @param value will update documentRoot, which is a Boolean type. + * + */ + public void setdocumentRoot( Boolean value ); + + /***************************************************************************************************** + * + * This method returns the value of documentRoot. + * + * @return This method will return the value of documentRoot, which is a Boolean type. + * + */ + public Boolean getdocumentRoot(); + /***************************************************************************************************** + * + * This method sets the value of jsonldPredicate. + * + * @param value will update jsonldPredicate, which is a String type. + * + */ + public void setjsonldPredicate( String value ); + + /***************************************************************************************************** + * + * This method sets the value of jsonldPredicate. + * + * @param value will update jsonldPredicate, which is a JsonldPredicate type. + * + */ + public void setjsonldPredicate( JsonldPredicate value ); + + /***************************************************************************************************** + * + * This method returns the value of jsonldPredicate. + * + * @return This method will return the value of jsonldPredicate, which is a Object type. + * + */ + public Object getjsonldPredicate(); + /***************************************************************************************************** + * + * This method sets the value of docParent. + * + * @param value will update docParent, which is a String type. + * + */ + public void setdocParent( String value ); + + /***************************************************************************************************** + * + * This method returns the value of docParent. + * + * @return This method will return the value of docParent, which is a String type. + * + */ + public String getdocParent(); + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ); + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String array. + * + */ + public void setdoc( String [] value ); + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a Object type. + * + */ + public Object getdoc(); + /***************************************************************************************************** + * + * This method sets the value of docAfter. + * + * @param value will update docAfter, which is a String type. + * + */ + public void setdocAfter( String value ); + + /***************************************************************************************************** + * + * This method returns the value of docAfter. + * + * @return This method will return the value of docAfter, which is a String type. + * + */ + public String getdocAfter(); + /***************************************************************************************************** + * + * This method sets the value of docChild. + * + * @param value will update docChild, which is a String type. + * + */ + public void setdocChild( String value ); + + /***************************************************************************************************** + * + * This method sets the value of docChild. + * + * @param value will update docChild, which is a String array. + * + */ + public void setdocChild( String [] value ); + + /***************************************************************************************************** + * + * This method returns the value of docChild. + * + * @return This method will return the value of docChild, which is a Object type. + * + */ + public Object getdocChild(); +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/ShellCommandRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/ShellCommandRequirement.java new file mode 100644 index 00000000..4b4b2e5d --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/ShellCommandRequirement.java @@ -0,0 +1,71 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Modify the behavior of CommandLineTool to generate a single string containing a shell command line. Each item in the argument list must be joined into a string separated by single spaces and quoted to prevent intepretation by the shell, unless `CommandLineBinding` for that argument contains `shellQuote: false`. If `shellQuote: false` is specified, the argument is joined into the command string without quoting, which allows the use of shell metacharacters such as `|` for pipes. +*/ +public class ShellCommandRequirement implements ProcessRequirement { + + /***************************************************************************************************** + * + * Always 'ShellCommandRequirement' + */ + String class_value = null; + + + public ShellCommandRequirement() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/Sink.java b/sdk-and-javadoc-generation/org/commonwl/lang/Sink.java new file mode 100644 index 00000000..93b8b084 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/Sink.java @@ -0,0 +1,92 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public interface Sink { + + /***************************************************************************************************** + * + * The method to use to merge multiple inbound links into a single array. If not specified, the default method is merge_nested. + */ + LinkMergeMethod linkMerge = null; + + /***************************************************************************************************** + * + * Specifies one or more workflow parameters that will provide input to the underlying step parameter. + */ + Object source = null; + + + /***************************************************************************************************** + * + * This method sets the value of linkMerge. + * + * @param value will update linkMerge, which is a LinkMergeMethod type. + * + */ + public void setlinkMerge( LinkMergeMethod value ); + + /***************************************************************************************************** + * + * This method returns the value of linkMerge. + * + * @return This method will return the value of linkMerge, which is a LinkMergeMethod type. + * + */ + public LinkMergeMethod getlinkMerge(); + /***************************************************************************************************** + * + * This method sets the value of source. + * + * @param value will update source, which is a String type. + * + */ + public void setsource( String value ); + + /***************************************************************************************************** + * + * This method sets the value of source. + * + * @param value will update source, which is a String array. + * + */ + public void setsource( String [] value ); + + /***************************************************************************************************** + * + * This method returns the value of source. + * + * @return This method will return the value of source, which is a Object type. + * + */ + public Object getsource(); +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/SoftwarePackage.java b/sdk-and-javadoc-generation/org/commonwl/lang/SoftwarePackage.java new file mode 100644 index 00000000..3b124a1c --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/SoftwarePackage.java @@ -0,0 +1,123 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class SoftwarePackage { + + /***************************************************************************************************** + * + * Must be one or more IRIs identifying resources for installing or enabling the software. Implementations may provide resolvers which map well-known software spec IRIs to some configuration action. For example, an IRI `https://packages.debian.org/jessie/bowtie` could be resolved with `apt-get install bowtie`. An IRI `https://anaconda.org/bioconda/bowtie` could be resolved with `conda install -c bioconda bowtie`. Tools may also provide IRIs to index entries such as [RRID](http://www.identifiers.org/rrid/), such as `http://identifiers.org/rrid/RRID:SCR_005476` + */ + String specs = null; + + /***************************************************************************************************** + * + * The common name of the software to be configured. + */ + String package_value = null; + + /***************************************************************************************************** + * + * The (optional) version of the software to configured. + */ + String version = null; + + + public SoftwarePackage() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of specs. + * + * @param value will update specs, which is a String type. + * + */ + public void setspecs( String value ) { + specs = value; + } + + /***************************************************************************************************** + * + * This method returns the value of specs. + * + * @return This method will return the value of specs, which is a String type. + * + */ + public String getspecs() { + return specs; + } + + /***************************************************************************************************** + * + * This method sets the value of package_value. + * + * @param value will update package_value, which is a String type. + * + */ + public void setpackage( String value ) { + package_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of package_value. + * + * @return This method will return the value of package_value, which is a String type. + * + */ + public String getpackage() { + return package_value; + } + + /***************************************************************************************************** + * + * This method sets the value of version. + * + * @param value will update version, which is a String type. + * + */ + public void setversion( String value ) { + version = value; + } + + /***************************************************************************************************** + * + * This method returns the value of version. + * + * @return This method will return the value of version, which is a String type. + * + */ + public String getversion() { + return version; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/SoftwareRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/SoftwareRequirement.java new file mode 100644 index 00000000..cdda3c76 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/SoftwareRequirement.java @@ -0,0 +1,99 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* A list of software packages that should be configured in the environment of the defined process. +*/ +public class SoftwareRequirement implements ProcessRequirement { + + /***************************************************************************************************** + * + * The list of software to be configured. + */ + SoftwarePackage packages = null; + + /***************************************************************************************************** + * + * Always 'SoftwareRequirement' + */ + String class_value = null; + + + public SoftwareRequirement() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of packages. + * + * @param value will update packages, which is a SoftwarePackage type. + * + */ + public void setpackages( SoftwarePackage value ) { + packages = value; + } + + /***************************************************************************************************** + * + * This method returns the value of packages. + * + * @return This method will return the value of packages, which is a SoftwarePackage type. + * + */ + public SoftwarePackage getpackages() { + return packages; + } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/SpecializeDef.java b/sdk-and-javadoc-generation/org/commonwl/lang/SpecializeDef.java new file mode 100644 index 00000000..db188efb --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/SpecializeDef.java @@ -0,0 +1,95 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +public class SpecializeDef { + + /***************************************************************************************************** + * + * The data type to be replaced + */ + String specializeFrom = null; + + /***************************************************************************************************** + * + * The new data type to replace with + */ + String specializeTo = null; + + + public SpecializeDef() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of specializeFrom. + * + * @param value will update specializeFrom, which is a String type. + * + */ + public void setspecializeFrom( String value ) { + specializeFrom = value; + } + + /***************************************************************************************************** + * + * This method returns the value of specializeFrom. + * + * @return This method will return the value of specializeFrom, which is a String type. + * + */ + public String getspecializeFrom() { + return specializeFrom; + } + + /***************************************************************************************************** + * + * This method sets the value of specializeTo. + * + * @param value will update specializeTo, which is a String type. + * + */ + public void setspecializeTo( String value ) { + specializeTo = value; + } + + /***************************************************************************************************** + * + * This method returns the value of specializeTo. + * + * @return This method will return the value of specializeTo, which is a String type. + * + */ + public String getspecializeTo() { + return specializeTo; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/StepInputExpressionRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/StepInputExpressionRequirement.java new file mode 100644 index 00000000..274bbde3 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/StepInputExpressionRequirement.java @@ -0,0 +1,71 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Indicate that the workflow platform must support the `valueFrom` field of [WorkflowStepInput](#WorkflowStepInput). +*/ +public class StepInputExpressionRequirement implements ProcessRequirement { + + /***************************************************************************************************** + * + * Always 'StepInputExpressionRequirement' + */ + String class_value = null; + + + public StepInputExpressionRequirement() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/SubworkflowFeatureRequirement.java b/sdk-and-javadoc-generation/org/commonwl/lang/SubworkflowFeatureRequirement.java new file mode 100644 index 00000000..f18f08b2 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/SubworkflowFeatureRequirement.java @@ -0,0 +1,71 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Indicates that the workflow platform must support nested workflows in the `run` field of [WorkflowStep](#WorkflowStep). +*/ +public class SubworkflowFeatureRequirement implements ProcessRequirement { + + /***************************************************************************************************** + * + * Always 'SubworkflowFeatureRequirement' + */ + String class_value = null; + + + public SubworkflowFeatureRequirement() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/Workflow.java b/sdk-and-javadoc-generation/org/commonwl/lang/Workflow.java new file mode 100644 index 00000000..81b21c0d --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/Workflow.java @@ -0,0 +1,452 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* A workflow describes a set of **steps** and the **dependencies** between those steps. When a step produces output that will be consumed by a second step, the first step is a dependency of the second step. +*/ +public class Workflow implements Process { + + String class_value = null; + + /***************************************************************************************************** + * + * The individual steps that make up the workflow. Each step is executed when all of its input data links are fufilled. An implementation may choose to execute the steps in a different order than listed and/or execute steps concurrently, provided that dependencies between steps are met. + */ + WorkflowStep [] steps = null; + + + /***************************************************************************************************** + * + * Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. + */ + WorkflowOutputParameter [] outputs = null; + + /***************************************************************************************************** + * + * Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option. + */ + Object requirements = null; + + /***************************************************************************************************** + * + * CWL document version. Always required at the document root. Not required for a Process embedded inside another Process. + */ + CWLVersion cwlVersion = null; + + /***************************************************************************************************** + * + * Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object. + */ + InputParameter [] inputs = null; + + /***************************************************************************************************** + * + * Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning. + */ + Any hints = null; + + /***************************************************************************************************** + * + * A long, human-readable description of this process object. + */ + String doc = null; + + /***************************************************************************************************** + * + * The unique identifier for this process object. + */ + String id = null; + + /***************************************************************************************************** + * + * A short, human-readable label of this process object. + */ + String label = null; + + + public Workflow() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of class_value. + * + * @param value will update class_value, which is a String type. + * + */ + public void setclass( String value ) { + class_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of class_value. + * + * @return This method will return the value of class_value, which is a String type. + * + */ + public String getclass() { + return class_value; + } + + /***************************************************************************************************** + * + * This method sets the value of steps. + * + * @param value will update steps, which is a WorkflowStep array. + * + */ + public void setsteps( WorkflowStep [] value ) { + steps = value; + } + + /***************************************************************************************************** + * + * This method returns the value of steps. + * + * @return This method will return the value of steps, which is a WorkflowStep array. + * + */ + public WorkflowStep [] getsteps() { + return steps; + } + + /***************************************************************************************************** + * + * This method sets the value of outputs. + * + * @param value will update outputs, which is a OutputParameter array. + * + */ + public void setoutputs( WorkflowOutputParameter [] value ) { + outputs = value; + } + + /***************************************************************************************************** + * + * This is a dummy method which has no functionality, and is required + * for implementing an interface method that was previously specialized. + * + * + */ + public void setoutputs( OutputParameter [] value ) { + + } + + /***************************************************************************************************** + * + * This method returns the value of outputs. + * + * @return This method will return the value of outputs, which is a WorkflowOutputParameter array. + * + */ + public WorkflowOutputParameter [] getoutputs() { + return outputs; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a StepInputExpressionRequirement type. + * + */ + public void setrequirements( StepInputExpressionRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a MultipleInputFeatureRequirement type. + * + */ + public void setrequirements( MultipleInputFeatureRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SoftwareRequirement type. + * + */ + public void setrequirements( SoftwareRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SchemaDefRequirement type. + * + */ + public void setrequirements( SchemaDefRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a InitialWorkDirRequirement type. + * + */ + public void setrequirements( InitialWorkDirRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a EnvVarRequirement type. + * + */ + public void setrequirements( EnvVarRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a DockerRequirement type. + * + */ + public void setrequirements( DockerRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ResourceRequirement type. + * + */ + public void setrequirements( ResourceRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a InlineJavascriptRequirement type. + * + */ + public void setrequirements( InlineJavascriptRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ShellCommandRequirement type. + * + */ + public void setrequirements( ShellCommandRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ScatterFeatureRequirement type. + * + */ + public void setrequirements( ScatterFeatureRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SubworkflowFeatureRequirement type. + * + */ + public void setrequirements( SubworkflowFeatureRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method returns the value of requirements. + * + * @return This method will return the value of requirements, which is a Object type. + * + */ + public Object getrequirements() { + return requirements; + } + + /***************************************************************************************************** + * + * This method sets the value of cwlVersion. + * + * @param value will update cwlVersion, which is a CWLVersion type. + * + */ + public void setcwlVersion( CWLVersion value ) { + cwlVersion = value; + } + + /***************************************************************************************************** + * + * This method returns the value of cwlVersion. + * + * @return This method will return the value of cwlVersion, which is a CWLVersion type. + * + */ + public CWLVersion getcwlVersion() { + return cwlVersion; + } + + /***************************************************************************************************** + * + * This method sets the value of inputs. + * + * @param value will update inputs, which is a InputParameter array. + * + */ + public void setinputs( InputParameter [] value ) { + inputs = value; + } + + /***************************************************************************************************** + * + * This method returns the value of inputs. + * + * @return This method will return the value of inputs, which is a InputParameter array. + * + */ + public InputParameter [] getinputs() { + return inputs; + } + + /***************************************************************************************************** + * + * This method sets the value of hints. + * + * @param value will update hints, which is a Any type. + * + */ + public void sethints( Any value ) { + hints = value; + } + + /***************************************************************************************************** + * + * This method returns the value of hints. + * + * @return This method will return the value of hints, which is a Any type. + * + */ + public Any gethints() { + return hints; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a String type. + * + */ + public String getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ) { + id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid() { + return id; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/WorkflowOutputParameter.java b/sdk-and-javadoc-generation/org/commonwl/lang/WorkflowOutputParameter.java new file mode 100644 index 00000000..53c12184 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/WorkflowOutputParameter.java @@ -0,0 +1,502 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Describe an output parameter of a workflow. The parameter must be connected to one or more parameters defined in the workflow that will provide the value of the output parameter. +*/ +public class WorkflowOutputParameter extends OutputParameter { + + /***************************************************************************************************** + * + * The method to use to merge multiple sources into a single array. If not specified, the default method is merge_nested. + */ + LinkMergeMethod linkMerge = null; + + /***************************************************************************************************** + * + * Specifies one or more workflow parameters that supply the value of to the output parameter. + */ + Object outputSource = null; + + /***************************************************************************************************** + * + * Specify valid types of data that may be assigned to this parameter. + */ + Object type = null; + + + /***************************************************************************************************** + * + * Describes how to handle the outputs of a process. + */ + CommandOutputBinding outputBinding = null; + + /***************************************************************************************************** + * + * The unique identifier for this parameter object. + */ + String id = null; + + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. + */ + Boolean streamable = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. For input parameters, this must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. For output parameters, this is the file format that will be assigned to the output parameter. + */ + Object format = null; + + /***************************************************************************************************** + * + * A documentation string for this type, or an array of strings which should be concatenated. + */ + Object doc = null; + + /***************************************************************************************************** + * + * Only valid when `type: File` or is an array of `items: File`. Describes files that must be included alongside the primary file(s). If the value is an expression, the value of `self` in the expression must be the primary input or output File to which this binding applies. If the value is a string, it specifies that the following pattern should be applied to the primary file: 1. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 2. Append the remainder of the string to the end of the file path. + */ + Object secondaryFiles = null; + + + /***************************************************************************************************** + * + * A short, human-readable label of this object. + */ + String label = null; + + + public WorkflowOutputParameter() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of linkMerge. + * + * @param value will update linkMerge, which is a LinkMergeMethod type. + * + */ + public void setlinkMerge( LinkMergeMethod value ) { + linkMerge = value; + } + + /***************************************************************************************************** + * + * This method returns the value of linkMerge. + * + * @return This method will return the value of linkMerge, which is a LinkMergeMethod type. + * + */ + public LinkMergeMethod getlinkMerge() { + return linkMerge; + } + + /***************************************************************************************************** + * + * This method sets the value of outputSource. + * + * @param value will update outputSource, which is a String type. + * + */ + public void setoutputSource( String value ) { + outputSource = value; + } + + /***************************************************************************************************** + * + * This method sets the value of outputSource. + * + * @param value will update outputSource, which is a String array. + * + */ + public void setoutputSource( String [] value ) { + outputSource = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outputSource. + * + * @return This method will return the value of outputSource, which is a Object type. + * + */ + public Object getoutputSource() { + return outputSource; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a OutputRecordSchema array. + * + */ + public void settype( OutputRecordSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a OutputEnumSchema array. + * + */ + public void settype( OutputEnumSchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String array. + * + */ + public void settype( String [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a OutputRecordSchema type. + * + */ + public void settype( OutputRecordSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a OutputEnumSchema type. + * + */ + public void settype( OutputEnumSchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CWLType array. + * + */ + public void settype( CWLType [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a OutputArraySchema type. + * + */ + public void settype( OutputArraySchema value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a OutputArraySchema array. + * + */ + public void settype( OutputArraySchema [] value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a CWLType type. + * + */ + public void settype( CWLType value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method sets the value of type. + * + * @param value will update type, which is a String type. + * + */ + public void settype( String value ) { + type = value; + } + + /***************************************************************************************************** + * + * This method returns the value of type. + * + * @return This method will return the value of type, which is a Object type. + * + */ + public Object gettype() { + return type; + } + + /***************************************************************************************************** + * + * This method sets the value of outputBinding. + * + * @param value will update outputBinding, which is a CommandOutputBinding type. + * + */ + public void setoutputBinding( CommandOutputBinding value ) { + outputBinding = value; + } + + /***************************************************************************************************** + * + * This method returns the value of outputBinding. + * + * @return This method will return the value of outputBinding, which is a CommandOutputBinding type. + * + */ + public CommandOutputBinding getoutputBinding() { + return outputBinding; + } + + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ) { + id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid() { + return id; + } + + /***************************************************************************************************** + * + * This method sets the value of streamable. + * + * @param value will update streamable, which is a Boolean type. + * + */ + public void setstreamable( Boolean value ) { + streamable = value; + } + + /***************************************************************************************************** + * + * This method returns the value of streamable. + * + * @return This method will return the value of streamable, which is a Boolean type. + * + */ + public Boolean getstreamable() { + return streamable; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a Expression array. + * + */ + public void setformat( Expression [] value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String type. + * + */ + public void setformat( String value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method sets the value of format. + * + * @param value will update format, which is a String array. + * + */ + public void setformat( String [] value ) { + format = value; + } + + /***************************************************************************************************** + * + * This method returns the value of format. + * + * @return This method will return the value of format, which is a Object type. + * + */ + public Object getformat() { + return format; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String array. + * + */ + public void setdoc( String [] value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a Object type. + * + */ + public Object getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression array. + * + */ + public void setsecondaryFiles( Expression [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String type. + * + */ + public void setsecondaryFiles( String value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a String array. + * + */ + public void setsecondaryFiles( String [] value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method sets the value of secondaryFiles. + * + * @param value will update secondaryFiles, which is a Expression type. + * + */ + public void setsecondaryFiles( Expression value ) { + secondaryFiles = value; + } + + /***************************************************************************************************** + * + * This method returns the value of secondaryFiles. + * + * @return This method will return the value of secondaryFiles, which is a Object type. + * + */ + public Object getsecondaryFiles() { + return secondaryFiles; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/WorkflowStep.java b/sdk-and-javadoc-generation/org/commonwl/lang/WorkflowStep.java new file mode 100644 index 00000000..b6ae2a5f --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/WorkflowStep.java @@ -0,0 +1,495 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* A workflow step is an executable element of a workflow. It specifies the underlying process implementation (such as `CommandLineTool` or another `Workflow`) in the `run` field and connects the input and output parameters of the underlying process to workflow parameters. +*/ +public class WorkflowStep { + + /***************************************************************************************************** + * + * Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this workflow step. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option. + */ + Object requirements = null; + + /***************************************************************************************************** + * + * Defines the input parameters of the workflow step. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used build a user interface for constructing the input object. + */ + WorkflowStepInput in = null; + + /***************************************************************************************************** + * + * Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this workflow step. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning. + */ + Any hints = null; + + Object scatter = null; + + /***************************************************************************************************** + * + * Required if `scatter` is an array of more than one element. + */ + ScatterMethod scatterMethod = null; + + /***************************************************************************************************** + * + * A long, human-readable description of this process object. + */ + String doc = null; + + /***************************************************************************************************** + * + * Specifies the process to run. + */ + Object run = null; + + /***************************************************************************************************** + * + * The unique identifier for this workflow step. + */ + String id = null; + + /***************************************************************************************************** + * + * A short, human-readable label of this process object. + */ + String label = null; + + /***************************************************************************************************** + * + * Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. + */ + Object out = null; + + + public WorkflowStep() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a StepInputExpressionRequirement type. + * + */ + public void setrequirements( StepInputExpressionRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a MultipleInputFeatureRequirement type. + * + */ + public void setrequirements( MultipleInputFeatureRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SoftwareRequirement type. + * + */ + public void setrequirements( SoftwareRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SchemaDefRequirement type. + * + */ + public void setrequirements( SchemaDefRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a InitialWorkDirRequirement type. + * + */ + public void setrequirements( InitialWorkDirRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a EnvVarRequirement type. + * + */ + public void setrequirements( EnvVarRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a DockerRequirement type. + * + */ + public void setrequirements( DockerRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ResourceRequirement type. + * + */ + public void setrequirements( ResourceRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a InlineJavascriptRequirement type. + * + */ + public void setrequirements( InlineJavascriptRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ShellCommandRequirement type. + * + */ + public void setrequirements( ShellCommandRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a ScatterFeatureRequirement type. + * + */ + public void setrequirements( ScatterFeatureRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method sets the value of requirements. + * + * @param value will update requirements, which is a SubworkflowFeatureRequirement type. + * + */ + public void setrequirements( SubworkflowFeatureRequirement value ) { + requirements = value; + } + + /***************************************************************************************************** + * + * This method returns the value of requirements. + * + * @return This method will return the value of requirements, which is a Object type. + * + */ + public Object getrequirements() { + return requirements; + } + + /***************************************************************************************************** + * + * This method sets the value of in. + * + * @param value will update in, which is a WorkflowStepInput type. + * + */ + public void setin( WorkflowStepInput value ) { + in = value; + } + + /***************************************************************************************************** + * + * This method returns the value of in. + * + * @return This method will return the value of in, which is a WorkflowStepInput type. + * + */ + public WorkflowStepInput getin() { + return in; + } + + /***************************************************************************************************** + * + * This method sets the value of hints. + * + * @param value will update hints, which is a Any type. + * + */ + public void sethints( Any value ) { + hints = value; + } + + /***************************************************************************************************** + * + * This method returns the value of hints. + * + * @return This method will return the value of hints, which is a Any type. + * + */ + public Any gethints() { + return hints; + } + + /***************************************************************************************************** + * + * This method sets the value of scatter. + * + * @param value will update scatter, which is a String type. + * + */ + public void setscatter( String value ) { + scatter = value; + } + + /***************************************************************************************************** + * + * This method sets the value of scatter. + * + * @param value will update scatter, which is a String array. + * + */ + public void setscatter( String [] value ) { + scatter = value; + } + + /***************************************************************************************************** + * + * This method returns the value of scatter. + * + * @return This method will return the value of scatter, which is a Object type. + * + */ + public Object getscatter() { + return scatter; + } + + /***************************************************************************************************** + * + * This method sets the value of scatterMethod. + * + * @param value will update scatterMethod, which is a ScatterMethod type. + * + */ + public void setscatterMethod( ScatterMethod value ) { + scatterMethod = value; + } + + /***************************************************************************************************** + * + * This method returns the value of scatterMethod. + * + * @return This method will return the value of scatterMethod, which is a ScatterMethod type. + * + */ + public ScatterMethod getscatterMethod() { + return scatterMethod; + } + + /***************************************************************************************************** + * + * This method sets the value of doc. + * + * @param value will update doc, which is a String type. + * + */ + public void setdoc( String value ) { + doc = value; + } + + /***************************************************************************************************** + * + * This method returns the value of doc. + * + * @return This method will return the value of doc, which is a String type. + * + */ + public String getdoc() { + return doc; + } + + /***************************************************************************************************** + * + * This method sets the value of run. + * + * @param value will update run, which is a CommandLineTool type. + * + */ + public void setrun( CommandLineTool value ) { + run = value; + } + + /***************************************************************************************************** + * + * This method sets the value of run. + * + * @param value will update run, which is a String type. + * + */ + public void setrun( String value ) { + run = value; + } + + /***************************************************************************************************** + * + * This method sets the value of run. + * + * @param value will update run, which is a Workflow type. + * + */ + public void setrun( Workflow value ) { + run = value; + } + + /***************************************************************************************************** + * + * This method sets the value of run. + * + * @param value will update run, which is a ExpressionTool type. + * + */ + public void setrun( ExpressionTool value ) { + run = value; + } + + /***************************************************************************************************** + * + * This method returns the value of run. + * + * @return This method will return the value of run, which is a Object type. + * + */ + public Object getrun() { + return run; + } + + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ) { + id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid() { + return id; + } + + /***************************************************************************************************** + * + * This method sets the value of label. + * + * @param value will update label, which is a String type. + * + */ + public void setlabel( String value ) { + label = value; + } + + /***************************************************************************************************** + * + * This method returns the value of label. + * + * @return This method will return the value of label, which is a String type. + * + */ + public String getlabel() { + return label; + } + + /***************************************************************************************************** + * + * This method sets the value of out. + * + * @param value will update out, which is a WorkflowStepOutput array. + * + */ + public void setout( WorkflowStepOutput [] value ) { + out = value; + } + + /***************************************************************************************************** + * + * This method sets the value of out. + * + * @param value will update out, which is a String array. + * + */ + public void setout( String [] value ) { + out = value; + } + + /***************************************************************************************************** + * + * This method returns the value of out. + * + * @return This method will return the value of out, which is a Object type. + * + */ + public Object getout() { + return out; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/WorkflowStepInput.java b/sdk-and-javadoc-generation/org/commonwl/lang/WorkflowStepInput.java new file mode 100644 index 00000000..1dea1033 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/WorkflowStepInput.java @@ -0,0 +1,206 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* The input of a workflow step connects an upstream parameter (from the workflow inputs, or the outputs of other workflows steps) with the input parameters of the underlying step. +*/ +public class WorkflowStepInput implements Sink { + + /***************************************************************************************************** + * + * The default value for this parameter if there is no `source` field. + */ + Any default_value = null; + + /***************************************************************************************************** + * + * A unique identifier for this workflow input parameter. + */ + String id = null; + + /***************************************************************************************************** + * + * To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must be specified in the workflow or workflow step requirements. If `valueFrom` is a constant string value, use this as the value for this input parameter. If `valueFrom` is a parameter reference or expression, it must be evaluated to yield the actual value to be assiged to the input field. The `self` value of in the parameter reference or expression must be the value of the parameter(s) specified in the `source` field, or null if there is no `source` field. The value of `inputs` in the parameter reference or expression must be the input object to the workflow step after assigning the `source` values and then scattering. The order of evaluating `valueFrom` among step input parameters is undefined and the result of evaluating `valueFrom` on a parameter must not be visible to evaluation of `valueFrom` on other parameters. + */ + Object valueFrom = null; + + + /***************************************************************************************************** + * + * The method to use to merge multiple inbound links into a single array. If not specified, the default method is merge_nested. + */ + LinkMergeMethod linkMerge = null; + + /***************************************************************************************************** + * + * Specifies one or more workflow parameters that will provide input to the underlying step parameter. + */ + Object source = null; + + + public WorkflowStepInput() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of default_value. + * + * @param value will update default_value, which is a Any type. + * + */ + public void setdefault( Any value ) { + default_value = value; + } + + /***************************************************************************************************** + * + * This method returns the value of default_value. + * + * @return This method will return the value of default_value, which is a Any type. + * + */ + public Any getdefault() { + return default_value; + } + + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ) { + id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid() { + return id; + } + + /***************************************************************************************************** + * + * This method sets the value of valueFrom. + * + * @param value will update valueFrom, which is a String type. + * + */ + public void setvalueFrom( String value ) { + valueFrom = value; + } + + /***************************************************************************************************** + * + * This method sets the value of valueFrom. + * + * @param value will update valueFrom, which is a Expression type. + * + */ + public void setvalueFrom( Expression value ) { + valueFrom = value; + } + + /***************************************************************************************************** + * + * This method returns the value of valueFrom. + * + * @return This method will return the value of valueFrom, which is a Object type. + * + */ + public Object getvalueFrom() { + return valueFrom; + } + + /***************************************************************************************************** + * + * This method sets the value of linkMerge. + * + * @param value will update linkMerge, which is a LinkMergeMethod type. + * + */ + public void setlinkMerge( LinkMergeMethod value ) { + linkMerge = value; + } + + /***************************************************************************************************** + * + * This method returns the value of linkMerge. + * + * @return This method will return the value of linkMerge, which is a LinkMergeMethod type. + * + */ + public LinkMergeMethod getlinkMerge() { + return linkMerge; + } + + /***************************************************************************************************** + * + * This method sets the value of source. + * + * @param value will update source, which is a String type. + * + */ + public void setsource( String value ) { + source = value; + } + + /***************************************************************************************************** + * + * This method sets the value of source. + * + * @param value will update source, which is a String array. + * + */ + public void setsource( String [] value ) { + source = value; + } + + /***************************************************************************************************** + * + * This method returns the value of source. + * + * @return This method will return the value of source, which is a Object type. + * + */ + public Object getsource() { + return source; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/WorkflowStepOutput.java b/sdk-and-javadoc-generation/org/commonwl/lang/WorkflowStepOutput.java new file mode 100644 index 00000000..cb37d61f --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/WorkflowStepOutput.java @@ -0,0 +1,71 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + +/***************************************************************************************************** +* +* Associate an output parameter of the underlying process with a workflow parameter. The workflow parameter (given in the `id` field) be may be used as a `source` to connect with input parameters of other workflow steps, or with an output parameter of the process. +*/ +public class WorkflowStepOutput { + + /***************************************************************************************************** + * + * A unique identifier for this workflow output parameter. This is the identifier to use in the `source` field of `WorkflowStepInput` to connect the output value to downstream parameters. + */ + String id = null; + + + public WorkflowStepOutput() { super(); } + + /***************************************************************************************************** + * + * This method sets the value of id. + * + * @param value will update id, which is a String type. + * + */ + public void setid( String value ) { + id = value; + } + + /***************************************************************************************************** + * + * This method returns the value of id. + * + * @return This method will return the value of id, which is a String type. + * + */ + public String getid() { + return id; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/stderr.java b/sdk-and-javadoc-generation/org/commonwl/lang/stderr.java new file mode 100644 index 00000000..d75b5c21 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/stderr.java @@ -0,0 +1,42 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + + /***************************************************************************************************** + * + * Only valid as a `type` for a `CommandLineTool` output with no `outputBinding` set. + */ +public enum stderr { + + + +} diff --git a/sdk-and-javadoc-generation/org/commonwl/lang/stdout.java b/sdk-and-javadoc-generation/org/commonwl/lang/stdout.java new file mode 100644 index 00000000..da57a288 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/lang/stdout.java @@ -0,0 +1,42 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.lang; + + /***************************************************************************************************** + * + * Only valid as a `type` for a `CommandLineTool` output with no `outputBinding` set. + */ +public enum stdout { + + + +} diff --git a/sdk-and-javadoc-generation/org/commonwl/util/CWLJavaCodeGenerator.java b/sdk-and-javadoc-generation/org/commonwl/util/CWLJavaCodeGenerator.java new file mode 100644 index 00000000..7b49ad91 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/util/CWLJavaCodeGenerator.java @@ -0,0 +1,330 @@ +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.util; + +import java.io.*; +import java.util.*; +import org.yaml.snakeyaml.*; +import org.commonwl.lang.*; + +public class CWLJavaCodeGenerator { + + /***************************************************************************************************** + * + * The String used for storing CWL filename. + */ + String CWL_FILE; + + /***************************************************************************************************** + * + * The String used for storing CWL Java code-generated class name. + */ + String CWL_JAVA_CLASS_NAME; + + /***************************************************************************************************** + * + * The String used for storing CWL Java code-generated filename. + */ + String CWL_JAVA_FILE; + + /***************************************************************************************************** + * + * The String used for storing CWL Java code-generated filename. + */ + String CWL_OBJECT = "CWL"; + + /***************************************************************************************************** + * + * The String used for storing if the CWL file is a CommandLineTool or Workflow. + */ + String TOOL_TYPE = ""; + + + /***************************************************************************************************** + * + * The CommandLineTool used for storing class in the CWL file. + */ + //CommandLineTool COMMAND_LINE_TOOL; + + /***************************************************************************************************** + * + * The CommandInputParameter used for storing inputs in the CWL file. + */ + //CommandInputParameter [] INPUTS; + + /***************************************************************************************************** + * + * The CommandOutputParameter used for storing outputs in the CWL file. + */ + //CommandOutputParameter [] OUTPUTS; + + public CWLJavaCodeGenerator( String cwlFile ) { + this.CWL_FILE = cwlFile; + } + + /***************************************************************************************************** + * + * This method starts the processing of the CWL file for populating the contents in a CommandLineTool. + * + * @throws java.lang.Exception is thrown if there issues with reading the file. + */ + public void processFile() throws Exception { + + CWL_JAVA_FILE = new String( CWL_FILE.trim() ); + CWL_JAVA_CLASS_NAME = new String( CWL_JAVA_FILE.substring( 0, CWL_JAVA_FILE.length() - 4 ) ); + CWL_JAVA_FILE = new String( CWL_JAVA_CLASS_NAME + ".java" ); + + InputStream cwlFile = new FileInputStream( CWL_FILE ); + Yaml yaml = new Yaml(); + Map contents = (Map) yaml.load(cwlFile); + processContents( contents ); + + } + + /***************************************************************************************************** + * + * This method adds a newline character to a string of text. + * + * @param text is a String of text. + */ + private String addNewline( String text ) { + return new String( text + "\n"); + } + + /***************************************************************************************************** + * + * This method adds a newline character to a string of text. + * + * @param text is a String of text. + */ + private String addIndentedNewline( String text ) { + return new String( " " + text + "\n"); + } + + /***************************************************************************************************** + * + * This method processing of the contents of a CWL file for populating a CommandLineTool instance. + * + * @param contents is a Map of the CWL YAML file. + */ + private void processContents( Map contents ) throws Exception { + + FileWriter cwlJavaFile = new FileWriter( CWL_JAVA_FILE ); + BufferedWriter cwlJavaBW = new BufferedWriter( cwlJavaFile ); + + cwlJavaBW.write( addNewline("import org.commonwl.lang.*;") ); + cwlJavaBW.write( addNewline("import org.commonwl.util.*;") ); + cwlJavaBW.write( addNewline("") ); + cwlJavaBW.write( addNewline( " public class " + CWL_JAVA_CLASS_NAME + "() {") ); + cwlJavaBW.write( addNewline("") ); + cwlJavaBW.write( addNewline( " public " + CWL_JAVA_CLASS_NAME + "() { }") ); + cwlJavaBW.write( addNewline("") ); + cwlJavaBW.write( addNewline( " public Object build() {") ); + cwlJavaBW.write( addNewline("") ); + + for( Object key : contents.keySet() ) { + + Object value = contents.get(key); + + if ( key.equals("class") ) { + + String class_type = (String) value; + cwlJavaBW.write( addIndentedNewline( value + " " + CWL_OBJECT + " = new " + CWL_OBJECT + "();" ) ); + cwlJavaBW.write( addNewline("") ); + + // Set the Tool type + TOOL_TYPE = new String( (String) value ); + + } + + if ( key.equals("inputs") ) { + + int numberOfInputs = ((ArrayList) value).size(); + int inputIndex = 0; + + for( Object inputPairs : (ArrayList) value ) { + + Map inputPairsValue = (Map) inputPairs; + + if (TOOL_TYPE.equals("CommandLineTool")) { + cwlJavaBW.write( addIndentedNewline( "CommandInputParameter [] inputs = new CommandInputParameter[" + numberOfInputs + "];" ) ); + } else { + cwlJavaBW.write( addIndentedNewline( "InputParameter [] inputs = new InputParameter[" + numberOfInputs + "];" ) ); + } + + for( Object attribute : inputPairsValue.keySet() ) { + + if ( attribute.equals("id") ) { + if (TOOL_TYPE.equals("CommandLineTool")) { + cwlJavaBW.write( addIndentedNewline( "inputs[" + inputIndex + "] = new CommandInputParameter();" ) ); + } else { + cwlJavaBW.write( addIndentedNewline( "inputs[" + inputIndex + "] = new InputParameter();" ) ); + } + cwlJavaBW.write( addIndentedNewline( "inputs[" + inputIndex + "].setid( \"" + (String) inputPairsValue.get( attribute ) + "\" );" ) ); + } + + if ( attribute.equals("type") ) { + cwlJavaBW.write( addIndentedNewline( "inputs[" + inputIndex + "].settype( \"" + (String) inputPairsValue.get( attribute ) + "\" );" ) ); + } + + } + + // Increment the index of the input + inputIndex = inputIndex + 1; + } + cwlJavaBW.write( addIndentedNewline( CWL_OBJECT + ".setinputs( inputs );" ) ); + cwlJavaBW.write( addNewline("") ); // Add a separator + } // end of inputs + + + if ( key.equals("outputs") ) { + + int numberOfOutputs = ((ArrayList) value).size(); + int outputIndex = 0; + + for( Object outputPairs : (ArrayList) value ) { + + Map outputPairsValue = (Map) outputPairs; + + if (TOOL_TYPE.equals("CommandLineTool")) { + cwlJavaBW.write( addIndentedNewline( "CommandOutputParameter [] outputs = new CommandOutputParameter[" + numberOfOutputs + "];" ) ); + } else { + cwlJavaBW.write( addIndentedNewline( "WorkflowOutputParameter [] outputs = new WorkflowOutputParameter[" + numberOfOutputs + "];" ) ); + } + + for( Object attribute : outputPairsValue.keySet() ) { + + if ( attribute.equals("id") ) { + if (TOOL_TYPE.equals("CommandLineTool")) { + cwlJavaBW.write( addIndentedNewline( "outputs[" + outputIndex + "] = new CommandInputParameter();" ) ); + } else { + cwlJavaBW.write( addIndentedNewline( "outputs[" + outputIndex + "] = new WorkflowOutputParameter();" ) ); + } + cwlJavaBW.write( addIndentedNewline( "outputs[" + outputIndex + "].setid( \"" + (String) outputPairsValue.get( attribute ) + "\" );" ) ); + } + + if ( attribute.equals("type") ) { + cwlJavaBW.write( addIndentedNewline( "outputs[" + outputIndex + "].settype( \"" + (String) outputPairsValue.get( attribute ) + "\" );" ) ); + } + + } + + // Increment the index of the input + outputIndex = outputIndex + 1; + } + cwlJavaBW.write( addIndentedNewline( CWL_OBJECT + ".setoutputs( outputs );" ) ); + cwlJavaBW.write( addNewline("") ); // Add a separator + } // end of outputs + + if ( key.equals("stdin") ) { + + String stdin = (String) value; + cwlJavaBW.write( addIndentedNewline( CWL_OBJECT + ".setstdin( \"" + stdin + "\" );" ) ); + cwlJavaBW.write( addNewline("") ); + + } + + if ( key.equals("stdout") ) { + + String stdout = (String) value; + cwlJavaBW.write( addIndentedNewline( CWL_OBJECT + ".setstdout( \"" + stdout + "\" );" ) ); + cwlJavaBW.write( addNewline("") ); + + } + + if ( key.equals("baseCommand") ) { + + String baseCommand = (String) value.toString(); + cwlJavaBW.write( addIndentedNewline( CWL_OBJECT + ".setbaseCommand( \"" + baseCommand.toString() + "\" );" ) ); + cwlJavaBW.write( addNewline("") ); + + } + + } + cwlJavaBW.write( addNewline(" return " + CWL_OBJECT + ";") ); + + cwlJavaBW.write( addNewline(" }") ); + cwlJavaBW.write( addNewline("") ); + cwlJavaBW.write( addNewline("}") ); + cwlJavaFile.flush(); + cwlJavaBW.close(); + + } + + + /************************************************************************* + * + * Purpose: To remove the brackets ([]) in a baseCommand. + * + * @param reference a String to be updated. + * + * @return an updated String. + * + */ + String removeBrackets( String reference ) { + return new String( reference.replace("[", "").replace("]", "").trim() ); + } + + /************************************************************************* + * + * Purpose: To remove the paranthesis "()" and dollar sign ($) + * standard input. + * + * @param reference a String to be updated. + * + * @return an updated String. + * + */ + String cleanStandardInput( String reference ) { + return new String( reference.replace("$", "").replace("(", "").replace(")", "").trim() ); + } + + + /************************************************************************* + * + * Purpose: Returns the first element of an ArrayList as a String. + * + * @param arrayList which is an ArrayList for retrieving its first element. + * + * @return an updated String. + * + */ + String getFirstElementOfArrayList( ArrayList arrayList ) { + + String firstElement = new String(""); + for ( Object e : arrayList ) { + firstElement = (String) e; + break; + } + return firstElement; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/util/CWLReader.java b/sdk-and-javadoc-generation/org/commonwl/util/CWLReader.java new file mode 100644 index 00000000..84067591 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/util/CWLReader.java @@ -0,0 +1,264 @@ +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.util; + +import java.io.*; +import java.util.*; +import org.yaml.snakeyaml.*; +import org.commonwl.lang.*; + +public class CWLReader { + + /***************************************************************************************************** + * + * The String used for storing CWL filename. + */ + String CWL_FILE; + + /***************************************************************************************************** + * + * The CommandLineTool used for storing class in the CWL file. + */ + CommandLineTool COMMAND_LINE_TOOL; + + /***************************************************************************************************** + * + * The CommandInputParameter used for storing inputs in the CWL file. + */ + CommandInputParameter [] INPUTS; + + /***************************************************************************************************** + * + * The CommandOutputParameter used for storing outputs in the CWL file. + */ + CommandOutputParameter [] OUTPUTS; + + + public CWLReader( String cwlFile ) { + this.CWL_FILE = cwlFile; + } + + /***************************************************************************************************** + * + * This method starts the processing of the CWL file for populating the contents in a CommandLineTool. + * + * @throws java.lang.Exception is thrown if there issues with reading the file. + */ + public void processFile() throws Exception { + InputStream cwlFile = new FileInputStream( CWL_FILE ); + Yaml yaml = new Yaml(); + Map contents = (Map) yaml.load(cwlFile); + for( Object key : contents.keySet() ) { + processContents( (String) key, contents.get(key) ); + } + } + + + /***************************************************************************************************** + * + * This method processing of the contents of a CWL file for populating a CommandLineTool instance. + * + * @param key is a String denoting the key of the element in the CWL file. + * @param value is an Object denoting the value of the element in the CWL file. + */ + private void processContents(String key, Object value ) { + if ( key.equals("class") ) { + processClass( (String) value ); + } + + if ( key.equals("inputs") ) { + for( Object inputPairs : (ArrayList) value ){ + processInputs( (Map) inputPairs ); + break; + } + COMMAND_LINE_TOOL.setinputs( INPUTS ); + } + + if ( key.equals("outputs") ) { + for( Object outputPairs : (ArrayList) value ){ + processOutputs( (Map) outputPairs ); + break; + } + COMMAND_LINE_TOOL.setoutputs( OUTPUTS ); + } + + if ( key.equals("baseCommand") ) { + COMMAND_LINE_TOOL.setbaseCommand( removeBrackets( getFirstElementOfArrayList( (ArrayList) value ) ) ); + } + + if ( key.equals("stdin") ) { + COMMAND_LINE_TOOL.setstdin( cleanStandardInput( (String) value ) ); + } + + if ( key.equals("stdout") ) { + COMMAND_LINE_TOOL.setstdout( (String) value ); + } + + + } + + + /***************************************************************************************************** + * + * This method processes the class in a CWL file, and updates the CommandLineTool contents. + * + * @param classType is a String of the type of the class (i.e. CommandLineTool). + */ + private void processClass(String classType ) { + if ( classType.equals("CommandLineTool") ) { + COMMAND_LINE_TOOL = new CommandLineTool(); + } + } + + /***************************************************************************************************** + * + * This method processes the intputs in a CWL file, and updates the CommandLineTool contents. + * + * @param inputs is a key-value pair Map of the inputs. + */ + private void processInputs( Map inputs ) { + + INPUTS = new CommandInputParameter[ inputs.size() ]; + + int counter = 0; + + for( Object attribute : inputs.keySet() ){ + + INPUTS[ counter ] = new CommandInputParameter(); + + if ( attribute.equals("id") ) { + INPUTS[counter].setid( (String) inputs.get( attribute ) ); + } + + if ( attribute.equals("type") ) { + INPUTS[counter].settype( (String) inputs.get( attribute ) ); + } + + } + } + + /***************************************************************************************************** + * + * This method processes the outputs in a CWL file, and updates the CommandLineTool contents. + * + * @param outputs is a key-value pair Map of the outputs. + */ + private void processOutputs( Map outputs ) { + + OUTPUTS = new CommandOutputParameter[ outputs.size() ]; + + int counter = 0; + + for( Object attribute : outputs.keySet() ){ + + OUTPUTS[ counter ] = new CommandOutputParameter(); + + if ( attribute.equals("id") ) { + OUTPUTS[counter].setid( (String) outputs.get( attribute ) ); + } + + if ( attribute.equals("type") ) { + OUTPUTS[counter].settype( (String) outputs.get( attribute ) ); + } + + if ( attribute.equals("outputBinding") ) { + Map outputBindingMap = (Map) outputs.get( attribute ); + CommandOutputBinding cob = new CommandOutputBinding(); + + for( Object outputBindingAttribute : outputBindingMap.keySet() ) { + if( outputBindingAttribute.equals("glob") ) { + cob.setglob( new String( (String)outputBindingMap.get(outputBindingAttribute) ) ); + } + } + OUTPUTS[counter].setoutputBinding( cob ); + } + } + } + + /************************************************************************* + * + * Purpose: To remove the brackets ([]) in a baseCommand. + * + * @param reference a String to be updated. + * + * @return an updated String. + * + */ + String removeBrackets( String reference ) { + return new String( reference.replace("[", "").replace("]", "").trim() ); + } + + /************************************************************************* + * + * Purpose: To remove the paranthesis "()" and dollar sign ($) + * standard input. + * + * @param reference a String to be updated. + * + * @return an updated String. + * + */ + String cleanStandardInput( String reference ) { + return new String( reference.replace("$", "").replace("(", "").replace(")", "").trim() ); + } + + + /************************************************************************* + * + * Purpose: Returns the first element of an ArrayList as a String. + * + * @param arrayList which is an ArrayList for retrieving its first element. + * + * @return an updated String. + * + */ + String getFirstElementOfArrayList( ArrayList arrayList ) { + + String firstElement = new String(""); + for ( Object e : arrayList ) { + firstElement = (String) e; + break; + } + return firstElement; + } + + /************************************************************************* + * + * Purpose: Returns the populated CommandLineTool instance. + * + * @return an CommandLineTool instance. + * + */ + public CommandLineTool getCommandLineToolInstance() { + return COMMAND_LINE_TOOL; + } + +} \ No newline at end of file diff --git a/sdk-and-javadoc-generation/org/commonwl/util/JSONReader.java b/sdk-and-javadoc-generation/org/commonwl/util/JSONReader.java new file mode 100644 index 00000000..7a562bfc --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/util/JSONReader.java @@ -0,0 +1,107 @@ + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.util; + +import java.io.*; +import java.util.*; + +import org.json.simple.*; +import org.json.simple.parser.*; + +/***************************************************************************************************** +* +* This is used reading and processing a JSON file. +*/ +public class JSONReader { + + /***************************************************************************************************** + * + * The String used for storing the JSON filename. + */ + String JSON_FILE; + + /***************************************************************************************************** + * + * The String used for storing the key of the root of a JSON file's contents. + */ + String ROOT_KEY; + + /***************************************************************************************************** + * + * The key-value pairs in a JSON file that sit underneath the root key in a JSON file. + */ + Map jsonMap = new HashMap(); + + public JSONReader( String jsonFile ) { + this.JSON_FILE = jsonFile; + } + + /***************************************************************************************************** + * + * This method will process a JSON file an store it's contents. + * + * @throws java.lang.Exception is thrown if there issues with reading the file. + */ + public void processFile() throws Exception { + + FileReader reader = new FileReader( JSON_FILE ); + + JSONParser parser = new JSONParser(); + + JSONObject jsonObject = (JSONObject) parser.parse(reader); + + Set keys = jsonObject.keySet(); + + for( Object root : keys ) { + ROOT_KEY = (String) root; + Map mapSubKeys = (Map ) jsonObject.get( root ); + + for( Object subKey : mapSubKeys.keySet() ) { + jsonMap.put( new String( root + "." + (String) subKey ), mapSubKeys.get( subKey ) ); + } + } + + } + + /***************************************************************************************************** + * + * This method is used to request the value using a key in the processed JSON file. + * + * @param key is a particular key, which is a String. + * + * @return a String value for a particular key. + * + */ + public String getValue( String key ) { + return jsonMap.get(key); + } +} diff --git a/sdk-and-javadoc-generation/org/commonwl/util/SystemCommandExecution.java b/sdk-and-javadoc-generation/org/commonwl/util/SystemCommandExecution.java new file mode 100644 index 00000000..e1193a28 --- /dev/null +++ b/sdk-and-javadoc-generation/org/commonwl/util/SystemCommandExecution.java @@ -0,0 +1,251 @@ + + +/***************************************************************************************************** +* +* Authors: +* +* Java SDK for CWL +* +* @author Paul Grosu (pgrosu@gmail.com), Northeastern University +* @version 0.20 +* @since April 28, 2016 +* +*

Alternate SDK (via Avro): +* +* Denis Yuen (denis.yuen@gmail.com) +* +* CWL Draft: +* +* Peter Amstutz (peter.amstutz@curoverse.com), Curoverse +* Nebojsa Tijanic (nebojsa.tijanic@sbgenomics.com), Seven Bridges Genomics +* +* Contributors: +* +* Luka Stojanovic (luka.stojanovic@sbgenomics.com), Seven Bridges Genomics +* John Chilton (jmchilton@gmail.com), Galaxy Project, Pennsylvania State University +* Michael R. Crusoe (crusoe@ucdavis.edu), University of California, Davis +* Herve Menager (herve.menager@gmail.com), Institut Pasteur +* Maxim Mikheev (mikhmv@biodatomics.com), BioDatomics +* Stian Soiland-Reyes (soiland-reyes@cs.manchester.ac.uk), University of Manchester +* +*****************************************************************************************************/ + +package org.commonwl.util; + +import java.io.*; + +/***************************************************************************************************** +* +* This is used for executing commands on the system. +*/ +public class SystemCommandExecution { + + /***************************************************************************************************** + * + * The String used for storing the standard input. + */ + private String StandardInput; + + /***************************************************************************************************** + * + * The String used for storing the standard error. + */ + private String StandardError; + + /***************************************************************************************************** + * + * The String used for storing the standard output. + */ + private String StandardOutput; + + /***************************************************************************************************** + * + * The Integer used for storing the return status code. + */ + private Integer statusCode; + + + + public Integer getStatusCode() { + return statusCode; + } + + public void setStatusCode(Integer statusCode) { + this.statusCode = statusCode; + } + + public SystemCommandExecution() { + this.StandardInput = new String(""); + this.StandardError = new String(""); + this.StandardOutput = new String(""); + } + + public SystemCommandExecution( String StandardInput ) { + this.StandardInput = StandardInput; + } + + /***************************************************************************************************** + * + * This method executes the command and returns a String array of the standard input, + * standard output, and standard error. + * + * @return a String array of the standard input, standard output, and standard error. + * + */ + public String [] executeCommand() { + + String stringStream = null; + String [] InputErrorOutput = new String[3]; + InputErrorOutput[0] = new String(""); + InputErrorOutput[1] = new String(""); + InputErrorOutput[2] = new String(""); + + StandardError = new String(""); + StandardOutput = new String(""); + + try { + + java.lang.Process process = Runtime.getRuntime().exec( StandardInput ); + + + + InputErrorOutput[0] = StandardInput; + + BufferedReader standardInputStream = new BufferedReader(new + InputStreamReader(process.getInputStream())); + + BufferedReader standardErrorStream = new BufferedReader(new + InputStreamReader(process.getErrorStream())); + + // Read the output from the command + while (( stringStream = standardInputStream.readLine() ) != null) { + if( StandardOutput.trim().length() == 0 ) { + StandardOutput = new String( stringStream ); + } else { + StandardOutput = new String( StandardOutput + "\n" + stringStream ); + } + } + InputErrorOutput[2] = StandardOutput; + + // Read any errors from the attempted command + while (( stringStream = standardErrorStream.readLine() ) != null) { + if( StandardError.trim().length() == 0 ) { + StandardError = new String( StandardError + " " + stringStream ); + } else { + StandardError = new String( StandardError + " " + stringStream ); + } + } + InputErrorOutput[1] = StandardError; + + this.statusCode=process.exitValue(); + } + catch (IOException exception) { + exception.printStackTrace(); + System.exit(-1); + } + + return InputErrorOutput; + + } + + /***************************************************************************************************** + * + * This method returns the last value of the standard input. + * + * @return a String of the standard input. + * + */ + public String getStandardInput() { + return StandardInput; + } + + /***************************************************************************************************** + * + * This method returns the last value of the standard error. + * + * @return a String of the standard error. + * + */ + public String getStandardError() { + return StandardError; + } + + /***************************************************************************************************** + * + * This method returns the last value of the standard output. + * + * @return a String of the standard output. + * + */ + public String getStandardOutput() { + return StandardOutput; + } + + /***************************************************************************************************** + * + * This method removes the "class" string from the class name, produced by the getClass() method. + * + * @param className a String of the class name. + * + * @return an updated String of the class name. + * + */ + public String cleanupClassName( String className ) { + return className.replace("class","").trim(); + } + + /***************************************************************************************************** + * + * This method is a helper method to process any object being requested to be run, such as + * the ones returned by getbaseCommand() which are actually a String type. The value is cast + * String and added to the standard input string. + * + * @param command a String of the standard input. + * + */ + public void extendExecutionCommand( Object command ) { + if ( cleanupClassName( command.getClass().getName() ).equals("java.lang.String") ) { + extendExecutionCommand( (String) command ) ; + } + } + + /***************************************************************************************************** + * + * This method is a method to process a String command being requested to be run. The value is + * added to the standard input string. + * + * @param command a String of the standard input. + * + */ + public void extendExecutionCommand( String command ) { + + if( StandardInput.trim().length() == 0 ) { + this.StandardInput = command; + } else { + this.StandardInput = this.StandardInput + " " + command; + } + } + + /***************************************************************************************************** + * + * This method resets the standard input String. + * + */ + public void newExecutionCommand() { + this.StandardInput = new String(""); + } + + + /***************************************************************************************************** + * + * This method sets the standard input String. + * + * @param inputText is a String of the standard input. + * + */ + public void setStandardInput( String inputText ) { + this.StandardInput = inputText; + } + + +} diff --git a/sdk-and-javadoc-generation/step0-download-v1_0-yaml-files.sh b/sdk-and-javadoc-generation/step0-download-v1_0-yaml-files.sh new file mode 100644 index 00000000..24308b18 --- /dev/null +++ b/sdk-and-javadoc-generation/step0-download-v1_0-yaml-files.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +curl -O https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/Process.yml +curl -O https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/Workflow.yml +curl -O https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/CommandLineTool.yml +curl -O https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/salad/schema_salad/metaschema/metaschema.yml +curl -O https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/salad/schema_salad/metaschema/metaschema_base.yml + +mv *.yml cwl-yaml-specs \ No newline at end of file diff --git a/sdk-and-javadoc-generation/step1-generate_sdk.sh b/sdk-and-javadoc-generation/step1-generate_sdk.sh new file mode 100755 index 00000000..cd8e24b7 --- /dev/null +++ b/sdk-and-javadoc-generation/step1-generate_sdk.sh @@ -0,0 +1,18 @@ +#!/bin/bash + +echo "Compiling the YAMLParser, CWLSDKBuilder and CreateCWLJavaSDK files..." +echo "" +javac YAMLParser.java +javac CWLSDKBuilder.java +javac CreateCWLJavaSDK.java + +echo "Creating the SDK folder..." +echo "" +rm -rf org/commonwl/lang +mkdir org +mkdir org/commonwl +mkdir org/commonwl/lang + +echo "Running the SDK creation process..." +echo "" +java CreateCWLJavaSDK cwl-yaml-specs/CommandLineTool.yml cwl-yaml-specs/Process.yml cwl-yaml-specs/Workflow.yml cwl-yaml-specs/metaschema_base.yml cwl-yaml-specs/metaschema.yml \ No newline at end of file diff --git a/sdk-and-javadoc-generation/step2-compile-sdk-files-for-jar.sh b/sdk-and-javadoc-generation/step2-compile-sdk-files-for-jar.sh new file mode 100755 index 00000000..4b50815e --- /dev/null +++ b/sdk-and-javadoc-generation/step2-compile-sdk-files-for-jar.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +for JavaFile in org/commonwl/lang/*.java; do + echo "Compiling: $JavaFile"; + javac $JavaFile; +done + +cd ../../.. \ No newline at end of file diff --git a/sdk-and-javadoc-generation/step3-compile-util-files-for-jar.sh b/sdk-and-javadoc-generation/step3-compile-util-files-for-jar.sh new file mode 100755 index 00000000..0a5ae81f --- /dev/null +++ b/sdk-and-javadoc-generation/step3-compile-util-files-for-jar.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +for JavaFile in org/commonwl/util/*.java; do + echo "Compiling: $JavaFile"; + javac -cp .:./lib/json-simple-1.1.1.jar:./lib/snakeyaml-1.16.jar $JavaFile; +done + +cd ../../.. \ No newline at end of file diff --git a/sdk-and-javadoc-generation/step4-generate-jar-files.sh b/sdk-and-javadoc-generation/step4-generate-jar-files.sh new file mode 100755 index 00000000..3cc80468 --- /dev/null +++ b/sdk-and-javadoc-generation/step4-generate-jar-files.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +rm lib/cwl.jar +jar cf lib/cwl.jar org + +cp lib/*jar ../lib \ No newline at end of file diff --git a/sdk-and-javadoc-generation/step5-generate-javadoc.sh b/sdk-and-javadoc-generation/step5-generate-javadoc.sh new file mode 100755 index 00000000..7c237cda --- /dev/null +++ b/sdk-and-javadoc-generation/step5-generate-javadoc.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +rm -rf javadoc +mkdir javadoc +cd javadoc +javadoc -cp ./lib/cwl.jar:./lib/json-simple-1.1.1.jar:./lib/snakeyaml-1.16.jar:. -version -private ../org/commonwl/lang/*.java ../org/commonwl/util/*.java +cd .. + +rm -rf ../javadoc +mkdir ../javadoc +cp -R javadoc ../ \ No newline at end of file diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Any.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Any.java deleted file mode 100644 index bf92975e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Any.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum Any { - ANY("Any"); - - private static String[] symbols = new String[] {"Any"}; - private String docVal; - - private Any(final String docVal) { - this.docVal = docVal; - } - - public static Any fromDocumentVal(final String docVal) { - for(final Any val : Any.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Any.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ArraySchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ArraySchema.java deleted file mode 100644 index ff57c37f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ArraySchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#ArraySchema
This interface is implemented by {@link ArraySchemaImpl}
- */ -public interface ArraySchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *

- * Defines the type of the array elements. *
- */ - - Object getItems(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - Array_name getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ArraySchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ArraySchemaImpl.java deleted file mode 100644 index 5197cb6a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ArraySchemaImpl.java +++ /dev/null @@ -1,128 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/salad#ArraySchema
- */ -public class ArraySchemaImpl extends SaveableImpl implements ArraySchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Object items; - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - public Object getItems() { - return this.items; - } - - private Array_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - public Array_name getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of ArraySchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ArraySchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ArraySchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Object items; - try { - items = - LoaderInstances - .uri_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("items"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - items = null; // won't be used but prevents compiler from complaining. - final String __message = "the `items` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Array_name type; - try { - type = - LoaderInstances - .typedsl_Array_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.items = (Object) items; - this.type = (Array_name) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("items", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Array_name.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Array_name.java deleted file mode 100644 index 91fdc1fe..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Array_name.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum Array_name { - ARRAY("array"); - - private static String[] symbols = new String[] {"array"}; - private String docVal; - - private Array_name(final String docVal) { - this.docVal = docVal; - } - - public static Array_name fromDocumentVal(final String docVal) { - for(final Array_name val : Array_name.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Array_name.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLArraySchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLArraySchema.java deleted file mode 100644 index 9003654e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLArraySchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CWLArraySchema
This interface is implemented by {@link CWLArraySchemaImpl}
- */ -public interface CWLArraySchema extends ArraySchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - Object getItems(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - Array_name getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLArraySchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLArraySchemaImpl.java deleted file mode 100644 index 8cf046fc..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLArraySchemaImpl.java +++ /dev/null @@ -1,128 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CWLArraySchema
- */ -public class CWLArraySchemaImpl extends SaveableImpl implements CWLArraySchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Object items; - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - public Object getItems() { - return this.items; - } - - private Array_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - public Array_name getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CWLArraySchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CWLArraySchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CWLArraySchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Object items; - try { - items = - LoaderInstances - .uri_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("items"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - items = null; // won't be used but prevents compiler from complaining. - final String __message = "the `items` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Array_name type; - try { - type = - LoaderInstances - .typedsl_Array_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.items = (Object) items; - this.type = (Array_name) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("items", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLRecordField.java deleted file mode 100644 index a5cb4193..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLRecordField.java +++ /dev/null @@ -1,51 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CWLRecordField
This interface is implemented by {@link CWLRecordFieldImpl}
- */ -public interface CWLRecordField extends RecordField, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - String getName(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - Object getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLRecordFieldImpl.java deleted file mode 100644 index 3dccc3d3..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLRecordFieldImpl.java +++ /dev/null @@ -1,175 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CWLRecordField
- */ -public class CWLRecordFieldImpl extends SaveableImpl implements CWLRecordField { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String name; - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - public String getName() { - return this.name; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - public Object getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CWLRecordFieldImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CWLRecordFieldImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CWLRecordFieldImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - if (name == null) { - if (__docRoot != null) { - name = __docRoot; - } else { - throw new ValidationException("Missing name"); - } - } - __baseUri = (String) name; - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.doc = (Object) doc; - this.name = (String) name; - this.type = (Object) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("doc", "name", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLRecordSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLRecordSchema.java deleted file mode 100644 index 4bdfc29e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLRecordSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CWLRecordSchema
This interface is implemented by {@link CWLRecordSchemaImpl}
- */ -public interface CWLRecordSchema extends RecordSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - java.util.Optional> getFields(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - Record_name getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLRecordSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLRecordSchemaImpl.java deleted file mode 100644 index 4e2aa4be..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLRecordSchemaImpl.java +++ /dev/null @@ -1,134 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CWLRecordSchema
- */ -public class CWLRecordSchemaImpl extends SaveableImpl implements CWLRecordSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional> fields; - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - public java.util.Optional> getFields() { - return this.fields; - } - - private Record_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - public Record_name getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CWLRecordSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CWLRecordSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CWLRecordSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional> fields; - - if (__doc.containsKey("fields")) { - try { - fields = - LoaderInstances - .idmap_fields_optional_array_of_CWLRecordField - .loadField(__doc.get("fields"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - fields = null; // won't be used but prevents compiler from complaining. - final String __message = "the `fields` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - fields = null; - } - Record_name type; - try { - type = - LoaderInstances - .typedsl_Record_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.fields = (java.util.Optional>) fields; - this.type = (Record_name) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("fields", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLType.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLType.java deleted file mode 100644 index e0037687..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLType.java +++ /dev/null @@ -1,45 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum CWLType { - NULL("null"), - BOOLEAN("boolean"), - INT("int"), - LONG("long"), - FLOAT("float"), - DOUBLE("double"), - STRING("string"), - FILE("File"), - DIRECTORY("Directory"); - - private static String[] symbols = new String[] {"null", "boolean", "int", "long", "float", "double", "string", "File", "Directory"}; - private String docVal; - - private CWLType(final String docVal) { - this.docVal = docVal; - } - - public static CWLType fromDocumentVal(final String docVal) { - for(final CWLType val : CWLType.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", CWLType.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLVersion.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLVersion.java deleted file mode 100644 index 02f81525..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CWLVersion.java +++ /dev/null @@ -1,50 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum CWLVersion { - DRAFT_2("draft-2"), - DRAFT_3_DEV1("draft-3.dev1"), - DRAFT_3_DEV2("draft-3.dev2"), - DRAFT_3_DEV3("draft-3.dev3"), - DRAFT_3_DEV4("draft-3.dev4"), - DRAFT_3_DEV5("draft-3.dev5"), - DRAFT_3("draft-3"), - DRAFT_4_DEV1("draft-4.dev1"), - DRAFT_4_DEV2("draft-4.dev2"), - DRAFT_4_DEV3("draft-4.dev3"), - V1_0_DEV4("v1.0.dev4"), - V1_0("v1.0"), - V1_1_0_DEV1("v1.1.0-dev1"), - V1_1("v1.1"); - - private static String[] symbols = new String[] {"draft-2", "draft-3.dev1", "draft-3.dev2", "draft-3.dev3", "draft-3.dev4", "draft-3.dev5", "draft-3", "draft-4.dev1", "draft-4.dev2", "draft-4.dev3", "v1.0.dev4", "v1.0", "v1.1.0-dev1", "v1.1"}; - private String docVal; - - private CWLVersion(final String docVal) { - this.docVal = docVal; - } - - public static CWLVersion fromDocumentVal(final String docVal) { - for(final CWLVersion val : CWLVersion.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", CWLVersion.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputArraySchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputArraySchema.java deleted file mode 100644 index 56eeef7c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputArraySchema.java +++ /dev/null @@ -1,70 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputArraySchema
This interface is implemented by {@link CommandInputArraySchemaImpl}
- */ -public interface CommandInputArraySchema extends InputArraySchema, CommandInputSchema, CommandLineBindable, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - Object getItems(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - Array_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputArraySchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputArraySchemaImpl.java deleted file mode 100644 index 9da0e555..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputArraySchemaImpl.java +++ /dev/null @@ -1,262 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputArraySchema
- */ -public class CommandInputArraySchemaImpl extends SaveableImpl implements CommandInputArraySchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private Object items; - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - public Object getItems() { - return this.items; - } - - private Array_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - public Array_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandInputArraySchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandInputArraySchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandInputArraySchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - Object items; - try { - items = - LoaderInstances - .uri_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("items"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - items = null; // won't be used but prevents compiler from complaining. - final String __message = "the `items` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Array_name type; - try { - type = - LoaderInstances - .typedsl_Array_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_CommandLineBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.items = (Object) items; - this.type = (Array_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("items", "type", "label", "doc", "name", "inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputEnumSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputEnumSchema.java deleted file mode 100644 index 0a97a945..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputEnumSchema.java +++ /dev/null @@ -1,70 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputEnumSchema
This interface is implemented by {@link CommandInputEnumSchemaImpl}
- */ -public interface CommandInputEnumSchema extends InputEnumSchema, CommandInputSchema, CommandLineBindable, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - java.util.List getSymbols(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - Enum_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputEnumSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputEnumSchemaImpl.java deleted file mode 100644 index c75f93ea..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputEnumSchemaImpl.java +++ /dev/null @@ -1,262 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputEnumSchema
- */ -public class CommandInputEnumSchemaImpl extends SaveableImpl implements CommandInputEnumSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.List symbols; - - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - public java.util.List getSymbols() { - return this.symbols; - } - - private Enum_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - public Enum_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandInputEnumSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandInputEnumSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandInputEnumSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.List symbols; - try { - symbols = - LoaderInstances - .uri_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("symbols"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - symbols = null; // won't be used but prevents compiler from complaining. - final String __message = "the `symbols` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Enum_name type; - try { - type = - LoaderInstances - .typedsl_Enum_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_CommandLineBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.name = (java.util.Optional) name; - this.symbols = (java.util.List) symbols; - this.type = (Enum_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("name", "symbols", "type", "label", "doc", "inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameter.java deleted file mode 100644 index 410b3a48..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameter.java +++ /dev/null @@ -1,180 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputParameter
This interface is implemented by {@link CommandInputParameterImpl}
- An input parameter for a CommandLineTool.
- */ -public interface CommandInputParameter extends InputParameter, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferrably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value to use for this parameter if the parameter is missing - * from the input object, or if the value of the parameter in the input - * object is `null`. Default values are applied before evaluating expressions - * (e.g. dependent `valueFrom` fields). - * *
- */ - - java.util.Optional getDefault(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandInputParameter/inputBinding
- *
- * Describes how to turns the input parameters of a process into - * command line arguments. - * *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameterImpl.java deleted file mode 100644 index ed59f1f2..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputParameterImpl.java +++ /dev/null @@ -1,493 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputParameter
- An input parameter for a CommandLineTool.
- */ -public class CommandInputParameterImpl extends SaveableImpl implements CommandInputParameter { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferrably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - private java.util.Optional default_; - - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value to use for this parameter if the parameter is missing - * from the input object, or if the value of the parameter in the input - * object is `null`. Default values are applied before evaluating expressions - * (e.g. dependent `valueFrom` fields). - * *
- */ - - public java.util.Optional getDefault() { - return this.default_; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandInputParameter/inputBinding
- *
- * Describes how to turns the input parameters of a process into - * command line arguments. - * *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandInputParameterImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandInputParameterImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandInputParameterImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - java.util.Optional default_; - - if (__doc.containsKey("default")) { - try { - default_ = - LoaderInstances - .optional_CWLObjectType - .loadField(__doc.get("default"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - default_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `default` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - default_ = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_stdin_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_CommandLineBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.doc = (Object) doc; - this.id = (java.util.Optional) id; - this.format = (Object) format; - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - this.default_ = (java.util.Optional) default_; - this.type = (Object) type; - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("label", "secondaryFiles", "streamable", "doc", "id", "format", "loadContents", "loadListing", "default", "type", "inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordField.java deleted file mode 100644 index 0d8ff342..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordField.java +++ /dev/null @@ -1,167 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputRecordField
This interface is implemented by {@link CommandInputRecordFieldImpl}
- */ -public interface CommandInputRecordField extends InputRecordField, CommandLineBindable, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - String getName(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferrably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordFieldImpl.java deleted file mode 100644 index 4521f10e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordFieldImpl.java +++ /dev/null @@ -1,452 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordField
- */ -public class CommandInputRecordFieldImpl extends SaveableImpl implements CommandInputRecordField { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String name; - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - public String getName() { - return this.name; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferrably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandInputRecordFieldImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandInputRecordFieldImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandInputRecordFieldImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - if (name == null) { - if (__docRoot != null) { - name = __docRoot; - } else { - throw new ValidationException("Missing name"); - } - } - __baseUri = (String) name; - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_CommandLineBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.doc = (Object) doc; - this.name = (String) name; - this.type = (Object) type; - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.format = (Object) format; - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("doc", "name", "type", "label", "secondaryFiles", "streamable", "format", "loadContents", "loadListing", "inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordSchema.java deleted file mode 100644 index 20b6db9d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordSchema.java +++ /dev/null @@ -1,70 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputRecordSchema
This interface is implemented by {@link CommandInputRecordSchemaImpl}
- */ -public interface CommandInputRecordSchema extends InputRecordSchema, CommandInputSchema, CommandLineBindable, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - java.util.Optional> getFields(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - Record_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordSchemaImpl.java deleted file mode 100644 index 2c546a5f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputRecordSchemaImpl.java +++ /dev/null @@ -1,268 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordSchema
- */ -public class CommandInputRecordSchemaImpl extends SaveableImpl implements CommandInputRecordSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.Optional> fields; - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - public java.util.Optional> getFields() { - return this.fields; - } - - private Record_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - public Record_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandInputRecordSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandInputRecordSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandInputRecordSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.Optional> fields; - - if (__doc.containsKey("fields")) { - try { - fields = - LoaderInstances - .idmap_fields_optional_array_of_CommandInputRecordField - .loadField(__doc.get("fields"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - fields = null; // won't be used but prevents compiler from complaining. - final String __message = "the `fields` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - fields = null; - } - Record_name type; - try { - type = - LoaderInstances - .typedsl_Record_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_CommandLineBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.fields = (java.util.Optional>) fields; - this.type = (Record_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("fields", "type", "label", "doc", "name", "inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputSchema.java deleted file mode 100644 index 1bd47582..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandInputSchema.java +++ /dev/null @@ -1,28 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputSchema
- */ -public interface CommandInputSchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindable.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindable.java deleted file mode 100644 index a4777934..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindable.java +++ /dev/null @@ -1,35 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineBindable
This interface is implemented by {@link CommandLineBindableImpl}
- */ -public interface CommandLineBindable extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindableImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindableImpl.java deleted file mode 100644 index 818a1cce..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindableImpl.java +++ /dev/null @@ -1,110 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandLineBindable
- */ -public class CommandLineBindableImpl extends SaveableImpl implements CommandLineBindable { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandLineBindableImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandLineBindableImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandLineBindableImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_CommandLineBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBinding.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBinding.java deleted file mode 100644 index f73e19ac..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBinding.java +++ /dev/null @@ -1,154 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineBinding
This interface is implemented by {@link CommandLineBindingImpl}
- - When listed under `inputBinding` in the input schema, the term - "value" refers to the the corresponding value in the input object. For - binding objects listed in `CommandLineTool.arguments`, the term "value" - refers to the effective value after evaluating `valueFrom`. - - The binding behavior when building the command line depends on the data - type of the value. If there is a mismatch between the type described by - the input schema and the effective value, such as resulting from an - expression evaluation, an implementation must use the data type of the - effective value. - - - **string**: Add `prefix` and the string to the command line. - - - **number**: Add `prefix` and decimal representation to command line. - - - **boolean**: If true, add `prefix` to the command line. If false, add - nothing. - - - **File**: Add `prefix` and the value of - [`File.path`](#File) to the command line. - - - **Directory**: Add `prefix` and the value of - [`Directory.path`](#Directory) to the command line. - - - **array**: If `itemSeparator` is specified, add `prefix` and the join - the array into a single string with `itemSeparator` separating the - items. Otherwise first add `prefix`, then recursively process - individual elements. - If the array is empty, it does not add anything to command line. - - - **object**: Add `prefix` only, and recursively add object fields for - which `inputBinding` is specified. - - - **null**: Add nothing. -
- */ -public interface CommandLineBinding extends InputBinding, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#InputBinding/loadContents
- *
- * Use of `loadContents` in `InputBinding` is deprecated. - * Preserved for v1.0 backwards compatability. Will be removed in - * CWL v2.0. Use `InputParameter.loadContents` instead. - * - * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/position
- *
- * The sorting key. Default position is 0. If the inputBinding is - * associated with an input parameter, then the value of `self` in the - * expression will be the value of the input parameter. Input parameter - * defaults (as specified by the `InputParameter.default` field) must be - * applied before evaluating the expression. Expressions must return a - * single value of type int or a null. - * *
- */ - - Object getPosition(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/prefix
- *
- * Command line prefix to add before the value. *
- */ - - java.util.Optional getPrefix(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/separate
- *
- * If true (default), then the prefix and value must be added as separate - * command line arguments; if false, prefix and value must be concatenated - * into a single command line argument. - * *
- */ - - java.util.Optional getSeparate(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/itemSeparator
- *
- * Join the array elements into a single string with the elements - * separated by by `itemSeparator`. - * *
- */ - - java.util.Optional getItemSeparator(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/valueFrom
- *
- * If `valueFrom` is a constant string value, use this as the value and - * apply the binding rules above. - * - * If `valueFrom` is an expression, evaluate the expression to yield the - * actual value to use to build the command line and apply the binding - * rules above. If the inputBinding is associated with an input - * parameter, the value of `self` in the expression will be the value of - * the input parameter. Input parameter defaults (as specified by the - * `InputParameter.default` field) must be applied before evaluating the - * expression. - * - * If the value of the associated input parameter is `null`, `valueFrom` is - * not evaluated and nothing is added to the command line. - * - * When a binding is part of the `CommandLineTool.arguments` field, - * the `valueFrom` field is required. - * *
- */ - - Object getValueFrom(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/shellQuote
- *
- * If `ShellCommandRequirement` is in the requirements for the current command, - * this controls whether the value is quoted on the command line (default is true). - * Use `shellQuote: false` to inject metacharacters for operations such as pipes. - * - * If `shellQuote` is true or not provided, the implementation must not - * permit interpretation of any shell metacharacters or directives. - * *
- */ - - java.util.Optional getShellQuote(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindingImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindingImpl.java deleted file mode 100644 index 023e4788..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineBindingImpl.java +++ /dev/null @@ -1,367 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandLineBinding
- - When listed under `inputBinding` in the input schema, the term - "value" refers to the the corresponding value in the input object. For - binding objects listed in `CommandLineTool.arguments`, the term "value" - refers to the effective value after evaluating `valueFrom`. - - The binding behavior when building the command line depends on the data - type of the value. If there is a mismatch between the type described by - the input schema and the effective value, such as resulting from an - expression evaluation, an implementation must use the data type of the - effective value. - - - **string**: Add `prefix` and the string to the command line. - - - **number**: Add `prefix` and decimal representation to command line. - - - **boolean**: If true, add `prefix` to the command line. If false, add - nothing. - - - **File**: Add `prefix` and the value of - [`File.path`](#File) to the command line. - - - **Directory**: Add `prefix` and the value of - [`Directory.path`](#Directory) to the command line. - - - **array**: If `itemSeparator` is specified, add `prefix` and the join - the array into a single string with `itemSeparator` separating the - items. Otherwise first add `prefix`, then recursively process - individual elements. - If the array is empty, it does not add anything to command line. - - - **object**: Add `prefix` only, and recursively add object fields for - which `inputBinding` is specified. - - - **null**: Add nothing. -
- */ -public class CommandLineBindingImpl extends SaveableImpl implements CommandLineBinding { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#InputBinding/loadContents
- *
- * Use of `loadContents` in `InputBinding` is deprecated. - * Preserved for v1.0 backwards compatability. Will be removed in - * CWL v2.0. Use `InputParameter.loadContents` instead. - * - * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private Object position; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/position
- *
- * The sorting key. Default position is 0. If the inputBinding is - * associated with an input parameter, then the value of `self` in the - * expression will be the value of the input parameter. Input parameter - * defaults (as specified by the `InputParameter.default` field) must be - * applied before evaluating the expression. Expressions must return a - * single value of type int or a null. - * *
- */ - - public Object getPosition() { - return this.position; - } - - private java.util.Optional prefix; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/prefix
- *
- * Command line prefix to add before the value. *
- */ - - public java.util.Optional getPrefix() { - return this.prefix; - } - - private java.util.Optional separate; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/separate
- *
- * If true (default), then the prefix and value must be added as separate - * command line arguments; if false, prefix and value must be concatenated - * into a single command line argument. - * *
- */ - - public java.util.Optional getSeparate() { - return this.separate; - } - - private java.util.Optional itemSeparator; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/itemSeparator
- *
- * Join the array elements into a single string with the elements - * separated by by `itemSeparator`. - * *
- */ - - public java.util.Optional getItemSeparator() { - return this.itemSeparator; - } - - private Object valueFrom; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/valueFrom
- *
- * If `valueFrom` is a constant string value, use this as the value and - * apply the binding rules above. - * - * If `valueFrom` is an expression, evaluate the expression to yield the - * actual value to use to build the command line and apply the binding - * rules above. If the inputBinding is associated with an input - * parameter, the value of `self` in the expression will be the value of - * the input parameter. Input parameter defaults (as specified by the - * `InputParameter.default` field) must be applied before evaluating the - * expression. - * - * If the value of the associated input parameter is `null`, `valueFrom` is - * not evaluated and nothing is added to the command line. - * - * When a binding is part of the `CommandLineTool.arguments` field, - * the `valueFrom` field is required. - * *
- */ - - public Object getValueFrom() { - return this.valueFrom; - } - - private java.util.Optional shellQuote; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/shellQuote
- *
- * If `ShellCommandRequirement` is in the requirements for the current command, - * this controls whether the value is quoted on the command line (default is true). - * Use `shellQuote: false` to inject metacharacters for operations such as pipes. - * - * If `shellQuote` is true or not provided, the implementation must not - * permit interpretation of any shell metacharacters or directives. - * *
- */ - - public java.util.Optional getShellQuote() { - return this.shellQuote; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandLineBindingImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandLineBindingImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandLineBindingImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - Object position; - - if (__doc.containsKey("position")) { - try { - position = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_ExpressionLoader - .loadField(__doc.get("position"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - position = null; // won't be used but prevents compiler from complaining. - final String __message = "the `position` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - position = null; - } - java.util.Optional prefix; - - if (__doc.containsKey("prefix")) { - try { - prefix = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("prefix"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - prefix = null; // won't be used but prevents compiler from complaining. - final String __message = "the `prefix` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - prefix = null; - } - java.util.Optional separate; - - if (__doc.containsKey("separate")) { - try { - separate = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("separate"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - separate = null; // won't be used but prevents compiler from complaining. - final String __message = "the `separate` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - separate = null; - } - java.util.Optional itemSeparator; - - if (__doc.containsKey("itemSeparator")) { - try { - itemSeparator = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("itemSeparator"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - itemSeparator = null; // won't be used but prevents compiler from complaining. - final String __message = "the `itemSeparator` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - itemSeparator = null; - } - Object valueFrom; - - if (__doc.containsKey("valueFrom")) { - try { - valueFrom = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("valueFrom"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - valueFrom = null; // won't be used but prevents compiler from complaining. - final String __message = "the `valueFrom` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - valueFrom = null; - } - java.util.Optional shellQuote; - - if (__doc.containsKey("shellQuote")) { - try { - shellQuote = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("shellQuote"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - shellQuote = null; // won't be used but prevents compiler from complaining. - final String __message = "the `shellQuote` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - shellQuote = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.loadContents = (java.util.Optional) loadContents; - this.position = (Object) position; - this.prefix = (java.util.Optional) prefix; - this.separate = (java.util.Optional) separate; - this.itemSeparator = (java.util.Optional) itemSeparator; - this.valueFrom = (Object) valueFrom; - this.shellQuote = (java.util.Optional) shellQuote; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("loadContents", "position", "prefix", "separate", "itemSeparator", "valueFrom", "shellQuote"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineTool.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineTool.java deleted file mode 100644 index 387e1bd0..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineTool.java +++ /dev/null @@ -1,216 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineTool
This interface is implemented by {@link CommandLineToolImpl}
- This defines the schema of the CWL Command Line Tool Description document. -
- */ -public interface CommandLineTool extends Process, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/class
- - */ - - CommandLineTool_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - java.util.List getInputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - java.util.List getOutputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - java.util.Optional> getRequirements(); - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - java.util.Optional> getHints(); - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - java.util.Optional getCwlVersion(); - /** - * Getter for property https://w3id.org/cwl/cwl#baseCommand
- *
- * Specifies the program to execute. If an array, the first element of - * the array is the command to execute, and subsequent elements are - * mandatory command line arguments. The elements in `baseCommand` must - * appear before any command line bindings from `inputBinding` or - * `arguments`. - * - * If `baseCommand` is not provided or is an empty array, the first - * element of the command line produced after processing `inputBinding` or - * `arguments` must be used as the program to execute. - * - * If the program includes a path separator character it must - * be an absolute path, otherwise it is an error. If the program does not - * include a path separator, search the `$PATH` variable in the runtime - * environment of the workflow runner find the absolute path of the - * executable. - * *
- */ - - Object getBaseCommand(); - /** - * Getter for property https://w3id.org/cwl/cwl#arguments
- *
- * Command line bindings which are not directly associated with input - * parameters. If the value is a string, it is used as a string literal - * argument. If it is an Expression, the result of the evaluation is used - * as an argument. - * *
- */ - - java.util.Optional> getArguments(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdin
- *
- * A path to a file whose contents must be piped into the command's - * standard input stream. - * *
- */ - - Object getStdin(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stderr
- *
- * Capture the command's standard error stream to a file written to - * the designated output directory. - * - * If `stderr` is a string, it specifies the file name to use. - * - * If `stderr` is an expression, the expression is evaluated and must - * return a string with the file name to use to capture stderr. If the - * return value is not a string, or the resulting path contains illegal - * characters (such as the path separator `/`) it is an error. - * *
- */ - - Object getStderr(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdout
- *
- * Capture the command's standard output stream to a file written to - * the designated output directory. - * - * If `stdout` is a string, it specifies the file name to use. - * - * If `stdout` is an expression, the expression is evaluated and must - * return a string with the file name to use to capture stdout. If the - * return value is not a string, or the resulting path contains illegal - * characters (such as the path separator `/`) it is an error. - * *
- */ - - Object getStdout(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/successCodes
- *
- * Exit codes that indicate the process completed successfully. - * *
- */ - - java.util.Optional> getSuccessCodes(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/temporaryFailCodes
- *
- * Exit codes that indicate the process failed due to a possibly - * temporary condition, where executing the process with the same - * runtime environment and inputs may produce different results. - * *
- */ - - java.util.Optional> getTemporaryFailCodes(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/permanentFailCodes
- *
- * Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail. *
- */ - - java.util.Optional> getPermanentFailCodes(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineToolImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineToolImpl.java deleted file mode 100644 index e7c3ac24..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineToolImpl.java +++ /dev/null @@ -1,655 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandLineTool
- This defines the schema of the CWL Command Line Tool Description document. -
- */ -public class CommandLineToolImpl extends SaveableImpl implements CommandLineTool { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private CommandLineTool_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/class
- - */ - - public CommandLineTool_class getClass_() { - return this.class_; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.List inputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - public java.util.List getInputs() { - return this.inputs; - } - - private java.util.List outputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - public java.util.List getOutputs() { - return this.outputs; - } - - private java.util.Optional> requirements; - - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - public java.util.Optional> getRequirements() { - return this.requirements; - } - - private java.util.Optional> hints; - - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - public java.util.Optional> getHints() { - return this.hints; - } - - private java.util.Optional cwlVersion; - - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - public java.util.Optional getCwlVersion() { - return this.cwlVersion; - } - - private Object baseCommand; - - /** - * Getter for property https://w3id.org/cwl/cwl#baseCommand
- *
- * Specifies the program to execute. If an array, the first element of - * the array is the command to execute, and subsequent elements are - * mandatory command line arguments. The elements in `baseCommand` must - * appear before any command line bindings from `inputBinding` or - * `arguments`. - * - * If `baseCommand` is not provided or is an empty array, the first - * element of the command line produced after processing `inputBinding` or - * `arguments` must be used as the program to execute. - * - * If the program includes a path separator character it must - * be an absolute path, otherwise it is an error. If the program does not - * include a path separator, search the `$PATH` variable in the runtime - * environment of the workflow runner find the absolute path of the - * executable. - * *
- */ - - public Object getBaseCommand() { - return this.baseCommand; - } - - private java.util.Optional> arguments; - - /** - * Getter for property https://w3id.org/cwl/cwl#arguments
- *
- * Command line bindings which are not directly associated with input - * parameters. If the value is a string, it is used as a string literal - * argument. If it is an Expression, the result of the evaluation is used - * as an argument. - * *
- */ - - public java.util.Optional> getArguments() { - return this.arguments; - } - - private Object stdin; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdin
- *
- * A path to a file whose contents must be piped into the command's - * standard input stream. - * *
- */ - - public Object getStdin() { - return this.stdin; - } - - private Object stderr; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stderr
- *
- * Capture the command's standard error stream to a file written to - * the designated output directory. - * - * If `stderr` is a string, it specifies the file name to use. - * - * If `stderr` is an expression, the expression is evaluated and must - * return a string with the file name to use to capture stderr. If the - * return value is not a string, or the resulting path contains illegal - * characters (such as the path separator `/`) it is an error. - * *
- */ - - public Object getStderr() { - return this.stderr; - } - - private Object stdout; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdout
- *
- * Capture the command's standard output stream to a file written to - * the designated output directory. - * - * If `stdout` is a string, it specifies the file name to use. - * - * If `stdout` is an expression, the expression is evaluated and must - * return a string with the file name to use to capture stdout. If the - * return value is not a string, or the resulting path contains illegal - * characters (such as the path separator `/`) it is an error. - * *
- */ - - public Object getStdout() { - return this.stdout; - } - - private java.util.Optional> successCodes; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/successCodes
- *
- * Exit codes that indicate the process completed successfully. - * *
- */ - - public java.util.Optional> getSuccessCodes() { - return this.successCodes; - } - - private java.util.Optional> temporaryFailCodes; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/temporaryFailCodes
- *
- * Exit codes that indicate the process failed due to a possibly - * temporary condition, where executing the process with the same - * runtime environment and inputs may produce different results. - * *
- */ - - public java.util.Optional> getTemporaryFailCodes() { - return this.temporaryFailCodes; - } - - private java.util.Optional> permanentFailCodes; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/permanentFailCodes
- *
- * Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail. *
- */ - - public java.util.Optional> getPermanentFailCodes() { - return this.permanentFailCodes; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandLineToolImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandLineToolImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandLineToolImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - CommandLineTool_class class_; - try { - class_ = - LoaderInstances - .uri_CommandLineTool_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.List inputs; - try { - inputs = - LoaderInstances - .idmap_inputs_array_of_CommandInputParameter - .loadField(__doc.get("inputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List outputs; - try { - outputs = - LoaderInstances - .idmap_outputs_array_of_CommandOutputParameter - .loadField(__doc.get("outputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> requirements; - - if (__doc.containsKey("requirements")) { - try { - requirements = - LoaderInstances - .idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement - .loadField(__doc.get("requirements"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - requirements = null; // won't be used but prevents compiler from complaining. - final String __message = "the `requirements` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - requirements = null; - } - java.util.Optional> hints; - - if (__doc.containsKey("hints")) { - try { - hints = - LoaderInstances - .idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance - .loadField(__doc.get("hints"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - hints = null; // won't be used but prevents compiler from complaining. - final String __message = "the `hints` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - hints = null; - } - java.util.Optional cwlVersion; - - if (__doc.containsKey("cwlVersion")) { - try { - cwlVersion = - LoaderInstances - .uri_optional_CWLVersion_False_True_None_None - .loadField(__doc.get("cwlVersion"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - cwlVersion = null; // won't be used but prevents compiler from complaining. - final String __message = "the `cwlVersion` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - cwlVersion = null; - } - Object baseCommand; - - if (__doc.containsKey("baseCommand")) { - try { - baseCommand = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("baseCommand"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - baseCommand = null; // won't be used but prevents compiler from complaining. - final String __message = "the `baseCommand` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - baseCommand = null; - } - java.util.Optional> arguments; - - if (__doc.containsKey("arguments")) { - try { - arguments = - LoaderInstances - .optional_array_of_union_of_StringInstance_or_ExpressionLoader_or_CommandLineBinding - .loadField(__doc.get("arguments"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - arguments = null; // won't be used but prevents compiler from complaining. - final String __message = "the `arguments` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - arguments = null; - } - Object stdin; - - if (__doc.containsKey("stdin")) { - try { - stdin = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("stdin"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - stdin = null; // won't be used but prevents compiler from complaining. - final String __message = "the `stdin` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - stdin = null; - } - Object stderr; - - if (__doc.containsKey("stderr")) { - try { - stderr = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("stderr"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - stderr = null; // won't be used but prevents compiler from complaining. - final String __message = "the `stderr` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - stderr = null; - } - Object stdout; - - if (__doc.containsKey("stdout")) { - try { - stdout = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("stdout"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - stdout = null; // won't be used but prevents compiler from complaining. - final String __message = "the `stdout` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - stdout = null; - } - java.util.Optional> successCodes; - - if (__doc.containsKey("successCodes")) { - try { - successCodes = - LoaderInstances - .optional_array_of_IntegerInstance - .loadField(__doc.get("successCodes"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - successCodes = null; // won't be used but prevents compiler from complaining. - final String __message = "the `successCodes` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - successCodes = null; - } - java.util.Optional> temporaryFailCodes; - - if (__doc.containsKey("temporaryFailCodes")) { - try { - temporaryFailCodes = - LoaderInstances - .optional_array_of_IntegerInstance - .loadField(__doc.get("temporaryFailCodes"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - temporaryFailCodes = null; // won't be used but prevents compiler from complaining. - final String __message = "the `temporaryFailCodes` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - temporaryFailCodes = null; - } - java.util.Optional> permanentFailCodes; - - if (__doc.containsKey("permanentFailCodes")) { - try { - permanentFailCodes = - LoaderInstances - .optional_array_of_IntegerInstance - .loadField(__doc.get("permanentFailCodes"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - permanentFailCodes = null; // won't be used but prevents compiler from complaining. - final String __message = "the `permanentFailCodes` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - permanentFailCodes = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (java.util.Optional) id; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.inputs = (java.util.List) inputs; - this.outputs = (java.util.List) outputs; - this.requirements = (java.util.Optional>) requirements; - this.hints = (java.util.Optional>) hints; - this.cwlVersion = (java.util.Optional) cwlVersion; - this.class_ = (CommandLineTool_class) class_; - this.baseCommand = (Object) baseCommand; - this.arguments = (java.util.Optional>) arguments; - this.stdin = (Object) stdin; - this.stderr = (Object) stderr; - this.stdout = (Object) stdout; - this.successCodes = (java.util.Optional>) successCodes; - this.temporaryFailCodes = (java.util.Optional>) temporaryFailCodes; - this.permanentFailCodes = (java.util.Optional>) permanentFailCodes; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id", "label", "doc", "inputs", "outputs", "requirements", "hints", "cwlVersion", "class", "baseCommand", "arguments", "stdin", "stderr", "stdout", "successCodes", "temporaryFailCodes", "permanentFailCodes"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineTool_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineTool_class.java deleted file mode 100644 index 2f18bc27..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandLineTool_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum CommandLineTool_class { - COMMANDLINETOOL("CommandLineTool"); - - private static String[] symbols = new String[] {"CommandLineTool"}; - private String docVal; - - private CommandLineTool_class(final String docVal) { - this.docVal = docVal; - } - - public static CommandLineTool_class fromDocumentVal(final String docVal) { - for(final CommandLineTool_class val : CommandLineTool_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", CommandLineTool_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputArraySchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputArraySchema.java deleted file mode 100644 index ce2a0994..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputArraySchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputArraySchema
This interface is implemented by {@link CommandOutputArraySchemaImpl}
- */ -public interface CommandOutputArraySchema extends OutputArraySchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - Object getItems(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - Array_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputArraySchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputArraySchemaImpl.java deleted file mode 100644 index 44253996..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputArraySchemaImpl.java +++ /dev/null @@ -1,232 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputArraySchema
- */ -public class CommandOutputArraySchemaImpl extends SaveableImpl implements CommandOutputArraySchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private Object items; - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - public Object getItems() { - return this.items; - } - - private Array_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - public Array_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandOutputArraySchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandOutputArraySchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandOutputArraySchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - Object items; - try { - items = - LoaderInstances - .uri_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("items"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - items = null; // won't be used but prevents compiler from complaining. - final String __message = "the `items` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Array_name type; - try { - type = - LoaderInstances - .typedsl_Array_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.items = (Object) items; - this.type = (Array_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("items", "type", "label", "doc", "name"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBinding.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBinding.java deleted file mode 100644 index 019a06db..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBinding.java +++ /dev/null @@ -1,125 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputBinding
This interface is implemented by {@link CommandOutputBindingImpl}
- Describes how to generate an output parameter based on the files produced - by a CommandLineTool. - - The output parameter value is generated by applying these operations in the - following order: - - - glob - - loadContents - - outputEval - - secondaryFiles -
- */ -public interface CommandOutputBinding extends LoadContents, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputBinding/glob
- *
- * Find files or directories relative to the output directory, using POSIX - * glob(3) pathname matching. If an array is provided, find files or - * directories that match any pattern in the array. If an expression is - * provided, the expression must return a string or an array of strings, - * which will then be evaluated as one or more glob patterns. Must only - * match and return files/directories which actually exist. - * - * If the value of glob is a relative path pattern (does not - * begin with a slash '/') then it is resolved relative to the - * output directory. If the value of the glob is an absolute - * path pattern (it does begin with a slash '/') then it must - * refer to a path within the output directory. It is an error - * if any glob resolves to a path outside the output directory. - * Specifically this means globs that resolve to paths outside the output - * directory are illegal. - * - * A glob may match a path within the output directory which is - * actually a symlink to another file. In this case, the - * expected behavior is for the resulting File/Directory object to take the - * `basename` (and corresponding `nameroot` and `nameext`) of the - * symlink. The `location` of the File/Directory is implementation - * dependent, but logically the File/Directory should have the same content - * as the symlink target. Platforms may stage output files/directories to - * cloud storage that lack the concept of a symlink. In - * this case file content and directories may be duplicated, or (to avoid - * duplication) the File/Directory `location` may refer to the symlink - * target. - * - * It is an error if a symlink in the output directory (or any - * symlink in a chain of links) refers to any file or directory - * that is not under an input or output directory. - * - * Implementations may shut down a container before globbing - * output, so globs and expressions must not assume access to the - * container filesystem except for declared input and output. - * *
- */ - - Object getGlob(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputBinding/outputEval
- *
- * Evaluate an expression to generate the output value. If - * `glob` was specified, the value of `self` must be an array - * containing file objects that were matched. If no files were - * matched, `self` must be a zero length array; if a single file - * was matched, the value of `self` is an array of a single - * element. Additionally, if `loadContents` is `true`, the File - * objects must include up to the first 64 KiB of file contents - * in the `contents` field. The exit code of the process is - * available in the expression as `runtime.exitCode`. - * *
- */ - - java.util.Optional getOutputEval(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBindingImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBindingImpl.java deleted file mode 100644 index 597ac2e8..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputBindingImpl.java +++ /dev/null @@ -1,269 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputBinding
- Describes how to generate an output parameter based on the files produced - by a CommandLineTool. - - The output parameter value is generated by applying these operations in the - following order: - - - glob - - loadContents - - outputEval - - secondaryFiles -
- */ -public class CommandOutputBindingImpl extends SaveableImpl implements CommandOutputBinding { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - private Object glob; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputBinding/glob
- *
- * Find files or directories relative to the output directory, using POSIX - * glob(3) pathname matching. If an array is provided, find files or - * directories that match any pattern in the array. If an expression is - * provided, the expression must return a string or an array of strings, - * which will then be evaluated as one or more glob patterns. Must only - * match and return files/directories which actually exist. - * - * If the value of glob is a relative path pattern (does not - * begin with a slash '/') then it is resolved relative to the - * output directory. If the value of the glob is an absolute - * path pattern (it does begin with a slash '/') then it must - * refer to a path within the output directory. It is an error - * if any glob resolves to a path outside the output directory. - * Specifically this means globs that resolve to paths outside the output - * directory are illegal. - * - * A glob may match a path within the output directory which is - * actually a symlink to another file. In this case, the - * expected behavior is for the resulting File/Directory object to take the - * `basename` (and corresponding `nameroot` and `nameext`) of the - * symlink. The `location` of the File/Directory is implementation - * dependent, but logically the File/Directory should have the same content - * as the symlink target. Platforms may stage output files/directories to - * cloud storage that lack the concept of a symlink. In - * this case file content and directories may be duplicated, or (to avoid - * duplication) the File/Directory `location` may refer to the symlink - * target. - * - * It is an error if a symlink in the output directory (or any - * symlink in a chain of links) refers to any file or directory - * that is not under an input or output directory. - * - * Implementations may shut down a container before globbing - * output, so globs and expressions must not assume access to the - * container filesystem except for declared input and output. - * *
- */ - - public Object getGlob() { - return this.glob; - } - - private java.util.Optional outputEval; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputBinding/outputEval
- *
- * Evaluate an expression to generate the output value. If - * `glob` was specified, the value of `self` must be an array - * containing file objects that were matched. If no files were - * matched, `self` must be a zero length array; if a single file - * was matched, the value of `self` is an array of a single - * element. Additionally, if `loadContents` is `true`, the File - * objects must include up to the first 64 KiB of file contents - * in the `contents` field. The exit code of the process is - * available in the expression as `runtime.exitCode`. - * *
- */ - - public java.util.Optional getOutputEval() { - return this.outputEval; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandOutputBindingImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandOutputBindingImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandOutputBindingImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - Object glob; - - if (__doc.containsKey("glob")) { - try { - glob = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader_or_array_of_StringInstance - .loadField(__doc.get("glob"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - glob = null; // won't be used but prevents compiler from complaining. - final String __message = "the `glob` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - glob = null; - } - java.util.Optional outputEval; - - if (__doc.containsKey("outputEval")) { - try { - outputEval = - LoaderInstances - .optional_ExpressionLoader - .loadField(__doc.get("outputEval"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputEval = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputEval` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - outputEval = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - this.glob = (Object) glob; - this.outputEval = (java.util.Optional) outputEval; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("loadContents", "loadListing", "glob", "outputEval"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputEnumSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputEnumSchema.java deleted file mode 100644 index bd5625b6..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputEnumSchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputEnumSchema
This interface is implemented by {@link CommandOutputEnumSchemaImpl}
- */ -public interface CommandOutputEnumSchema extends OutputEnumSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - java.util.List getSymbols(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - Enum_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputEnumSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputEnumSchemaImpl.java deleted file mode 100644 index 136bbd2d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputEnumSchemaImpl.java +++ /dev/null @@ -1,232 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputEnumSchema
- */ -public class CommandOutputEnumSchemaImpl extends SaveableImpl implements CommandOutputEnumSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.List symbols; - - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - public java.util.List getSymbols() { - return this.symbols; - } - - private Enum_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - public Enum_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandOutputEnumSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandOutputEnumSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandOutputEnumSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.List symbols; - try { - symbols = - LoaderInstances - .uri_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("symbols"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - symbols = null; // won't be used but prevents compiler from complaining. - final String __message = "the `symbols` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Enum_name type; - try { - type = - LoaderInstances - .typedsl_Enum_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.name = (java.util.Optional) name; - this.symbols = (java.util.List) symbols; - this.type = (Enum_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("name", "symbols", "type", "label", "doc"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameter.java deleted file mode 100644 index 72ae65c2..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameter.java +++ /dev/null @@ -1,137 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputParameter
This interface is implemented by {@link CommandOutputParameterImpl}
- An output parameter for a CommandLineTool.
- */ -public interface CommandOutputParameter extends OutputParameter, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputParameter/outputBinding
- *
- * Describes how to generate this output object based on the files produced by a CommandLineTool *
- */ - - java.util.Optional getOutputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameterImpl.java deleted file mode 100644 index b0b445e8..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputParameterImpl.java +++ /dev/null @@ -1,381 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputParameter
- An output parameter for a CommandLineTool.
- */ -public class CommandOutputParameterImpl extends SaveableImpl implements CommandOutputParameter { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional outputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputParameter/outputBinding
- *
- * Describes how to generate this output object based on the files produced by a CommandLineTool *
- */ - - public java.util.Optional getOutputBinding() { - return this.outputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandOutputParameterImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandOutputParameterImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandOutputParameterImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_stdout_or_stderr_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional outputBinding; - - if (__doc.containsKey("outputBinding")) { - try { - outputBinding = - LoaderInstances - .optional_CommandOutputBinding - .loadField(__doc.get("outputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - outputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.doc = (Object) doc; - this.id = (java.util.Optional) id; - this.format = (Object) format; - this.type = (Object) type; - this.outputBinding = (java.util.Optional) outputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("label", "secondaryFiles", "streamable", "doc", "id", "format", "type", "outputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordField.java deleted file mode 100644 index e26042b5..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordField.java +++ /dev/null @@ -1,139 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputRecordField
This interface is implemented by {@link CommandOutputRecordFieldImpl}
- */ -public interface CommandOutputRecordField extends OutputRecordField, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - String getName(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputRecordField/outputBinding
- *
- * Describes how to generate this output object based on the files - * produced by a CommandLineTool - * *
- */ - - java.util.Optional getOutputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordFieldImpl.java deleted file mode 100644 index 39b9f786..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordFieldImpl.java +++ /dev/null @@ -1,378 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordField
- */ -public class CommandOutputRecordFieldImpl extends SaveableImpl implements CommandOutputRecordField { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String name; - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - public String getName() { - return this.name; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private java.util.Optional outputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputRecordField/outputBinding
- *
- * Describes how to generate this output object based on the files - * produced by a CommandLineTool - * *
- */ - - public java.util.Optional getOutputBinding() { - return this.outputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandOutputRecordFieldImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandOutputRecordFieldImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandOutputRecordFieldImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - if (name == null) { - if (__docRoot != null) { - name = __docRoot; - } else { - throw new ValidationException("Missing name"); - } - } - __baseUri = (String) name; - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional outputBinding; - - if (__doc.containsKey("outputBinding")) { - try { - outputBinding = - LoaderInstances - .optional_CommandOutputBinding - .loadField(__doc.get("outputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - outputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.doc = (Object) doc; - this.name = (String) name; - this.type = (Object) type; - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.format = (Object) format; - this.outputBinding = (java.util.Optional) outputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("doc", "name", "type", "label", "secondaryFiles", "streamable", "format", "outputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordSchema.java deleted file mode 100644 index af27b61d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordSchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputRecordSchema
This interface is implemented by {@link CommandOutputRecordSchemaImpl}
- */ -public interface CommandOutputRecordSchema extends OutputRecordSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - java.util.Optional> getFields(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - Record_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordSchemaImpl.java deleted file mode 100644 index 36219652..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/CommandOutputRecordSchemaImpl.java +++ /dev/null @@ -1,238 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordSchema
- */ -public class CommandOutputRecordSchemaImpl extends SaveableImpl implements CommandOutputRecordSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.Optional> fields; - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - public java.util.Optional> getFields() { - return this.fields; - } - - private Record_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - public Record_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of CommandOutputRecordSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandOutputRecordSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandOutputRecordSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.Optional> fields; - - if (__doc.containsKey("fields")) { - try { - fields = - LoaderInstances - .idmap_fields_optional_array_of_CommandOutputRecordField - .loadField(__doc.get("fields"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - fields = null; // won't be used but prevents compiler from complaining. - final String __message = "the `fields` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - fields = null; - } - Record_name type; - try { - type = - LoaderInstances - .typedsl_Record_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.fields = (java.util.Optional>) fields; - this.type = (Record_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("fields", "type", "label", "doc", "name"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Directory.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Directory.java deleted file mode 100644 index 44fb4f24..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Directory.java +++ /dev/null @@ -1,154 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Directory
This interface is implemented by {@link DirectoryImpl}
- Represents a directory to present to a command line tool. - - Directories are represented as objects with `class` of `Directory`. Directory objects have - a number of properties that provide metadata about the directory. - - The `location` property of a Directory is a URI that uniquely identifies - the directory. Implementations must support the file:// URI scheme and may - support other schemes such as http://. Alternately to `location`, - implementations must also accept the `path` property on Directory, which - must be a filesystem path available on the same host as the CWL runner (for - inputs) or the runtime environment of a command line tool execution (for - command line tool outputs). - - A Directory object may have a `listing` field. This is a list of File and - Directory objects that are contained in the Directory. For each entry in - `listing`, the `basename` property defines the name of the File or - Subdirectory when staged to disk. If `listing` is not provided, the - implementation must have some way of fetching the Directory listing at - runtime based on the `location` field. - - If a Directory does not have `location`, it is a Directory literal. A - Directory literal must provide `listing`. Directory literals must be - created on disk at runtime as needed. - - The resources in a Directory literal do not need to have any implied - relationship in their `location`. For example, a Directory listing may - contain two files located on different hosts. It is the responsibility of - the runtime to ensure that those files are staged to disk appropriately. - Secondary files associated with files in `listing` must also be staged to - the same Directory. - - When executing a CommandLineTool, Directories must be recursively staged - first and have local values of `path` assigend. - - Directory objects in CommandLineTool output must provide either a - `location` URI or a `path` property in the context of the tool execution - runtime (local to the compute node, or within the executing container). - - An ExpressionTool may forward file references from input to output by using - the same value for `location`. - - Name conflicts (the same `basename` appearing multiple times in `listing` - or in any entry in `secondaryFiles` in the listing) is a fatal error. -
- */ -public interface Directory extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Directory/class
- *
- * Must be `Directory` to indicate this object describes a Directory. *
- */ - - Directory_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#Directory/location
- *
- * An IRI that identifies the directory resource. This may be a relative - * reference, in which case it must be resolved using the base IRI of the - * document. The location may refer to a local or remote resource. If - * the `listing` field is not set, the implementation must use the - * location IRI to retrieve directory listing. If an implementation is - * unable to retrieve the directory listing stored at a remote resource (due to - * unsupported protocol, access denied, or other issue) it must signal an - * error. - * - * If the `location` field is not provided, the `listing` field must be - * provided. The implementation must assign a unique identifier for - * the `location` field. - * - * If the `path` field is provided but the `location` field is not, an - * implementation may assign the value of the `path` field to `location`, - * then follow the rules above. - * *
- */ - - java.util.Optional getLocation(); - /** - * Getter for property https://w3id.org/cwl/cwl#path
- *
- * The local path where the Directory is made available prior to executing a - * CommandLineTool. This must be set by the implementation. This field - * must not be used in any other context. The command line tool being - * executed must be able to to access the directory at `path` using the POSIX - * `opendir(2)` syscall. - * - * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * `<space>`, `<tab>`, and `<newline>`) or characters - * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) - * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) - * then implementations may terminate the process with a - * `permanentFailure`. - * *
- */ - - java.util.Optional getPath(); - /** - * Getter for property https://w3id.org/cwl/cwl#Directory/basename
- *
- * The base name of the directory, that is, the name of the file without any - * leading directory path. The base name must not contain a slash `/`. - * - * If not provided, the implementation must set this field based on the - * `location` field by taking the final path component after parsing - * `location` as an IRI. If `basename` is provided, it is not required to - * match the value from `location`. - * - * When this file is made available to a CommandLineTool, it must be named - * with `basename`, i.e. the final component of the `path` field must match - * `basename`. - * *
- */ - - java.util.Optional getBasename(); - /** - * Getter for property https://w3id.org/cwl/cwl#listing
- *
- * List of files or subdirectories contained in this directory. The name - * of each file or subdirectory is determined by the `basename` field of - * each `File` or `Directory` object. It is an error if a `File` shares a - * `basename` with any other entry in `listing`. If two or more - * `Directory` object share the same `basename`, this must be treated as - * equivalent to a single subdirectory with the listings recursively - * merged. - * *
- */ - - java.util.Optional> getListing(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DirectoryImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/DirectoryImpl.java deleted file mode 100644 index ebfc1eba..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DirectoryImpl.java +++ /dev/null @@ -1,315 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#Directory
- Represents a directory to present to a command line tool. - - Directories are represented as objects with `class` of `Directory`. Directory objects have - a number of properties that provide metadata about the directory. - - The `location` property of a Directory is a URI that uniquely identifies - the directory. Implementations must support the file:// URI scheme and may - support other schemes such as http://. Alternately to `location`, - implementations must also accept the `path` property on Directory, which - must be a filesystem path available on the same host as the CWL runner (for - inputs) or the runtime environment of a command line tool execution (for - command line tool outputs). - - A Directory object may have a `listing` field. This is a list of File and - Directory objects that are contained in the Directory. For each entry in - `listing`, the `basename` property defines the name of the File or - Subdirectory when staged to disk. If `listing` is not provided, the - implementation must have some way of fetching the Directory listing at - runtime based on the `location` field. - - If a Directory does not have `location`, it is a Directory literal. A - Directory literal must provide `listing`. Directory literals must be - created on disk at runtime as needed. - - The resources in a Directory literal do not need to have any implied - relationship in their `location`. For example, a Directory listing may - contain two files located on different hosts. It is the responsibility of - the runtime to ensure that those files are staged to disk appropriately. - Secondary files associated with files in `listing` must also be staged to - the same Directory. - - When executing a CommandLineTool, Directories must be recursively staged - first and have local values of `path` assigend. - - Directory objects in CommandLineTool output must provide either a - `location` URI or a `path` property in the context of the tool execution - runtime (local to the compute node, or within the executing container). - - An ExpressionTool may forward file references from input to output by using - the same value for `location`. - - Name conflicts (the same `basename` appearing multiple times in `listing` - or in any entry in `secondaryFiles` in the listing) is a fatal error. -
- */ -public class DirectoryImpl extends SaveableImpl implements Directory { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Directory_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#Directory/class
- *
- * Must be `Directory` to indicate this object describes a Directory. *
- */ - - public Directory_class getClass_() { - return this.class_; - } - - private java.util.Optional location; - - /** - * Getter for property https://w3id.org/cwl/cwl#Directory/location
- *
- * An IRI that identifies the directory resource. This may be a relative - * reference, in which case it must be resolved using the base IRI of the - * document. The location may refer to a local or remote resource. If - * the `listing` field is not set, the implementation must use the - * location IRI to retrieve directory listing. If an implementation is - * unable to retrieve the directory listing stored at a remote resource (due to - * unsupported protocol, access denied, or other issue) it must signal an - * error. - * - * If the `location` field is not provided, the `listing` field must be - * provided. The implementation must assign a unique identifier for - * the `location` field. - * - * If the `path` field is provided but the `location` field is not, an - * implementation may assign the value of the `path` field to `location`, - * then follow the rules above. - * *
- */ - - public java.util.Optional getLocation() { - return this.location; - } - - private java.util.Optional path; - - /** - * Getter for property https://w3id.org/cwl/cwl#path
- *
- * The local path where the Directory is made available prior to executing a - * CommandLineTool. This must be set by the implementation. This field - * must not be used in any other context. The command line tool being - * executed must be able to to access the directory at `path` using the POSIX - * `opendir(2)` syscall. - * - * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * `<space>`, `<tab>`, and `<newline>`) or characters - * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) - * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) - * then implementations may terminate the process with a - * `permanentFailure`. - * *
- */ - - public java.util.Optional getPath() { - return this.path; - } - - private java.util.Optional basename; - - /** - * Getter for property https://w3id.org/cwl/cwl#Directory/basename
- *
- * The base name of the directory, that is, the name of the file without any - * leading directory path. The base name must not contain a slash `/`. - * - * If not provided, the implementation must set this field based on the - * `location` field by taking the final path component after parsing - * `location` as an IRI. If `basename` is provided, it is not required to - * match the value from `location`. - * - * When this file is made available to a CommandLineTool, it must be named - * with `basename`, i.e. the final component of the `path` field must match - * `basename`. - * *
- */ - - public java.util.Optional getBasename() { - return this.basename; - } - - private java.util.Optional> listing; - - /** - * Getter for property https://w3id.org/cwl/cwl#listing
- *
- * List of files or subdirectories contained in this directory. The name - * of each file or subdirectory is determined by the `basename` field of - * each `File` or `Directory` object. It is an error if a `File` shares a - * `basename` with any other entry in `listing`. If two or more - * `Directory` object share the same `basename`, this must be treated as - * equivalent to a single subdirectory with the listings recursively - * merged. - * *
- */ - - public java.util.Optional> getListing() { - return this.listing; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of DirectoryImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public DirectoryImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("DirectoryImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Directory_class class_; - try { - class_ = - LoaderInstances - .uri_Directory_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional location; - - if (__doc.containsKey("location")) { - try { - location = - LoaderInstances - .uri_optional_StringInstance_False_False_None_None - .loadField(__doc.get("location"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - location = null; // won't be used but prevents compiler from complaining. - final String __message = "the `location` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - location = null; - } - java.util.Optional path; - - if (__doc.containsKey("path")) { - try { - path = - LoaderInstances - .uri_optional_StringInstance_False_False_None_None - .loadField(__doc.get("path"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - path = null; // won't be used but prevents compiler from complaining. - final String __message = "the `path` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - path = null; - } - java.util.Optional basename; - - if (__doc.containsKey("basename")) { - try { - basename = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("basename"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - basename = null; // won't be used but prevents compiler from complaining. - final String __message = "the `basename` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - basename = null; - } - java.util.Optional> listing; - - if (__doc.containsKey("listing")) { - try { - listing = - LoaderInstances - .optional_array_of_union_of_File_or_Directory - .loadField(__doc.get("listing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - listing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `listing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - listing = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (Directory_class) class_; - this.location = (java.util.Optional) location; - this.path = (java.util.Optional) path; - this.basename = (java.util.Optional) basename; - this.listing = (java.util.Optional>) listing; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "location", "path", "basename", "listing"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Directory_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Directory_class.java deleted file mode 100644 index a3116455..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Directory_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum Directory_class { - DIRECTORY("Directory"); - - private static String[] symbols = new String[] {"Directory"}; - private String docVal; - - private Directory_class(final String docVal) { - this.docVal = docVal; - } - - public static Directory_class fromDocumentVal(final String docVal) { - for(final Directory_class val : Directory_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Directory_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Dirent.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Dirent.java deleted file mode 100644 index ec831d32..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Dirent.java +++ /dev/null @@ -1,79 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Dirent
This interface is implemented by {@link DirentImpl}
- Define a file or subdirectory that must be placed in the designated output - directory prior to executing the command line tool. May be the result of - executing an expression, such as building a configuration file from a - template. -
- */ -public interface Dirent extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#entryname
- *
- * The name of the file or subdirectory to create in the output directory. - * If `entry` is a File or Directory, the `entryname` field overrides the value - * of `basename` of the File or Directory object. Optional. - * *
- */ - - Object getEntryname(); - /** - * Getter for property https://w3id.org/cwl/cwl#entry
- *
- * If the value is a string literal or an expression which evaluates to a - * string, a new file must be created with the string as the file contents. - * - * If the value is an expression that evaluates to a `File` object, this - * indicates the referenced file should be added to the designated output - * directory prior to executing the tool. - * - * If the value is an expression that evaluates to a `Dirent` object, this - * indicates that the File or Directory in `entry` should be added to the - * designated output directory with the name in `entryname`. - * - * If `writable` is false, the file may be made available using a bind - * mount or file system link to avoid unnecessary copying of the input - * file. - * *
- */ - - Object getEntry(); - /** - * Getter for property https://w3id.org/cwl/cwl#Dirent/writable
- *
- * If true, the file or directory must be writable by the tool. Changes - * to the file or directory must be isolated and not visible by any other - * CommandLineTool process. This may be implemented by making a copy of - * the original file or directory. Default false (files and directories - * read-only by default). - * - * A directory marked as `writable: true` implies that all files and - * subdirectories are recursively writable as well. - * *
- */ - - java.util.Optional getWritable(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DirentImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/DirentImpl.java deleted file mode 100644 index 16d7fdd1..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DirentImpl.java +++ /dev/null @@ -1,194 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#Dirent
- Define a file or subdirectory that must be placed in the designated output - directory prior to executing the command line tool. May be the result of - executing an expression, such as building a configuration file from a - template. -
- */ -public class DirentImpl extends SaveableImpl implements Dirent { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Object entryname; - - /** - * Getter for property https://w3id.org/cwl/cwl#entryname
- *
- * The name of the file or subdirectory to create in the output directory. - * If `entry` is a File or Directory, the `entryname` field overrides the value - * of `basename` of the File or Directory object. Optional. - * *
- */ - - public Object getEntryname() { - return this.entryname; - } - - private Object entry; - - /** - * Getter for property https://w3id.org/cwl/cwl#entry
- *
- * If the value is a string literal or an expression which evaluates to a - * string, a new file must be created with the string as the file contents. - * - * If the value is an expression that evaluates to a `File` object, this - * indicates the referenced file should be added to the designated output - * directory prior to executing the tool. - * - * If the value is an expression that evaluates to a `Dirent` object, this - * indicates that the File or Directory in `entry` should be added to the - * designated output directory with the name in `entryname`. - * - * If `writable` is false, the file may be made available using a bind - * mount or file system link to avoid unnecessary copying of the input - * file. - * *
- */ - - public Object getEntry() { - return this.entry; - } - - private java.util.Optional writable; - - /** - * Getter for property https://w3id.org/cwl/cwl#Dirent/writable
- *
- * If true, the file or directory must be writable by the tool. Changes - * to the file or directory must be isolated and not visible by any other - * CommandLineTool process. This may be implemented by making a copy of - * the original file or directory. Default false (files and directories - * read-only by default). - * - * A directory marked as `writable: true` implies that all files and - * subdirectories are recursively writable as well. - * *
- */ - - public java.util.Optional getWritable() { - return this.writable; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of DirentImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public DirentImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("DirentImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Object entryname; - - if (__doc.containsKey("entryname")) { - try { - entryname = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("entryname"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - entryname = null; // won't be used but prevents compiler from complaining. - final String __message = "the `entryname` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - entryname = null; - } - Object entry; - try { - entry = - LoaderInstances - .union_of_StringInstance_or_ExpressionLoader - .loadField(__doc.get("entry"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - entry = null; // won't be used but prevents compiler from complaining. - final String __message = "the `entry` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional writable; - - if (__doc.containsKey("writable")) { - try { - writable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("writable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - writable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `writable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - writable = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.entryname = (Object) entryname; - this.entry = (Object) entry; - this.writable = (java.util.Optional) writable; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("entryname", "entry", "writable"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirement.java deleted file mode 100644 index d9d065a5..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirement.java +++ /dev/null @@ -1,138 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#DockerRequirement
This interface is implemented by {@link DockerRequirementImpl}
- Indicates that a workflow component should be run in a - [Docker](http://docker.com) or Docker-compatible (such as - [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and - specifies how to fetch or build the image. - - If a CommandLineTool lists `DockerRequirement` under - `hints` (or `requirements`), it may (or must) be run in the specified Docker - container. - - The platform must first acquire or install the correct Docker image as - specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`. - - The platform must execute the tool in the container using `docker run` with - the appropriate Docker image and tool command line. - - The workflow platform may provide input files and the designated output - directory through the use of volume bind mounts. The platform should rewrite - file paths in the input object to correspond to the Docker bind mounted - locations. That is, the platform should rewrite values in the parameter context - such as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths - within the container. The platform must ensure that `runtime.outdir` and - `runtime.tmpdir` are distinct directories. - - When running a tool contained in Docker, the workflow platform must not - assume anything about the contents of the Docker container, such as the - presence or absence of specific software, except to assume that the - generated command line represents a valid command within the runtime - environment of the container. - - A container image may specify an - [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint) - and/or - [CMD](https://docs.docker.com/engine/reference/builder/#cmd). - Command line arguments will be appended after all elements of - ENTRYPOINT, and will override all elements specified using CMD (in - other words, CMD is only used when the CommandLineTool definition - produces an empty command line). - - Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility - concerns of the implicit hidden execution point (For further discussion, see - [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable - CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD. - CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the - `requirements` section. - - ## Interaction with other requirements - - If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a - DockerRequirement, the environment variables must be provided to Docker - using `--env` or `--env-file` and interact with the container's preexisting - environment as defined by Docker. -
- */ -public interface DockerRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/class
- *
- * Always 'DockerRequirement' *
- */ - - DockerRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerPull
- *
- * Specify a Docker image to retrieve using `docker pull`. Can contain the - * immutable digest to ensure an exact container is used: - * `dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2` - * *
- */ - - java.util.Optional getDockerPull(); - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerLoad
- *
- * Specify a HTTP URL from which to download a Docker image using `docker load`. *
- */ - - java.util.Optional getDockerLoad(); - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerFile
- *
- * Supply the contents of a Dockerfile which will be built using `docker build`. *
- */ - - java.util.Optional getDockerFile(); - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerImport
- *
- * Provide HTTP URL to download and gunzip a Docker images using `docker import. *
- */ - - java.util.Optional getDockerImport(); - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerImageId
- *
- * The image id that will be used for `docker run`. May be a - * human-readable image name or the image identifier hash. May be skipped - * if `dockerPull` is specified, in which case the `dockerPull` image id - * must be used. - * *
- */ - - java.util.Optional getDockerImageId(); - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerOutputDirectory
- *
- * Set the designated output directory to a specific location inside the - * Docker container. - * *
- */ - - java.util.Optional getDockerOutputDirectory(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirementImpl.java deleted file mode 100644 index 3f132d70..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirementImpl.java +++ /dev/null @@ -1,345 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#DockerRequirement
- Indicates that a workflow component should be run in a - [Docker](http://docker.com) or Docker-compatible (such as - [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and - specifies how to fetch or build the image. - - If a CommandLineTool lists `DockerRequirement` under - `hints` (or `requirements`), it may (or must) be run in the specified Docker - container. - - The platform must first acquire or install the correct Docker image as - specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`. - - The platform must execute the tool in the container using `docker run` with - the appropriate Docker image and tool command line. - - The workflow platform may provide input files and the designated output - directory through the use of volume bind mounts. The platform should rewrite - file paths in the input object to correspond to the Docker bind mounted - locations. That is, the platform should rewrite values in the parameter context - such as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths - within the container. The platform must ensure that `runtime.outdir` and - `runtime.tmpdir` are distinct directories. - - When running a tool contained in Docker, the workflow platform must not - assume anything about the contents of the Docker container, such as the - presence or absence of specific software, except to assume that the - generated command line represents a valid command within the runtime - environment of the container. - - A container image may specify an - [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint) - and/or - [CMD](https://docs.docker.com/engine/reference/builder/#cmd). - Command line arguments will be appended after all elements of - ENTRYPOINT, and will override all elements specified using CMD (in - other words, CMD is only used when the CommandLineTool definition - produces an empty command line). - - Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility - concerns of the implicit hidden execution point (For further discussion, see - [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable - CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD. - CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the - `requirements` section. - - ## Interaction with other requirements - - If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a - DockerRequirement, the environment variables must be provided to Docker - using `--env` or `--env-file` and interact with the container's preexisting - environment as defined by Docker. -
- */ -public class DockerRequirementImpl extends SaveableImpl implements DockerRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private DockerRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/class
- *
- * Always 'DockerRequirement' *
- */ - - public DockerRequirement_class getClass_() { - return this.class_; - } - - private java.util.Optional dockerPull; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerPull
- *
- * Specify a Docker image to retrieve using `docker pull`. Can contain the - * immutable digest to ensure an exact container is used: - * `dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2` - * *
- */ - - public java.util.Optional getDockerPull() { - return this.dockerPull; - } - - private java.util.Optional dockerLoad; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerLoad
- *
- * Specify a HTTP URL from which to download a Docker image using `docker load`. *
- */ - - public java.util.Optional getDockerLoad() { - return this.dockerLoad; - } - - private java.util.Optional dockerFile; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerFile
- *
- * Supply the contents of a Dockerfile which will be built using `docker build`. *
- */ - - public java.util.Optional getDockerFile() { - return this.dockerFile; - } - - private java.util.Optional dockerImport; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerImport
- *
- * Provide HTTP URL to download and gunzip a Docker images using `docker import. *
- */ - - public java.util.Optional getDockerImport() { - return this.dockerImport; - } - - private java.util.Optional dockerImageId; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerImageId
- *
- * The image id that will be used for `docker run`. May be a - * human-readable image name or the image identifier hash. May be skipped - * if `dockerPull` is specified, in which case the `dockerPull` image id - * must be used. - * *
- */ - - public java.util.Optional getDockerImageId() { - return this.dockerImageId; - } - - private java.util.Optional dockerOutputDirectory; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerOutputDirectory
- *
- * Set the designated output directory to a specific location inside the - * Docker container. - * *
- */ - - public java.util.Optional getDockerOutputDirectory() { - return this.dockerOutputDirectory; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of DockerRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public DockerRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("DockerRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - DockerRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_DockerRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional dockerPull; - - if (__doc.containsKey("dockerPull")) { - try { - dockerPull = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dockerPull"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dockerPull = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dockerPull` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dockerPull = null; - } - java.util.Optional dockerLoad; - - if (__doc.containsKey("dockerLoad")) { - try { - dockerLoad = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dockerLoad"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dockerLoad = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dockerLoad` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dockerLoad = null; - } - java.util.Optional dockerFile; - - if (__doc.containsKey("dockerFile")) { - try { - dockerFile = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dockerFile"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dockerFile = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dockerFile` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dockerFile = null; - } - java.util.Optional dockerImport; - - if (__doc.containsKey("dockerImport")) { - try { - dockerImport = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dockerImport"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dockerImport = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dockerImport` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dockerImport = null; - } - java.util.Optional dockerImageId; - - if (__doc.containsKey("dockerImageId")) { - try { - dockerImageId = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dockerImageId"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dockerImageId = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dockerImageId` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dockerImageId = null; - } - java.util.Optional dockerOutputDirectory; - - if (__doc.containsKey("dockerOutputDirectory")) { - try { - dockerOutputDirectory = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dockerOutputDirectory"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dockerOutputDirectory = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dockerOutputDirectory` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dockerOutputDirectory = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (DockerRequirement_class) class_; - this.dockerPull = (java.util.Optional) dockerPull; - this.dockerLoad = (java.util.Optional) dockerLoad; - this.dockerFile = (java.util.Optional) dockerFile; - this.dockerImport = (java.util.Optional) dockerImport; - this.dockerImageId = (java.util.Optional) dockerImageId; - this.dockerOutputDirectory = (java.util.Optional) dockerOutputDirectory; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "dockerPull", "dockerLoad", "dockerFile", "dockerImport", "dockerImageId", "dockerOutputDirectory"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirement_class.java deleted file mode 100644 index a130d08e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/DockerRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum DockerRequirement_class { - DOCKERREQUIREMENT("DockerRequirement"); - - private static String[] symbols = new String[] {"DockerRequirement"}; - private String docVal; - - private DockerRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static DockerRequirement_class fromDocumentVal(final String docVal) { - for(final DockerRequirement_class val : DockerRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", DockerRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Documented.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Documented.java deleted file mode 100644 index 234977d7..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Documented.java +++ /dev/null @@ -1,35 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#Documented
- */ -public interface Documented extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnumSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnumSchema.java deleted file mode 100644 index 0fc88977..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnumSchema.java +++ /dev/null @@ -1,50 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#EnumSchema
This interface is implemented by {@link EnumSchemaImpl}
- Define an enumerated type. -
- */ -public interface EnumSchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#EnumSchema/name
- - */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - java.util.List getSymbols(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - Enum_name getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnumSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnumSchemaImpl.java deleted file mode 100644 index 48ca5347..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnumSchemaImpl.java +++ /dev/null @@ -1,173 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/salad#EnumSchema
- Define an enumerated type. -
- */ -public class EnumSchemaImpl extends SaveableImpl implements EnumSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/salad#EnumSchema/name
- - */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.List symbols; - - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - public java.util.List getSymbols() { - return this.symbols; - } - - private Enum_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - public Enum_name getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of EnumSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public EnumSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("EnumSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.List symbols; - try { - symbols = - LoaderInstances - .uri_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("symbols"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - symbols = null; // won't be used but prevents compiler from complaining. - final String __message = "the `symbols` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Enum_name type; - try { - type = - LoaderInstances - .typedsl_Enum_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.name = (java.util.Optional) name; - this.symbols = (java.util.List) symbols; - this.type = (Enum_name) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("name", "symbols", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Enum_name.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Enum_name.java deleted file mode 100644 index 9c03e65e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Enum_name.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum Enum_name { - ENUM("enum"); - - private static String[] symbols = new String[] {"enum"}; - private String docVal; - - private Enum_name(final String docVal) { - this.docVal = docVal; - } - - public static Enum_name fromDocumentVal(final String docVal) { - for(final Enum_name val : Enum_name.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Enum_name.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirement.java deleted file mode 100644 index adbc73a3..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirement.java +++ /dev/null @@ -1,45 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#EnvVarRequirement
This interface is implemented by {@link EnvVarRequirementImpl}
- Define a list of environment variables which will be set in the - execution environment of the tool. See `EnvironmentDef` for details. -
- */ -public interface EnvVarRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/class
- *
- * Always 'EnvVarRequirement' *
- */ - - EnvVarRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/envDef
- *
- * The list of environment variables. *
- */ - - java.util.List getEnvDef(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirementImpl.java deleted file mode 100644 index feeb54f3..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirementImpl.java +++ /dev/null @@ -1,131 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#EnvVarRequirement
- Define a list of environment variables which will be set in the - execution environment of the tool. See `EnvironmentDef` for details. -
- */ -public class EnvVarRequirementImpl extends SaveableImpl implements EnvVarRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private EnvVarRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/class
- *
- * Always 'EnvVarRequirement' *
- */ - - public EnvVarRequirement_class getClass_() { - return this.class_; - } - - private java.util.List envDef; - - /** - * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/envDef
- *
- * The list of environment variables. *
- */ - - public java.util.List getEnvDef() { - return this.envDef; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of EnvVarRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public EnvVarRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("EnvVarRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - EnvVarRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_EnvVarRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List envDef; - try { - envDef = - LoaderInstances - .idmap_envDef_array_of_EnvironmentDef - .loadField(__doc.get("envDef"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - envDef = null; // won't be used but prevents compiler from complaining. - final String __message = "the `envDef` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (EnvVarRequirement_class) class_; - this.envDef = (java.util.List) envDef; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "envDef"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirement_class.java deleted file mode 100644 index afe066c2..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvVarRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum EnvVarRequirement_class { - ENVVARREQUIREMENT("EnvVarRequirement"); - - private static String[] symbols = new String[] {"EnvVarRequirement"}; - private String docVal; - - private EnvVarRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static EnvVarRequirement_class fromDocumentVal(final String docVal) { - for(final EnvVarRequirement_class val : EnvVarRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", EnvVarRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvironmentDef.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvironmentDef.java deleted file mode 100644 index 4a634b31..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvironmentDef.java +++ /dev/null @@ -1,46 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#EnvironmentDef
This interface is implemented by {@link EnvironmentDefImpl}
- Define an environment variable that will be set in the runtime environment - by the workflow platform when executing the command line tool. May be the - result of executing an expression, such as getting a parameter from input. -
- */ -public interface EnvironmentDef extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#EnvironmentDef/envName
- *
- * The environment variable name *
- */ - - String getEnvName(); - /** - * Getter for property https://w3id.org/cwl/cwl#EnvironmentDef/envValue
- *
- * The environment variable value *
- */ - - Object getEnvValue(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvironmentDefImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvironmentDefImpl.java deleted file mode 100644 index 0dcbfe75..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/EnvironmentDefImpl.java +++ /dev/null @@ -1,132 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#EnvironmentDef
- Define an environment variable that will be set in the runtime environment - by the workflow platform when executing the command line tool. May be the - result of executing an expression, such as getting a parameter from input. -
- */ -public class EnvironmentDefImpl extends SaveableImpl implements EnvironmentDef { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String envName; - - /** - * Getter for property https://w3id.org/cwl/cwl#EnvironmentDef/envName
- *
- * The environment variable name *
- */ - - public String getEnvName() { - return this.envName; - } - - private Object envValue; - - /** - * Getter for property https://w3id.org/cwl/cwl#EnvironmentDef/envValue
- *
- * The environment variable value *
- */ - - public Object getEnvValue() { - return this.envValue; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of EnvironmentDefImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public EnvironmentDefImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("EnvironmentDefImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String envName; - try { - envName = - LoaderInstances - .StringInstance - .loadField(__doc.get("envName"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - envName = null; // won't be used but prevents compiler from complaining. - final String __message = "the `envName` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object envValue; - try { - envValue = - LoaderInstances - .union_of_StringInstance_or_ExpressionLoader - .loadField(__doc.get("envValue"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - envValue = null; // won't be used but prevents compiler from complaining. - final String __message = "the `envValue` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.envName = (String) envName; - this.envValue = (Object) envValue; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("envName", "envValue"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Expression.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Expression.java deleted file mode 100644 index e34232e8..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Expression.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum Expression { - EXPRESSIONPLACEHOLDER("ExpressionPlaceholder"); - - private static String[] symbols = new String[] {"ExpressionPlaceholder"}; - private String docVal; - - private Expression(final String docVal) { - this.docVal = docVal; - } - - public static Expression fromDocumentVal(final String docVal) { - for(final Expression val : Expression.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Expression.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionTool.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionTool.java deleted file mode 100644 index 51a8163d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionTool.java +++ /dev/null @@ -1,132 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ExpressionTool
This interface is implemented by {@link ExpressionToolImpl}
- An ExpressionTool is a type of Process object that can be run by itself - or as a Workflow step. It executes a pure Javascript expression that has - access to the same input parameters as a workflow. It is meant to be used - sparingly as a way to isolate complex Javascript expressions that need to - operate on input data and produce some result; perhaps just a - rearrangement of the inputs. No Docker software container is required - or allowed. -
- */ -public interface ExpressionTool extends Process, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#ExpressionTool/class
- - */ - - ExpressionTool_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - java.util.List getInputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - java.util.List getOutputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - java.util.Optional> getRequirements(); - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - java.util.Optional> getHints(); - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - java.util.Optional getCwlVersion(); - /** - * Getter for property https://w3id.org/cwl/cwl#ExpressionTool/expression
- *
- * The expression to execute. The expression must return a JSON object which - * matches the output parameters of the ExpressionTool. - * *
- */ - - String getExpression(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolImpl.java deleted file mode 100644 index aac4f8a2..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolImpl.java +++ /dev/null @@ -1,404 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#ExpressionTool
- An ExpressionTool is a type of Process object that can be run by itself - or as a Workflow step. It executes a pure Javascript expression that has - access to the same input parameters as a workflow. It is meant to be used - sparingly as a way to isolate complex Javascript expressions that need to - operate on input data and produce some result; perhaps just a - rearrangement of the inputs. No Docker software container is required - or allowed. -
- */ -public class ExpressionToolImpl extends SaveableImpl implements ExpressionTool { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private ExpressionTool_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#ExpressionTool/class
- - */ - - public ExpressionTool_class getClass_() { - return this.class_; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.List inputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - public java.util.List getInputs() { - return this.inputs; - } - - private java.util.List outputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - public java.util.List getOutputs() { - return this.outputs; - } - - private java.util.Optional> requirements; - - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - public java.util.Optional> getRequirements() { - return this.requirements; - } - - private java.util.Optional> hints; - - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - public java.util.Optional> getHints() { - return this.hints; - } - - private java.util.Optional cwlVersion; - - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - public java.util.Optional getCwlVersion() { - return this.cwlVersion; - } - - private String expression; - - /** - * Getter for property https://w3id.org/cwl/cwl#ExpressionTool/expression
- *
- * The expression to execute. The expression must return a JSON object which - * matches the output parameters of the ExpressionTool. - * *
- */ - - public String getExpression() { - return this.expression; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of ExpressionToolImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ExpressionToolImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ExpressionToolImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - ExpressionTool_class class_; - try { - class_ = - LoaderInstances - .uri_ExpressionTool_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.List inputs; - try { - inputs = - LoaderInstances - .idmap_inputs_array_of_WorkflowInputParameter - .loadField(__doc.get("inputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List outputs; - try { - outputs = - LoaderInstances - .idmap_outputs_array_of_ExpressionToolOutputParameter - .loadField(__doc.get("outputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> requirements; - - if (__doc.containsKey("requirements")) { - try { - requirements = - LoaderInstances - .idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement - .loadField(__doc.get("requirements"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - requirements = null; // won't be used but prevents compiler from complaining. - final String __message = "the `requirements` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - requirements = null; - } - java.util.Optional> hints; - - if (__doc.containsKey("hints")) { - try { - hints = - LoaderInstances - .idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance - .loadField(__doc.get("hints"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - hints = null; // won't be used but prevents compiler from complaining. - final String __message = "the `hints` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - hints = null; - } - java.util.Optional cwlVersion; - - if (__doc.containsKey("cwlVersion")) { - try { - cwlVersion = - LoaderInstances - .uri_optional_CWLVersion_False_True_None_None - .loadField(__doc.get("cwlVersion"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - cwlVersion = null; // won't be used but prevents compiler from complaining. - final String __message = "the `cwlVersion` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - cwlVersion = null; - } - String expression; - try { - expression = - LoaderInstances - .ExpressionLoader - .loadField(__doc.get("expression"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - expression = null; // won't be used but prevents compiler from complaining. - final String __message = "the `expression` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (java.util.Optional) id; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.inputs = (java.util.List) inputs; - this.outputs = (java.util.List) outputs; - this.requirements = (java.util.Optional>) requirements; - this.hints = (java.util.Optional>) hints; - this.cwlVersion = (java.util.Optional) cwlVersion; - this.class_ = (ExpressionTool_class) class_; - this.expression = (String) expression; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id", "label", "doc", "inputs", "outputs", "requirements", "hints", "cwlVersion", "class", "expression"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameter.java deleted file mode 100644 index 614d46ab..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameter.java +++ /dev/null @@ -1,129 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ExpressionToolOutputParameter
This interface is implemented by {@link ExpressionToolOutputParameterImpl}
- */ -public interface ExpressionToolOutputParameter extends OutputParameter, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - Object getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameterImpl.java deleted file mode 100644 index 5bca916e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionToolOutputParameterImpl.java +++ /dev/null @@ -1,350 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#ExpressionToolOutputParameter
- */ -public class ExpressionToolOutputParameterImpl extends SaveableImpl implements ExpressionToolOutputParameter { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - public Object getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of ExpressionToolOutputParameterImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ExpressionToolOutputParameterImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ExpressionToolOutputParameterImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.doc = (Object) doc; - this.id = (java.util.Optional) id; - this.format = (Object) format; - this.type = (Object) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("label", "secondaryFiles", "streamable", "doc", "id", "format", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionTool_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionTool_class.java deleted file mode 100644 index ecafc318..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ExpressionTool_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum ExpressionTool_class { - EXPRESSIONTOOL("ExpressionTool"); - - private static String[] symbols = new String[] {"ExpressionTool"}; - private String docVal; - - private ExpressionTool_class(final String docVal) { - this.docVal = docVal; - } - - public static ExpressionTool_class fromDocumentVal(final String docVal) { - for(final ExpressionTool_class val : ExpressionTool_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", ExpressionTool_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/FieldBase.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/FieldBase.java deleted file mode 100644 index ee318343..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/FieldBase.java +++ /dev/null @@ -1,96 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#FieldBase
- */ -public interface FieldBase extends Labeled, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/File.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/File.java deleted file mode 100644 index 2bf6414a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/File.java +++ /dev/null @@ -1,278 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#File
This interface is implemented by {@link FileImpl}
- Represents a file (or group of files when `secondaryFiles` is provided) that - will be accessible by tools using standard POSIX file system call API such as - open(2) and read(2). - - Files are represented as objects with `class` of `File`. File objects have - a number of properties that provide metadata about the file. - - The `location` property of a File is a URI that uniquely identifies the - file. Implementations must support the file:// URI scheme and may support - other schemes such as http://. The value of `location` may also be a - relative reference, in which case it must be resolved relative to the URI - of the document it appears in. Alternately to `location`, implementations - must also accept the `path` property on File, which must be a filesystem - path available on the same host as the CWL runner (for inputs) or the - runtime environment of a command line tool execution (for command line tool - outputs). - - If no `location` or `path` is specified, a file object must specify - `contents` with the UTF-8 text content of the file. This is a "file - literal". File literals do not correspond to external resources, but are - created on disk with `contents` with when needed for a executing a tool. - Where appropriate, expressions can return file literals to define new files - on a runtime. The maximum size of `contents` is 64 kilobytes. - - The `basename` property defines the filename on disk where the file is - staged. This may differ from the resource name. If not provided, - `basename` must be computed from the last path part of `location` and made - available to expressions. - - The `secondaryFiles` property is a list of File or Directory objects that - must be staged in the same directory as the primary file. It is an error - for file names to be duplicated in `secondaryFiles`. - - The `size` property is the size in bytes of the File. It must be computed - from the resource and made available to expressions. The `checksum` field - contains a cryptographic hash of the file content for use it verifying file - contents. Implementations may, at user option, enable or disable - computation of the `checksum` field for performance or other reasons. - However, the ability to compute output checksums is required to pass the - CWL conformance test suite. - - When executing a CommandLineTool, the files and secondary files may be - staged to an arbitrary directory, but must use the value of `basename` for - the filename. The `path` property must be file path in the context of the - tool execution runtime (local to the compute node, or within the executing - container). All computed properties should be available to expressions. - File literals also must be staged and `path` must be set. - - When collecting CommandLineTool outputs, `glob` matching returns file paths - (with the `path` property) and the derived properties. This can all be - modified by `outputEval`. Alternately, if the file `cwl.output.json` is - present in the output, `outputBinding` is ignored. - - File objects in the output must provide either a `location` URI or a `path` - property in the context of the tool execution runtime (local to the compute - node, or within the executing container). - - When evaluating an ExpressionTool, file objects must be referenced via - `location` (the expression tool does not have access to files on disk so - `path` is meaningless) or as file literals. It is legal to return a file - object with an existing `location` but a different `basename`. The - `loadContents` field of ExpressionTool inputs behaves the same as on - CommandLineTool inputs, however it is not meaningful on the outputs. - - An ExpressionTool may forward file references from input to output by using - the same value for `location`. -
- */ -public interface File extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#File/class
- *
- * Must be `File` to indicate this object describes a file. *
- */ - - File_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/location
- *
- * An IRI that identifies the file resource. This may be a relative - * reference, in which case it must be resolved using the base IRI of the - * document. The location may refer to a local or remote resource; the - * implementation must use the IRI to retrieve file content. If an - * implementation is unable to retrieve the file content stored at a - * remote resource (due to unsupported protocol, access denied, or other - * issue) it must signal an error. - * - * If the `location` field is not provided, the `contents` field must be - * provided. The implementation must assign a unique identifier for - * the `location` field. - * - * If the `path` field is provided but the `location` field is not, an - * implementation may assign the value of the `path` field to `location`, - * then follow the rules above. - * *
- */ - - java.util.Optional getLocation(); - /** - * Getter for property https://w3id.org/cwl/cwl#path
- *
- * The local host path where the File is available when a CommandLineTool is - * executed. This field must be set by the implementation. The final - * path component must match the value of `basename`. This field - * must not be used in any other context. The command line tool being - * executed must be able to to access the file at `path` using the POSIX - * `open(2)` syscall. - * - * As a special case, if the `path` field is provided but the `location` - * field is not, an implementation may assign the value of the `path` - * field to `location`, and remove the `path` field. - * - * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * `<space>`, `<tab>`, and `<newline>`) or characters - * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) - * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) - * then implementations may terminate the process with a - * `permanentFailure`. - * *
- */ - - java.util.Optional getPath(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/basename
- *
- * The base name of the file, that is, the name of the file without any - * leading directory path. The base name must not contain a slash `/`. - * - * If not provided, the implementation must set this field based on the - * `location` field by taking the final path component after parsing - * `location` as an IRI. If `basename` is provided, it is not required to - * match the value from `location`. - * - * When this file is made available to a CommandLineTool, it must be named - * with `basename`, i.e. the final component of the `path` field must match - * `basename`. - * *
- */ - - java.util.Optional getBasename(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/dirname
- *
- * The name of the directory containing file, that is, the path leading up - * to the final slash in the path such that `dirname + '/' + basename == - * path`. - * - * The implementation must set this field based on the value of `path` - * prior to evaluating parameter references or expressions in a - * CommandLineTool document. This field must not be used in any other - * context. - * *
- */ - - java.util.Optional getDirname(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/nameroot
- *
- * The basename root such that `nameroot + nameext == basename`, and - * `nameext` is empty or begins with a period and contains at most one - * period. For the purposess of path splitting leading periods on the - * basename are ignored; a basename of `.cshrc` will have a nameroot of - * `.cshrc`. - * - * The implementation must set this field automatically based on the value - * of `basename` prior to evaluating parameter references or expressions. - * *
- */ - - java.util.Optional getNameroot(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/nameext
- *
- * The basename extension such that `nameroot + nameext == basename`, and - * `nameext` is empty or begins with a period and contains at most one - * period. Leading periods on the basename are ignored; a basename of - * `.cshrc` will have an empty `nameext`. - * - * The implementation must set this field automatically based on the value - * of `basename` prior to evaluating parameter references or expressions. - * *
- */ - - java.util.Optional getNameext(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/checksum
- *
- * Optional hash code for validating file integrity. Currently must be in the form - * "sha1$ + hexadecimal string" using the SHA-1 algorithm. - * *
- */ - - java.util.Optional getChecksum(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/size
- *
- * Optional file size *
- */ - - Object getSize(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * A list of additional files or directories that are associated with the - * primary file and must be transferred alongside the primary file. - * Examples include indexes of the primary file, or external references - * which must be included when loading primary document. A file object - * listed in `secondaryFiles` may itself include `secondaryFiles` for - * which the same rules apply. - * *
- */ - - java.util.Optional> getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * The format of the file: this must be an IRI of a concept node that - * represents the file format, preferrably defined within an ontology. - * If no ontology is available, file formats may be tested by exact match. - * - * Reasoning about format compatability must be done by checking that an - * input file format is the same, `owl:equivalentClass` or - * `rdfs:subClassOf` the format required by the input parameter. - * `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if - * `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer - * `<C> owl:subclassOf <A>`. - * - * File format ontologies may be provided in the "$schemas" metadata at the - * root of the document. If no ontologies are specified in `$schemas`, the - * runtime may perform exact file format matches. - * *
- */ - - java.util.Optional getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/contents
- *
- * File contents literal. Maximum of 64 KiB. - * - * If neither `location` nor `path` is provided, `contents` must be - * non-null. The implementation must assign a unique identifier for the - * `location` field. When the file is staged as input to CommandLineTool, - * the value of `contents` must be written to a file. - * - * If `loadContents` of `inputBinding` or `outputBinding` is true and - * `location` is valid, the implementation must read up to the first 64 - * KiB of text from the file and place it in the "contents" field. - * *
- */ - - java.util.Optional getContents(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/FileImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/FileImpl.java deleted file mode 100644 index 9f53483f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/FileImpl.java +++ /dev/null @@ -1,600 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#File
- Represents a file (or group of files when `secondaryFiles` is provided) that - will be accessible by tools using standard POSIX file system call API such as - open(2) and read(2). - - Files are represented as objects with `class` of `File`. File objects have - a number of properties that provide metadata about the file. - - The `location` property of a File is a URI that uniquely identifies the - file. Implementations must support the file:// URI scheme and may support - other schemes such as http://. The value of `location` may also be a - relative reference, in which case it must be resolved relative to the URI - of the document it appears in. Alternately to `location`, implementations - must also accept the `path` property on File, which must be a filesystem - path available on the same host as the CWL runner (for inputs) or the - runtime environment of a command line tool execution (for command line tool - outputs). - - If no `location` or `path` is specified, a file object must specify - `contents` with the UTF-8 text content of the file. This is a "file - literal". File literals do not correspond to external resources, but are - created on disk with `contents` with when needed for a executing a tool. - Where appropriate, expressions can return file literals to define new files - on a runtime. The maximum size of `contents` is 64 kilobytes. - - The `basename` property defines the filename on disk where the file is - staged. This may differ from the resource name. If not provided, - `basename` must be computed from the last path part of `location` and made - available to expressions. - - The `secondaryFiles` property is a list of File or Directory objects that - must be staged in the same directory as the primary file. It is an error - for file names to be duplicated in `secondaryFiles`. - - The `size` property is the size in bytes of the File. It must be computed - from the resource and made available to expressions. The `checksum` field - contains a cryptographic hash of the file content for use it verifying file - contents. Implementations may, at user option, enable or disable - computation of the `checksum` field for performance or other reasons. - However, the ability to compute output checksums is required to pass the - CWL conformance test suite. - - When executing a CommandLineTool, the files and secondary files may be - staged to an arbitrary directory, but must use the value of `basename` for - the filename. The `path` property must be file path in the context of the - tool execution runtime (local to the compute node, or within the executing - container). All computed properties should be available to expressions. - File literals also must be staged and `path` must be set. - - When collecting CommandLineTool outputs, `glob` matching returns file paths - (with the `path` property) and the derived properties. This can all be - modified by `outputEval`. Alternately, if the file `cwl.output.json` is - present in the output, `outputBinding` is ignored. - - File objects in the output must provide either a `location` URI or a `path` - property in the context of the tool execution runtime (local to the compute - node, or within the executing container). - - When evaluating an ExpressionTool, file objects must be referenced via - `location` (the expression tool does not have access to files on disk so - `path` is meaningless) or as file literals. It is legal to return a file - object with an existing `location` but a different `basename`. The - `loadContents` field of ExpressionTool inputs behaves the same as on - CommandLineTool inputs, however it is not meaningful on the outputs. - - An ExpressionTool may forward file references from input to output by using - the same value for `location`. -
- */ -public class FileImpl extends SaveableImpl implements File { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private File_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/class
- *
- * Must be `File` to indicate this object describes a file. *
- */ - - public File_class getClass_() { - return this.class_; - } - - private java.util.Optional location; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/location
- *
- * An IRI that identifies the file resource. This may be a relative - * reference, in which case it must be resolved using the base IRI of the - * document. The location may refer to a local or remote resource; the - * implementation must use the IRI to retrieve file content. If an - * implementation is unable to retrieve the file content stored at a - * remote resource (due to unsupported protocol, access denied, or other - * issue) it must signal an error. - * - * If the `location` field is not provided, the `contents` field must be - * provided. The implementation must assign a unique identifier for - * the `location` field. - * - * If the `path` field is provided but the `location` field is not, an - * implementation may assign the value of the `path` field to `location`, - * then follow the rules above. - * *
- */ - - public java.util.Optional getLocation() { - return this.location; - } - - private java.util.Optional path; - - /** - * Getter for property https://w3id.org/cwl/cwl#path
- *
- * The local host path where the File is available when a CommandLineTool is - * executed. This field must be set by the implementation. The final - * path component must match the value of `basename`. This field - * must not be used in any other context. The command line tool being - * executed must be able to to access the file at `path` using the POSIX - * `open(2)` syscall. - * - * As a special case, if the `path` field is provided but the `location` - * field is not, an implementation may assign the value of the `path` - * field to `location`, and remove the `path` field. - * - * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * `<space>`, `<tab>`, and `<newline>`) or characters - * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) - * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) - * then implementations may terminate the process with a - * `permanentFailure`. - * *
- */ - - public java.util.Optional getPath() { - return this.path; - } - - private java.util.Optional basename; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/basename
- *
- * The base name of the file, that is, the name of the file without any - * leading directory path. The base name must not contain a slash `/`. - * - * If not provided, the implementation must set this field based on the - * `location` field by taking the final path component after parsing - * `location` as an IRI. If `basename` is provided, it is not required to - * match the value from `location`. - * - * When this file is made available to a CommandLineTool, it must be named - * with `basename`, i.e. the final component of the `path` field must match - * `basename`. - * *
- */ - - public java.util.Optional getBasename() { - return this.basename; - } - - private java.util.Optional dirname; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/dirname
- *
- * The name of the directory containing file, that is, the path leading up - * to the final slash in the path such that `dirname + '/' + basename == - * path`. - * - * The implementation must set this field based on the value of `path` - * prior to evaluating parameter references or expressions in a - * CommandLineTool document. This field must not be used in any other - * context. - * *
- */ - - public java.util.Optional getDirname() { - return this.dirname; - } - - private java.util.Optional nameroot; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/nameroot
- *
- * The basename root such that `nameroot + nameext == basename`, and - * `nameext` is empty or begins with a period and contains at most one - * period. For the purposess of path splitting leading periods on the - * basename are ignored; a basename of `.cshrc` will have a nameroot of - * `.cshrc`. - * - * The implementation must set this field automatically based on the value - * of `basename` prior to evaluating parameter references or expressions. - * *
- */ - - public java.util.Optional getNameroot() { - return this.nameroot; - } - - private java.util.Optional nameext; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/nameext
- *
- * The basename extension such that `nameroot + nameext == basename`, and - * `nameext` is empty or begins with a period and contains at most one - * period. Leading periods on the basename are ignored; a basename of - * `.cshrc` will have an empty `nameext`. - * - * The implementation must set this field automatically based on the value - * of `basename` prior to evaluating parameter references or expressions. - * *
- */ - - public java.util.Optional getNameext() { - return this.nameext; - } - - private java.util.Optional checksum; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/checksum
- *
- * Optional hash code for validating file integrity. Currently must be in the form - * "sha1$ + hexadecimal string" using the SHA-1 algorithm. - * *
- */ - - public java.util.Optional getChecksum() { - return this.checksum; - } - - private Object size; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/size
- *
- * Optional file size *
- */ - - public Object getSize() { - return this.size; - } - - private java.util.Optional> secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * A list of additional files or directories that are associated with the - * primary file and must be transferred alongside the primary file. - * Examples include indexes of the primary file, or external references - * which must be included when loading primary document. A file object - * listed in `secondaryFiles` may itself include `secondaryFiles` for - * which the same rules apply. - * *
- */ - - public java.util.Optional> getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * The format of the file: this must be an IRI of a concept node that - * represents the file format, preferrably defined within an ontology. - * If no ontology is available, file formats may be tested by exact match. - * - * Reasoning about format compatability must be done by checking that an - * input file format is the same, `owl:equivalentClass` or - * `rdfs:subClassOf` the format required by the input parameter. - * `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if - * `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer - * `<C> owl:subclassOf <A>`. - * - * File format ontologies may be provided in the "$schemas" metadata at the - * root of the document. If no ontologies are specified in `$schemas`, the - * runtime may perform exact file format matches. - * *
- */ - - public java.util.Optional getFormat() { - return this.format; - } - - private java.util.Optional contents; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/contents
- *
- * File contents literal. Maximum of 64 KiB. - * - * If neither `location` nor `path` is provided, `contents` must be - * non-null. The implementation must assign a unique identifier for the - * `location` field. When the file is staged as input to CommandLineTool, - * the value of `contents` must be written to a file. - * - * If `loadContents` of `inputBinding` or `outputBinding` is true and - * `location` is valid, the implementation must read up to the first 64 - * KiB of text from the file and place it in the "contents" field. - * *
- */ - - public java.util.Optional getContents() { - return this.contents; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of FileImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public FileImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("FileImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - File_class class_; - try { - class_ = - LoaderInstances - .uri_File_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional location; - - if (__doc.containsKey("location")) { - try { - location = - LoaderInstances - .uri_optional_StringInstance_False_False_None_None - .loadField(__doc.get("location"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - location = null; // won't be used but prevents compiler from complaining. - final String __message = "the `location` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - location = null; - } - java.util.Optional path; - - if (__doc.containsKey("path")) { - try { - path = - LoaderInstances - .uri_optional_StringInstance_False_False_None_None - .loadField(__doc.get("path"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - path = null; // won't be used but prevents compiler from complaining. - final String __message = "the `path` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - path = null; - } - java.util.Optional basename; - - if (__doc.containsKey("basename")) { - try { - basename = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("basename"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - basename = null; // won't be used but prevents compiler from complaining. - final String __message = "the `basename` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - basename = null; - } - java.util.Optional dirname; - - if (__doc.containsKey("dirname")) { - try { - dirname = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dirname"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dirname = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dirname` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dirname = null; - } - java.util.Optional nameroot; - - if (__doc.containsKey("nameroot")) { - try { - nameroot = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("nameroot"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - nameroot = null; // won't be used but prevents compiler from complaining. - final String __message = "the `nameroot` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - nameroot = null; - } - java.util.Optional nameext; - - if (__doc.containsKey("nameext")) { - try { - nameext = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("nameext"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - nameext = null; // won't be used but prevents compiler from complaining. - final String __message = "the `nameext` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - nameext = null; - } - java.util.Optional checksum; - - if (__doc.containsKey("checksum")) { - try { - checksum = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("checksum"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - checksum = null; // won't be used but prevents compiler from complaining. - final String __message = "the `checksum` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - checksum = null; - } - Object size; - - if (__doc.containsKey("size")) { - try { - size = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance - .loadField(__doc.get("size"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - size = null; // won't be used but prevents compiler from complaining. - final String __message = "the `size` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - size = null; - } - java.util.Optional> secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_optional_array_of_union_of_File_or_Directory - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_optional_StringInstance_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional contents; - - if (__doc.containsKey("contents")) { - try { - contents = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("contents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - contents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `contents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - contents = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (File_class) class_; - this.location = (java.util.Optional) location; - this.path = (java.util.Optional) path; - this.basename = (java.util.Optional) basename; - this.dirname = (java.util.Optional) dirname; - this.nameroot = (java.util.Optional) nameroot; - this.nameext = (java.util.Optional) nameext; - this.checksum = (java.util.Optional) checksum; - this.size = (Object) size; - this.secondaryFiles = (java.util.Optional>) secondaryFiles; - this.format = (java.util.Optional) format; - this.contents = (java.util.Optional) contents; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "location", "path", "basename", "dirname", "nameroot", "nameext", "checksum", "size", "secondaryFiles", "format", "contents"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/File_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/File_class.java deleted file mode 100644 index c362b611..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/File_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum File_class { - FILE("File"); - - private static String[] symbols = new String[] {"File"}; - private String docVal; - - private File_class(final String docVal) { - this.docVal = docVal; - } - - public static File_class fromDocumentVal(final String docVal) { - for(final File_class val : File_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", File_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/IOSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/IOSchema.java deleted file mode 100644 index 2ede6fdf..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/IOSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#IOSchema
- */ -public interface IOSchema extends Labeled, Documented, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Identified.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Identified.java deleted file mode 100644 index cbab3751..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Identified.java +++ /dev/null @@ -1,28 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Identified
- */ -public interface Identified extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirement.java deleted file mode 100644 index 993b1cdd..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirement.java +++ /dev/null @@ -1,55 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InitialWorkDirRequirement
This interface is implemented by {@link InitialWorkDirRequirementImpl}
- Define a list of files and subdirectories that must be created by the workflow platform in the designated output directory prior to executing the command line tool.
- */ -public interface InitialWorkDirRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#InitialWorkDirRequirement/class
- *
- * InitialWorkDirRequirement *
- */ - - InitialWorkDirRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#listing
- *
- * The list of files or subdirectories that must be placed in the - * designated output directory prior to executing the command line tool. - * - * May be an expression. If so, the expression return value must validate as - * `{type: array, items: ["null", File, File[], Directory, Directory[], Dirent]}`. - * - * Files or Directories which are listed in the input parameters and - * appear in the `InitialWorkDirRequirement` listing must have their - * `path` set to their staged location in the designated output directory. - * If the same File or Directory appears more than once in the - * `InitialWorkDirRequirement` listing, the implementation must choose - * exactly one value for `path`; how this value is chosen is undefined. - * *
- */ - - Object getListing(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirementImpl.java deleted file mode 100644 index 585a6681..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirementImpl.java +++ /dev/null @@ -1,141 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InitialWorkDirRequirement
- Define a list of files and subdirectories that must be created by the workflow platform in the designated output directory prior to executing the command line tool.
- */ -public class InitialWorkDirRequirementImpl extends SaveableImpl implements InitialWorkDirRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private InitialWorkDirRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#InitialWorkDirRequirement/class
- *
- * InitialWorkDirRequirement *
- */ - - public InitialWorkDirRequirement_class getClass_() { - return this.class_; - } - - private Object listing; - - /** - * Getter for property https://w3id.org/cwl/cwl#listing
- *
- * The list of files or subdirectories that must be placed in the - * designated output directory prior to executing the command line tool. - * - * May be an expression. If so, the expression return value must validate as - * `{type: array, items: ["null", File, File[], Directory, Directory[], Dirent]}`. - * - * Files or Directories which are listed in the input parameters and - * appear in the `InitialWorkDirRequirement` listing must have their - * `path` set to their staged location in the designated output directory. - * If the same File or Directory appears more than once in the - * `InitialWorkDirRequirement` listing, the implementation must choose - * exactly one value for `path`; how this value is chosen is undefined. - * *
- */ - - public Object getListing() { - return this.listing; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of InitialWorkDirRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InitialWorkDirRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InitialWorkDirRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - InitialWorkDirRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_InitialWorkDirRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object listing; - try { - listing = - LoaderInstances - .union_of_array_of_union_of_NullInstance_or_File_or_array_of_union_of_File_or_Directory_or_Directory_or_Dirent_or_ExpressionLoader_or_ExpressionLoader - .loadField(__doc.get("listing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - listing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `listing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (InitialWorkDirRequirement_class) class_; - this.listing = (Object) listing; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "listing"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirement_class.java deleted file mode 100644 index d19b43d3..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InitialWorkDirRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum InitialWorkDirRequirement_class { - INITIALWORKDIRREQUIREMENT("InitialWorkDirRequirement"); - - private static String[] symbols = new String[] {"InitialWorkDirRequirement"}; - private String docVal; - - private InitialWorkDirRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static InitialWorkDirRequirement_class fromDocumentVal(final String docVal) { - for(final InitialWorkDirRequirement_class val : InitialWorkDirRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", InitialWorkDirRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirement.java deleted file mode 100644 index ce361717..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirement.java +++ /dev/null @@ -1,49 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InlineJavascriptRequirement
This interface is implemented by {@link InlineJavascriptRequirementImpl}
- Indicates that the workflow platform must support inline Javascript expressions. - If this requirement is not present, the workflow platform must not perform expression - interpolatation. -
- */ -public interface InlineJavascriptRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/class
- *
- * Always 'InlineJavascriptRequirement' *
- */ - - InlineJavascriptRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/expressionLib
- *
- * Additional code fragments that will also be inserted - * before executing the expression code. Allows for function definitions that may - * be called from CWL expressions. - * *
- */ - - java.util.Optional> getExpressionLib(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirementImpl.java deleted file mode 100644 index d3fecbc1..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirementImpl.java +++ /dev/null @@ -1,141 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InlineJavascriptRequirement
- Indicates that the workflow platform must support inline Javascript expressions. - If this requirement is not present, the workflow platform must not perform expression - interpolatation. -
- */ -public class InlineJavascriptRequirementImpl extends SaveableImpl implements InlineJavascriptRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private InlineJavascriptRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/class
- *
- * Always 'InlineJavascriptRequirement' *
- */ - - public InlineJavascriptRequirement_class getClass_() { - return this.class_; - } - - private java.util.Optional> expressionLib; - - /** - * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/expressionLib
- *
- * Additional code fragments that will also be inserted - * before executing the expression code. Allows for function definitions that may - * be called from CWL expressions. - * *
- */ - - public java.util.Optional> getExpressionLib() { - return this.expressionLib; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of InlineJavascriptRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InlineJavascriptRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InlineJavascriptRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - InlineJavascriptRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_InlineJavascriptRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> expressionLib; - - if (__doc.containsKey("expressionLib")) { - try { - expressionLib = - LoaderInstances - .optional_array_of_StringInstance - .loadField(__doc.get("expressionLib"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - expressionLib = null; // won't be used but prevents compiler from complaining. - final String __message = "the `expressionLib` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - expressionLib = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (InlineJavascriptRequirement_class) class_; - this.expressionLib = (java.util.Optional>) expressionLib; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "expressionLib"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirement_class.java deleted file mode 100644 index 888e7a3c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InlineJavascriptRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum InlineJavascriptRequirement_class { - INLINEJAVASCRIPTREQUIREMENT("InlineJavascriptRequirement"); - - private static String[] symbols = new String[] {"InlineJavascriptRequirement"}; - private String docVal; - - private InlineJavascriptRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static InlineJavascriptRequirement_class fromDocumentVal(final String docVal) { - for(final InlineJavascriptRequirement_class val : InlineJavascriptRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", InlineJavascriptRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirement.java deleted file mode 100644 index 9e47cb5c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirement.java +++ /dev/null @@ -1,72 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InplaceUpdateRequirement
This interface is implemented by {@link InplaceUpdateRequirementImpl}
- - If `inplaceUpdate` is true, then an implementation supporting this - feature may permit tools to directly update files with `writable: - true` in InitialWorkDirRequirement. That is, as an optimization, - files may be destructively modified in place as opposed to copied - and updated. - - An implementation must ensure that only one workflow step may - access a writable file at a time. It is an error if a file which - is writable by one workflow step file is accessed (for reading or - writing) by any other workflow step running independently. - However, a file which has been updated in a previous completed - step may be used as input to multiple steps, provided it is - read-only in every step. - - Workflow steps which modify a file must produce the modified file - as output. Downstream steps which futher process the file must - use the output of previous steps, and not refer to a common input - (this is necessary for both ordering and correctness). - - Workflow authors should provide this in the `hints` section. The - intent of this feature is that workflows produce the same results - whether or not InplaceUpdateRequirement is supported by the - implementation, and this feature is primarily available as an - optimization for particular environments. - - Users and implementers should be aware that workflows that - destructively modify inputs may not be repeatable or reproducible. - In particular, enabling this feature implies that WorkReuse should - not be enabled. -
- */ -public interface InplaceUpdateRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/class
- *
- * Always 'InplaceUpdateRequirement' *
- */ - - InplaceUpdateRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/inplaceUpdate
- - */ - - Boolean getInplaceUpdate(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirementImpl.java deleted file mode 100644 index 539cfafd..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirementImpl.java +++ /dev/null @@ -1,158 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InplaceUpdateRequirement
- - If `inplaceUpdate` is true, then an implementation supporting this - feature may permit tools to directly update files with `writable: - true` in InitialWorkDirRequirement. That is, as an optimization, - files may be destructively modified in place as opposed to copied - and updated. - - An implementation must ensure that only one workflow step may - access a writable file at a time. It is an error if a file which - is writable by one workflow step file is accessed (for reading or - writing) by any other workflow step running independently. - However, a file which has been updated in a previous completed - step may be used as input to multiple steps, provided it is - read-only in every step. - - Workflow steps which modify a file must produce the modified file - as output. Downstream steps which futher process the file must - use the output of previous steps, and not refer to a common input - (this is necessary for both ordering and correctness). - - Workflow authors should provide this in the `hints` section. The - intent of this feature is that workflows produce the same results - whether or not InplaceUpdateRequirement is supported by the - implementation, and this feature is primarily available as an - optimization for particular environments. - - Users and implementers should be aware that workflows that - destructively modify inputs may not be repeatable or reproducible. - In particular, enabling this feature implies that WorkReuse should - not be enabled. -
- */ -public class InplaceUpdateRequirementImpl extends SaveableImpl implements InplaceUpdateRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private InplaceUpdateRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/class
- *
- * Always 'InplaceUpdateRequirement' *
- */ - - public InplaceUpdateRequirement_class getClass_() { - return this.class_; - } - - private Boolean inplaceUpdate; - - /** - * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/inplaceUpdate
- - */ - - public Boolean getInplaceUpdate() { - return this.inplaceUpdate; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of InplaceUpdateRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InplaceUpdateRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InplaceUpdateRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - InplaceUpdateRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_InplaceUpdateRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Boolean inplaceUpdate; - try { - inplaceUpdate = - LoaderInstances - .BooleanInstance - .loadField(__doc.get("inplaceUpdate"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inplaceUpdate = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inplaceUpdate` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (InplaceUpdateRequirement_class) class_; - this.inplaceUpdate = (Boolean) inplaceUpdate; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "inplaceUpdate"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirement_class.java deleted file mode 100644 index e86b7130..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InplaceUpdateRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum InplaceUpdateRequirement_class { - INPLACEUPDATEREQUIREMENT("InplaceUpdateRequirement"); - - private static String[] symbols = new String[] {"InplaceUpdateRequirement"}; - private String docVal; - - private InplaceUpdateRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static InplaceUpdateRequirement_class fromDocumentVal(final String docVal) { - for(final InplaceUpdateRequirement_class val : InplaceUpdateRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", InplaceUpdateRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputArraySchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputArraySchema.java deleted file mode 100644 index 0d9bb5ac..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputArraySchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputArraySchema
This interface is implemented by {@link InputArraySchemaImpl}
- */ -public interface InputArraySchema extends CWLArraySchema, InputSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - Object getItems(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - Array_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputArraySchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputArraySchemaImpl.java deleted file mode 100644 index 86bed2fe..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputArraySchemaImpl.java +++ /dev/null @@ -1,232 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InputArraySchema
- */ -public class InputArraySchemaImpl extends SaveableImpl implements InputArraySchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private Object items; - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - public Object getItems() { - return this.items; - } - - private Array_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - public Array_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of InputArraySchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InputArraySchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InputArraySchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - Object items; - try { - items = - LoaderInstances - .uri_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("items"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - items = null; // won't be used but prevents compiler from complaining. - final String __message = "the `items` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Array_name type; - try { - type = - LoaderInstances - .typedsl_Array_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.items = (Object) items; - this.type = (Array_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("items", "type", "label", "doc", "name"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBinding.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBinding.java deleted file mode 100644 index 7fceba16..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBinding.java +++ /dev/null @@ -1,43 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputBinding
This interface is implemented by {@link InputBindingImpl}
- */ -public interface InputBinding extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#InputBinding/loadContents
- *
- * Use of `loadContents` in `InputBinding` is deprecated. - * Preserved for v1.0 backwards compatability. Will be removed in - * CWL v2.0. Use `InputParameter.loadContents` instead. - * - * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - java.util.Optional getLoadContents(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBindingImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBindingImpl.java deleted file mode 100644 index 79bd3638..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputBindingImpl.java +++ /dev/null @@ -1,118 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InputBinding
- */ -public class InputBindingImpl extends SaveableImpl implements InputBinding { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#InputBinding/loadContents
- *
- * Use of `loadContents` in `InputBinding` is deprecated. - * Preserved for v1.0 backwards compatability. Will be removed in - * CWL v2.0. Use `InputParameter.loadContents` instead. - * - * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of InputBindingImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InputBindingImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InputBindingImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.loadContents = (java.util.Optional) loadContents; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("loadContents"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputEnumSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputEnumSchema.java deleted file mode 100644 index fa9dce07..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputEnumSchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputEnumSchema
This interface is implemented by {@link InputEnumSchemaImpl}
- */ -public interface InputEnumSchema extends EnumSchema, InputSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - java.util.List getSymbols(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - Enum_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputEnumSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputEnumSchemaImpl.java deleted file mode 100644 index bd91a6a0..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputEnumSchemaImpl.java +++ /dev/null @@ -1,232 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InputEnumSchema
- */ -public class InputEnumSchemaImpl extends SaveableImpl implements InputEnumSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.List symbols; - - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - public java.util.List getSymbols() { - return this.symbols; - } - - private Enum_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - public Enum_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of InputEnumSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InputEnumSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InputEnumSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.List symbols; - try { - symbols = - LoaderInstances - .uri_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("symbols"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - symbols = null; // won't be used but prevents compiler from complaining. - final String __message = "the `symbols` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Enum_name type; - try { - type = - LoaderInstances - .typedsl_Enum_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.name = (java.util.Optional) name; - this.symbols = (java.util.List) symbols; - this.type = (Enum_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("name", "symbols", "type", "label", "doc"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputFormat.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputFormat.java deleted file mode 100644 index 379d3f95..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputFormat.java +++ /dev/null @@ -1,41 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputFormat
- */ -public interface InputFormat extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferrably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputParameter.java deleted file mode 100644 index e3d87d6b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputParameter.java +++ /dev/null @@ -1,155 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputParameter
- */ -public interface InputParameter extends Parameter, InputFormat, LoadContents, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferrably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value to use for this parameter if the parameter is missing - * from the input object, or if the value of the parameter in the input - * object is `null`. Default values are applied before evaluating expressions - * (e.g. dependent `valueFrom` fields). - * *
- */ - - java.util.Optional getDefault(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordField.java deleted file mode 100644 index 4da330ac..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordField.java +++ /dev/null @@ -1,160 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputRecordField
This interface is implemented by {@link InputRecordFieldImpl}
- */ -public interface InputRecordField extends CWLRecordField, FieldBase, InputFormat, LoadContents, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - String getName(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferrably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordFieldImpl.java deleted file mode 100644 index 9dfadc92..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordFieldImpl.java +++ /dev/null @@ -1,422 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordField
- */ -public class InputRecordFieldImpl extends SaveableImpl implements InputRecordField { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String name; - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - public String getName() { - return this.name; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferrably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of InputRecordFieldImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InputRecordFieldImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InputRecordFieldImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - if (name == null) { - if (__docRoot != null) { - name = __docRoot; - } else { - throw new ValidationException("Missing name"); - } - } - __baseUri = (String) name; - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.doc = (Object) doc; - this.name = (String) name; - this.type = (Object) type; - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.format = (Object) format; - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("doc", "name", "type", "label", "secondaryFiles", "streamable", "format", "loadContents", "loadListing"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordSchema.java deleted file mode 100644 index ece42164..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordSchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputRecordSchema
This interface is implemented by {@link InputRecordSchemaImpl}
- */ -public interface InputRecordSchema extends CWLRecordSchema, InputSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - java.util.Optional> getFields(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - Record_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordSchemaImpl.java deleted file mode 100644 index 4405ca00..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputRecordSchemaImpl.java +++ /dev/null @@ -1,238 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordSchema
- */ -public class InputRecordSchemaImpl extends SaveableImpl implements InputRecordSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.Optional> fields; - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - public java.util.Optional> getFields() { - return this.fields; - } - - private Record_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - public Record_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of InputRecordSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InputRecordSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InputRecordSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.Optional> fields; - - if (__doc.containsKey("fields")) { - try { - fields = - LoaderInstances - .idmap_fields_optional_array_of_InputRecordField - .loadField(__doc.get("fields"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - fields = null; // won't be used but prevents compiler from complaining. - final String __message = "the `fields` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - fields = null; - } - Record_name type; - try { - type = - LoaderInstances - .typedsl_Record_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.fields = (java.util.Optional>) fields; - this.type = (Record_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("fields", "type", "label", "doc", "name"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputSchema.java deleted file mode 100644 index 6b8ac168..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/InputSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputSchema
- */ -public interface InputSchema extends IOSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Labeled.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Labeled.java deleted file mode 100644 index 389a5254..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Labeled.java +++ /dev/null @@ -1,35 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Labeled
- */ -public interface Labeled extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LinkMergeMethod.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/LinkMergeMethod.java deleted file mode 100644 index eb0d1546..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LinkMergeMethod.java +++ /dev/null @@ -1,38 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum LinkMergeMethod { - MERGE_NESTED("merge_nested"), - MERGE_FLATTENED("merge_flattened"); - - private static String[] symbols = new String[] {"merge_nested", "merge_flattened"}; - private String docVal; - - private LinkMergeMethod(final String docVal) { - this.docVal = docVal; - } - - public static LinkMergeMethod fromDocumentVal(final String docVal) { - for(final LinkMergeMethod val : LinkMergeMethod.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", LinkMergeMethod.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadContents.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadContents.java deleted file mode 100644 index c3433e39..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadContents.java +++ /dev/null @@ -1,56 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#LoadContents
- */ -public interface LoadContents extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingEnum.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingEnum.java deleted file mode 100644 index c3a489d5..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingEnum.java +++ /dev/null @@ -1,39 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum LoadListingEnum { - NO_LISTING("no_listing"), - SHALLOW_LISTING("shallow_listing"), - DEEP_LISTING("deep_listing"); - - private static String[] symbols = new String[] {"no_listing", "shallow_listing", "deep_listing"}; - private String docVal; - - private LoadListingEnum(final String docVal) { - this.docVal = docVal; - } - - public static LoadListingEnum fromDocumentVal(final String docVal) { - for(final LoadListingEnum val : LoadListingEnum.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", LoadListingEnum.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirement.java deleted file mode 100644 index 056180cb..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirement.java +++ /dev/null @@ -1,44 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#LoadListingRequirement
This interface is implemented by {@link LoadListingRequirementImpl}
- Specify the desired behavior for loading the `listing` field of - a Directory object for use by expressions. -
- */ -public interface LoadListingRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/class
- *
- * Always 'LoadListingRequirement' *
- */ - - LoadListingRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/loadListing
- - */ - - java.util.Optional getLoadListing(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirementImpl.java deleted file mode 100644 index 8923f1eb..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirementImpl.java +++ /dev/null @@ -1,136 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#LoadListingRequirement
- Specify the desired behavior for loading the `listing` field of - a Directory object for use by expressions. -
- */ -public class LoadListingRequirementImpl extends SaveableImpl implements LoadListingRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private LoadListingRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/class
- *
- * Always 'LoadListingRequirement' *
- */ - - public LoadListingRequirement_class getClass_() { - return this.class_; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/loadListing
- - */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of LoadListingRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public LoadListingRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("LoadListingRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - LoadListingRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_LoadListingRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (LoadListingRequirement_class) class_; - this.loadListing = (java.util.Optional) loadListing; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "loadListing"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirement_class.java deleted file mode 100644 index 1abcc983..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/LoadListingRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum LoadListingRequirement_class { - LOADLISTINGREQUIREMENT("LoadListingRequirement"); - - private static String[] symbols = new String[] {"LoadListingRequirement"}; - private String docVal; - - private LoadListingRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static LoadListingRequirement_class fromDocumentVal(final String docVal) { - for(final LoadListingRequirement_class val : LoadListingRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", LoadListingRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MapSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/MapSchema.java deleted file mode 100644 index 4e0f7419..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MapSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#MapSchema
This interface is implemented by {@link MapSchemaImpl}
- */ -public interface MapSchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `map` *
- */ - - Map_name getType(); - /** - * Getter for property https://w3id.org/cwl/salad#values
- *
- * Defines the type of the map elements. *
- */ - - Object getValues(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MapSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/MapSchemaImpl.java deleted file mode 100644 index 7cb05c82..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MapSchemaImpl.java +++ /dev/null @@ -1,128 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/salad#MapSchema
- */ -public class MapSchemaImpl extends SaveableImpl implements MapSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Map_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `map` *
- */ - - public Map_name getType() { - return this.type; - } - - private Object values; - - /** - * Getter for property https://w3id.org/cwl/salad#values
- *
- * Defines the type of the map elements. *
- */ - - public Object getValues() { - return this.values; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of MapSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public MapSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("MapSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Map_name type; - try { - type = - LoaderInstances - .typedsl_Map_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object values; - try { - values = - LoaderInstances - .uri_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("values"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - values = null; // won't be used but prevents compiler from complaining. - final String __message = "the `values` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.type = (Map_name) type; - this.values = (Object) values; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("type", "values"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Map_name.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Map_name.java deleted file mode 100644 index a42d8669..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Map_name.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum Map_name { - MAP("map"); - - private static String[] symbols = new String[] {"map"}; - private String docVal; - - private Map_name(final String docVal) { - this.docVal = docVal; - } - - public static Map_name fromDocumentVal(final String docVal) { - for(final Map_name val : Map_name.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Map_name.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirement.java deleted file mode 100644 index 905d851c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirement.java +++ /dev/null @@ -1,38 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement
This interface is implemented by {@link MultipleInputFeatureRequirementImpl}
- Indicates that the workflow platform must support multiple inbound data links - listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput). -
- */ -public interface MultipleInputFeatureRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement/class
- *
- * Always 'MultipleInputFeatureRequirement' *
- */ - - MultipleInputFeatureRequirement_class getClass_(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirementImpl.java deleted file mode 100644 index 8343a743..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirementImpl.java +++ /dev/null @@ -1,107 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement
- Indicates that the workflow platform must support multiple inbound data links - listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput). -
- */ -public class MultipleInputFeatureRequirementImpl extends SaveableImpl implements MultipleInputFeatureRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private MultipleInputFeatureRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement/class
- *
- * Always 'MultipleInputFeatureRequirement' *
- */ - - public MultipleInputFeatureRequirement_class getClass_() { - return this.class_; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of MultipleInputFeatureRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public MultipleInputFeatureRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("MultipleInputFeatureRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - MultipleInputFeatureRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_MultipleInputFeatureRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (MultipleInputFeatureRequirement_class) class_; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirement_class.java deleted file mode 100644 index fce3949b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/MultipleInputFeatureRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum MultipleInputFeatureRequirement_class { - MULTIPLEINPUTFEATUREREQUIREMENT("MultipleInputFeatureRequirement"); - - private static String[] symbols = new String[] {"MultipleInputFeatureRequirement"}; - private String docVal; - - private MultipleInputFeatureRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static MultipleInputFeatureRequirement_class fromDocumentVal(final String docVal) { - for(final MultipleInputFeatureRequirement_class val : MultipleInputFeatureRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", MultipleInputFeatureRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccess.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccess.java deleted file mode 100644 index 137c4304..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccess.java +++ /dev/null @@ -1,57 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#NetworkAccess
This interface is implemented by {@link NetworkAccessImpl}
- Indicate whether a process requires outgoing IPv4/IPv6 network - access. Choice of IPv4 or IPv6 is implementation and site - specific, correct tools must support both. - - If `networkAccess` is false or not specified, tools must not - assume network access, except for localhost (the loopback device). - - If `networkAccess` is true, the tool must be able to make outgoing - connections to network resources. Resources may be on a private - subnet or the public Internet. However, implementations and sites - may apply their own security policies to restrict what is - accessible by the tool. - - Enabling network access does not imply a publically routable IP - address or the ability to accept inbound connections. -
- */ -public interface NetworkAccess extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/class
- *
- * Always 'NetworkAccess' *
- */ - - NetworkAccess_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/networkAccess
- - */ - - Object getNetworkAccess(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccessImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccessImpl.java deleted file mode 100644 index 7468c94f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccessImpl.java +++ /dev/null @@ -1,143 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#NetworkAccess
- Indicate whether a process requires outgoing IPv4/IPv6 network - access. Choice of IPv4 or IPv6 is implementation and site - specific, correct tools must support both. - - If `networkAccess` is false or not specified, tools must not - assume network access, except for localhost (the loopback device). - - If `networkAccess` is true, the tool must be able to make outgoing - connections to network resources. Resources may be on a private - subnet or the public Internet. However, implementations and sites - may apply their own security policies to restrict what is - accessible by the tool. - - Enabling network access does not imply a publically routable IP - address or the ability to accept inbound connections. -
- */ -public class NetworkAccessImpl extends SaveableImpl implements NetworkAccess { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private NetworkAccess_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/class
- *
- * Always 'NetworkAccess' *
- */ - - public NetworkAccess_class getClass_() { - return this.class_; - } - - private Object networkAccess; - - /** - * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/networkAccess
- - */ - - public Object getNetworkAccess() { - return this.networkAccess; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of NetworkAccessImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public NetworkAccessImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("NetworkAccessImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - NetworkAccess_class class_; - try { - class_ = - LoaderInstances - .uri_NetworkAccess_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object networkAccess; - try { - networkAccess = - LoaderInstances - .union_of_BooleanInstance_or_ExpressionLoader - .loadField(__doc.get("networkAccess"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - networkAccess = null; // won't be used but prevents compiler from complaining. - final String __message = "the `networkAccess` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (NetworkAccess_class) class_; - this.networkAccess = (Object) networkAccess; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "networkAccess"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccess_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccess_class.java deleted file mode 100644 index d0f48225..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/NetworkAccess_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum NetworkAccess_class { - NETWORKACCESS("NetworkAccess"); - - private static String[] symbols = new String[] {"NetworkAccess"}; - private String docVal; - - private NetworkAccess_class(final String docVal) { - this.docVal = docVal; - } - - public static NetworkAccess_class fromDocumentVal(final String docVal) { - for(final NetworkAccess_class val : NetworkAccess_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", NetworkAccess_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputArraySchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputArraySchema.java deleted file mode 100644 index d26d6ae9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputArraySchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputArraySchema
This interface is implemented by {@link OutputArraySchemaImpl}
- */ -public interface OutputArraySchema extends CWLArraySchema, OutputSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - Object getItems(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - Array_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputArraySchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputArraySchemaImpl.java deleted file mode 100644 index 9261e32c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputArraySchemaImpl.java +++ /dev/null @@ -1,232 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputArraySchema
- */ -public class OutputArraySchemaImpl extends SaveableImpl implements OutputArraySchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private Object items; - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - public Object getItems() { - return this.items; - } - - private Array_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - public Array_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of OutputArraySchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public OutputArraySchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("OutputArraySchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - Object items; - try { - items = - LoaderInstances - .uri_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("items"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - items = null; // won't be used but prevents compiler from complaining. - final String __message = "the `items` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Array_name type; - try { - type = - LoaderInstances - .typedsl_Array_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.items = (Object) items; - this.type = (Array_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("items", "type", "label", "doc", "name"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputEnumSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputEnumSchema.java deleted file mode 100644 index aee84a8a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputEnumSchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputEnumSchema
This interface is implemented by {@link OutputEnumSchemaImpl}
- */ -public interface OutputEnumSchema extends EnumSchema, OutputSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - java.util.List getSymbols(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - Enum_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputEnumSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputEnumSchemaImpl.java deleted file mode 100644 index 0b691ae0..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputEnumSchemaImpl.java +++ /dev/null @@ -1,232 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputEnumSchema
- */ -public class OutputEnumSchemaImpl extends SaveableImpl implements OutputEnumSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.List symbols; - - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - public java.util.List getSymbols() { - return this.symbols; - } - - private Enum_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - public Enum_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of OutputEnumSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public OutputEnumSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("OutputEnumSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.List symbols; - try { - symbols = - LoaderInstances - .uri_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("symbols"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - symbols = null; // won't be used but prevents compiler from complaining. - final String __message = "the `symbols` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Enum_name type; - try { - type = - LoaderInstances - .typedsl_Enum_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.name = (java.util.Optional) name; - this.symbols = (java.util.List) symbols; - this.type = (Enum_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("name", "symbols", "type", "label", "doc"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputFormat.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputFormat.java deleted file mode 100644 index 6fc88bf8..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputFormat.java +++ /dev/null @@ -1,39 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputFormat
- */ -public interface OutputFormat extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputParameter.java deleted file mode 100644 index eddf67a2..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputParameter.java +++ /dev/null @@ -1,114 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputParameter
- */ -public interface OutputParameter extends Parameter, OutputFormat, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordField.java deleted file mode 100644 index 7fa04694..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordField.java +++ /dev/null @@ -1,130 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputRecordField
This interface is implemented by {@link OutputRecordFieldImpl}
- */ -public interface OutputRecordField extends CWLRecordField, FieldBase, OutputFormat, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - String getName(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordFieldImpl.java deleted file mode 100644 index f43a03e9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordFieldImpl.java +++ /dev/null @@ -1,346 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordField
- */ -public class OutputRecordFieldImpl extends SaveableImpl implements OutputRecordField { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String name; - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - public String getName() { - return this.name; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - public Object getFormat() { - return this.format; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of OutputRecordFieldImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public OutputRecordFieldImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("OutputRecordFieldImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - if (name == null) { - if (__docRoot != null) { - name = __docRoot; - } else { - throw new ValidationException("Missing name"); - } - } - __baseUri = (String) name; - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.doc = (Object) doc; - this.name = (String) name; - this.type = (Object) type; - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.format = (Object) format; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("doc", "name", "type", "label", "secondaryFiles", "streamable", "format"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordSchema.java deleted file mode 100644 index 60914e74..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordSchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputRecordSchema
This interface is implemented by {@link OutputRecordSchemaImpl}
- */ -public interface OutputRecordSchema extends CWLRecordSchema, OutputSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - java.util.Optional> getFields(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - Record_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordSchemaImpl.java deleted file mode 100644 index 8cdacaae..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputRecordSchemaImpl.java +++ /dev/null @@ -1,238 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordSchema
- */ -public class OutputRecordSchemaImpl extends SaveableImpl implements OutputRecordSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.Optional> fields; - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - public java.util.Optional> getFields() { - return this.fields; - } - - private Record_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - public Record_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of OutputRecordSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public OutputRecordSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("OutputRecordSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.Optional> fields; - - if (__doc.containsKey("fields")) { - try { - fields = - LoaderInstances - .idmap_fields_optional_array_of_OutputRecordField - .loadField(__doc.get("fields"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - fields = null; // won't be used but prevents compiler from complaining. - final String __message = "the `fields` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - fields = null; - } - Record_name type; - try { - type = - LoaderInstances - .typedsl_Record_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.fields = (java.util.Optional>) fields; - this.type = (Record_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("fields", "type", "label", "doc", "name"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputSchema.java deleted file mode 100644 index 4980babb..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/OutputSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputSchema
- */ -public interface OutputSchema extends IOSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Parameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Parameter.java deleted file mode 100644 index 0c69293a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Parameter.java +++ /dev/null @@ -1,105 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Parameter
- Define an input or output parameter to a process. -
- */ -public interface Parameter extends FieldBase, Documented, Identified, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/PrimitiveType.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/PrimitiveType.java deleted file mode 100644 index a6774d37..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/PrimitiveType.java +++ /dev/null @@ -1,43 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum PrimitiveType { - NULL("null"), - BOOLEAN("boolean"), - INT("int"), - LONG("long"), - FLOAT("float"), - DOUBLE("double"), - STRING("string"); - - private static String[] symbols = new String[] {"null", "boolean", "int", "long", "float", "double", "string"}; - private String docVal; - - private PrimitiveType(final String docVal) { - this.docVal = docVal; - } - - public static PrimitiveType fromDocumentVal(final String docVal) { - for(final PrimitiveType val : PrimitiveType.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", PrimitiveType.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Process.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Process.java deleted file mode 100644 index 270750c2..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Process.java +++ /dev/null @@ -1,107 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Process
- - The base executable type in CWL is the `Process` object defined by the - document. Note that the `Process` object is abstract and cannot be - directly executed. -
- */ -public interface Process extends Identified, Labeled, Documented, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - java.util.List getInputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - java.util.List getOutputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - java.util.Optional> getRequirements(); - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - java.util.Optional> getHints(); - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - java.util.Optional getCwlVersion(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ProcessRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ProcessRequirement.java deleted file mode 100644 index 2c658b3a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ProcessRequirement.java +++ /dev/null @@ -1,35 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ProcessRequirement
- A process requirement declares a prerequisite that may or must be fulfilled - before executing a process. See [`Process.hints`](#process) and - [`Process.requirements`](#process). - - Process requirements are the primary mechanism for specifying extensions to - the CWL core specification. -
- */ -public interface ProcessRequirement extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/RecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/RecordField.java deleted file mode 100644 index 30249bfd..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/RecordField.java +++ /dev/null @@ -1,54 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#RecordField
This interface is implemented by {@link RecordFieldImpl}
- A field of a record.
- */ -public interface RecordField extends Documented, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - String getName(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type. If it is an array, it indicates - * that the field type is a union type of its elements. - * Its elements may be duplicated. - * *
- */ - - Object getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/RecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/RecordFieldImpl.java deleted file mode 100644 index aa1d316a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/RecordFieldImpl.java +++ /dev/null @@ -1,178 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/salad#RecordField
- A field of a record.
- */ -public class RecordFieldImpl extends SaveableImpl implements RecordField { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String name; - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - public String getName() { - return this.name; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type. If it is an array, it indicates - * that the field type is a union type of its elements. - * Its elements may be duplicated. - * *
- */ - - public Object getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of RecordFieldImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public RecordFieldImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("RecordFieldImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - if (name == null) { - if (__docRoot != null) { - name = __docRoot; - } else { - throw new ValidationException("Missing name"); - } - } - __baseUri = (String) name; - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.doc = (Object) doc; - this.name = (String) name; - this.type = (Object) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("doc", "name", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/RecordSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/RecordSchema.java deleted file mode 100644 index d8a5966f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/RecordSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#RecordSchema
This interface is implemented by {@link RecordSchemaImpl}
- */ -public interface RecordSchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - java.util.Optional> getFields(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - Record_name getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/RecordSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/RecordSchemaImpl.java deleted file mode 100644 index 38f3f08f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/RecordSchemaImpl.java +++ /dev/null @@ -1,134 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/salad#RecordSchema
- */ -public class RecordSchemaImpl extends SaveableImpl implements RecordSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional> fields; - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - public java.util.Optional> getFields() { - return this.fields; - } - - private Record_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - public Record_name getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of RecordSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public RecordSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("RecordSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional> fields; - - if (__doc.containsKey("fields")) { - try { - fields = - LoaderInstances - .idmap_fields_optional_array_of_RecordField - .loadField(__doc.get("fields"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - fields = null; // won't be used but prevents compiler from complaining. - final String __message = "the `fields` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - fields = null; - } - Record_name type; - try { - type = - LoaderInstances - .typedsl_Record_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.fields = (java.util.Optional>) fields; - this.type = (Record_name) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("fields", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Record_name.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Record_name.java deleted file mode 100644 index 9dad005d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Record_name.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum Record_name { - RECORD("record"); - - private static String[] symbols = new String[] {"record"}; - private String docVal; - - private Record_name(final String docVal) { - this.docVal = docVal; - } - - public static Record_name fromDocumentVal(final String docVal) { - for(final Record_name val : Record_name.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Record_name.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirement.java deleted file mode 100644 index 5d7e16a9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirement.java +++ /dev/null @@ -1,112 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ResourceRequirement
This interface is implemented by {@link ResourceRequirementImpl}
- Specify basic hardware resource requirements. - - "min" is the minimum amount of a resource that must be reserved to schedule - a job. If "min" cannot be satisfied, the job should not be run. - - "max" is the maximum amount of a resource that the job shall be permitted - to use. If a node has sufficient resources, multiple jobs may be scheduled - on a single node provided each job's "max" resource requirements are - met. If a job attempts to exceed its "max" resource allocation, an - implementation may deny additional resources, which may result in job - failure. - - If "min" is specified but "max" is not, then "max" == "min" - If "max" is specified by "min" is not, then "min" == "max". - - It is an error if max < min. - - It is an error if the value of any of these fields is negative. - - If neither "min" nor "max" is specified for a resource, use the default values below. -
- */ -public interface ResourceRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/class
- *
- * Always 'ResourceRequirement' *
- */ - - ResourceRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/coresMin
- *
- * Minimum reserved number of CPU cores (default is 1) *
- */ - - Object getCoresMin(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/coresMax
- *
- * Maximum reserved number of CPU cores *
- */ - - Object getCoresMax(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/ramMin
- *
- * Minimum reserved RAM in mebibytes (2**20) (default is 256) *
- */ - - Object getRamMin(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/ramMax
- *
- * Maximum reserved RAM in mebibytes (2**20) *
- */ - - Object getRamMax(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/tmpdirMin
- *
- * Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024) *
- */ - - Object getTmpdirMin(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/tmpdirMax
- *
- * Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) *
- */ - - Object getTmpdirMax(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/outdirMin
- *
- * Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024) *
- */ - - Object getOutdirMin(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/outdirMax
- *
- * Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) *
- */ - - Object getOutdirMax(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirementImpl.java deleted file mode 100644 index 0deae6e7..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirementImpl.java +++ /dev/null @@ -1,365 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#ResourceRequirement
- Specify basic hardware resource requirements. - - "min" is the minimum amount of a resource that must be reserved to schedule - a job. If "min" cannot be satisfied, the job should not be run. - - "max" is the maximum amount of a resource that the job shall be permitted - to use. If a node has sufficient resources, multiple jobs may be scheduled - on a single node provided each job's "max" resource requirements are - met. If a job attempts to exceed its "max" resource allocation, an - implementation may deny additional resources, which may result in job - failure. - - If "min" is specified but "max" is not, then "max" == "min" - If "max" is specified by "min" is not, then "min" == "max". - - It is an error if max < min. - - It is an error if the value of any of these fields is negative. - - If neither "min" nor "max" is specified for a resource, use the default values below. -
- */ -public class ResourceRequirementImpl extends SaveableImpl implements ResourceRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private ResourceRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/class
- *
- * Always 'ResourceRequirement' *
- */ - - public ResourceRequirement_class getClass_() { - return this.class_; - } - - private Object coresMin; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/coresMin
- *
- * Minimum reserved number of CPU cores (default is 1) *
- */ - - public Object getCoresMin() { - return this.coresMin; - } - - private Object coresMax; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/coresMax
- *
- * Maximum reserved number of CPU cores *
- */ - - public Object getCoresMax() { - return this.coresMax; - } - - private Object ramMin; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/ramMin
- *
- * Minimum reserved RAM in mebibytes (2**20) (default is 256) *
- */ - - public Object getRamMin() { - return this.ramMin; - } - - private Object ramMax; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/ramMax
- *
- * Maximum reserved RAM in mebibytes (2**20) *
- */ - - public Object getRamMax() { - return this.ramMax; - } - - private Object tmpdirMin; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/tmpdirMin
- *
- * Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024) *
- */ - - public Object getTmpdirMin() { - return this.tmpdirMin; - } - - private Object tmpdirMax; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/tmpdirMax
- *
- * Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) *
- */ - - public Object getTmpdirMax() { - return this.tmpdirMax; - } - - private Object outdirMin; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/outdirMin
- *
- * Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024) *
- */ - - public Object getOutdirMin() { - return this.outdirMin; - } - - private Object outdirMax; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/outdirMax
- *
- * Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) *
- */ - - public Object getOutdirMax() { - return this.outdirMax; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of ResourceRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ResourceRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ResourceRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - ResourceRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_ResourceRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object coresMin; - - if (__doc.containsKey("coresMin")) { - try { - coresMin = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_ExpressionLoader - .loadField(__doc.get("coresMin"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - coresMin = null; // won't be used but prevents compiler from complaining. - final String __message = "the `coresMin` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - coresMin = null; - } - Object coresMax; - - if (__doc.containsKey("coresMax")) { - try { - coresMax = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_ExpressionLoader - .loadField(__doc.get("coresMax"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - coresMax = null; // won't be used but prevents compiler from complaining. - final String __message = "the `coresMax` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - coresMax = null; - } - Object ramMin; - - if (__doc.containsKey("ramMin")) { - try { - ramMin = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_ExpressionLoader - .loadField(__doc.get("ramMin"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - ramMin = null; // won't be used but prevents compiler from complaining. - final String __message = "the `ramMin` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - ramMin = null; - } - Object ramMax; - - if (__doc.containsKey("ramMax")) { - try { - ramMax = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_ExpressionLoader - .loadField(__doc.get("ramMax"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - ramMax = null; // won't be used but prevents compiler from complaining. - final String __message = "the `ramMax` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - ramMax = null; - } - Object tmpdirMin; - - if (__doc.containsKey("tmpdirMin")) { - try { - tmpdirMin = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_ExpressionLoader - .loadField(__doc.get("tmpdirMin"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - tmpdirMin = null; // won't be used but prevents compiler from complaining. - final String __message = "the `tmpdirMin` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - tmpdirMin = null; - } - Object tmpdirMax; - - if (__doc.containsKey("tmpdirMax")) { - try { - tmpdirMax = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_ExpressionLoader - .loadField(__doc.get("tmpdirMax"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - tmpdirMax = null; // won't be used but prevents compiler from complaining. - final String __message = "the `tmpdirMax` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - tmpdirMax = null; - } - Object outdirMin; - - if (__doc.containsKey("outdirMin")) { - try { - outdirMin = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_ExpressionLoader - .loadField(__doc.get("outdirMin"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outdirMin = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outdirMin` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - outdirMin = null; - } - Object outdirMax; - - if (__doc.containsKey("outdirMax")) { - try { - outdirMax = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_ExpressionLoader - .loadField(__doc.get("outdirMax"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outdirMax = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outdirMax` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - outdirMax = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (ResourceRequirement_class) class_; - this.coresMin = (Object) coresMin; - this.coresMax = (Object) coresMax; - this.ramMin = (Object) ramMin; - this.ramMax = (Object) ramMax; - this.tmpdirMin = (Object) tmpdirMin; - this.tmpdirMax = (Object) tmpdirMax; - this.outdirMin = (Object) outdirMin; - this.outdirMax = (Object) outdirMax; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirement_class.java deleted file mode 100644 index 846cbedc..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ResourceRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum ResourceRequirement_class { - RESOURCEREQUIREMENT("ResourceRequirement"); - - private static String[] symbols = new String[] {"ResourceRequirement"}; - private String docVal; - - private ResourceRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static ResourceRequirement_class fromDocumentVal(final String docVal) { - for(final ResourceRequirement_class val : ResourceRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", ResourceRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirement.java deleted file mode 100644 index 350e1c52..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirement.java +++ /dev/null @@ -1,38 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ScatterFeatureRequirement
This interface is implemented by {@link ScatterFeatureRequirementImpl}
- Indicates that the workflow platform must support the `scatter` and - `scatterMethod` fields of [WorkflowStep](#WorkflowStep). -
- */ -public interface ScatterFeatureRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#ScatterFeatureRequirement/class
- *
- * Always 'ScatterFeatureRequirement' *
- */ - - ScatterFeatureRequirement_class getClass_(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirementImpl.java deleted file mode 100644 index b722b7d7..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirementImpl.java +++ /dev/null @@ -1,107 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#ScatterFeatureRequirement
- Indicates that the workflow platform must support the `scatter` and - `scatterMethod` fields of [WorkflowStep](#WorkflowStep). -
- */ -public class ScatterFeatureRequirementImpl extends SaveableImpl implements ScatterFeatureRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private ScatterFeatureRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#ScatterFeatureRequirement/class
- *
- * Always 'ScatterFeatureRequirement' *
- */ - - public ScatterFeatureRequirement_class getClass_() { - return this.class_; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of ScatterFeatureRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ScatterFeatureRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ScatterFeatureRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - ScatterFeatureRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_ScatterFeatureRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (ScatterFeatureRequirement_class) class_; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirement_class.java deleted file mode 100644 index 63f85244..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterFeatureRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum ScatterFeatureRequirement_class { - SCATTERFEATUREREQUIREMENT("ScatterFeatureRequirement"); - - private static String[] symbols = new String[] {"ScatterFeatureRequirement"}; - private String docVal; - - private ScatterFeatureRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static ScatterFeatureRequirement_class fromDocumentVal(final String docVal) { - for(final ScatterFeatureRequirement_class val : ScatterFeatureRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", ScatterFeatureRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterMethod.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterMethod.java deleted file mode 100644 index dd530a96..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ScatterMethod.java +++ /dev/null @@ -1,39 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum ScatterMethod { - DOTPRODUCT("dotproduct"), - NESTED_CROSSPRODUCT("nested_crossproduct"), - FLAT_CROSSPRODUCT("flat_crossproduct"); - - private static String[] symbols = new String[] {"dotproduct", "nested_crossproduct", "flat_crossproduct"}; - private String docVal; - - private ScatterMethod(final String docVal) { - this.docVal = docVal; - } - - public static ScatterMethod fromDocumentVal(final String docVal) { - for(final ScatterMethod val : ScatterMethod.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", ScatterMethod.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirement.java deleted file mode 100644 index 824b7f33..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirement.java +++ /dev/null @@ -1,50 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#SchemaDefRequirement
This interface is implemented by {@link SchemaDefRequirementImpl}
- This field consists of an array of type definitions which must be used when - interpreting the `inputs` and `outputs` fields. When a `type` field - contain a IRI, the implementation must check if the type is defined in - `schemaDefs` and use that definition. If the type is not found in - `schemaDefs`, it is an error. The entries in `schemaDefs` must be - processed in the order listed such that later schema definitions may refer - to earlier schema definitions. -
- */ -public interface SchemaDefRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/class
- *
- * Always 'SchemaDefRequirement' *
- */ - - SchemaDefRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/types
- *
- * The list of type definitions. *
- */ - - java.util.List getTypes(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirementImpl.java deleted file mode 100644 index c8a65893..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirementImpl.java +++ /dev/null @@ -1,136 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#SchemaDefRequirement
- This field consists of an array of type definitions which must be used when - interpreting the `inputs` and `outputs` fields. When a `type` field - contain a IRI, the implementation must check if the type is defined in - `schemaDefs` and use that definition. If the type is not found in - `schemaDefs`, it is an error. The entries in `schemaDefs` must be - processed in the order listed such that later schema definitions may refer - to earlier schema definitions. -
- */ -public class SchemaDefRequirementImpl extends SaveableImpl implements SchemaDefRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private SchemaDefRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/class
- *
- * Always 'SchemaDefRequirement' *
- */ - - public SchemaDefRequirement_class getClass_() { - return this.class_; - } - - private java.util.List types; - - /** - * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/types
- *
- * The list of type definitions. *
- */ - - public java.util.List getTypes() { - return this.types; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of SchemaDefRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public SchemaDefRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("SchemaDefRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - SchemaDefRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_SchemaDefRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List types; - try { - types = - LoaderInstances - .array_of_union_of_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema - .loadField(__doc.get("types"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - types = null; // won't be used but prevents compiler from complaining. - final String __message = "the `types` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (SchemaDefRequirement_class) class_; - this.types = (java.util.List) types; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "types"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirement_class.java deleted file mode 100644 index 22a8cb87..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SchemaDefRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum SchemaDefRequirement_class { - SCHEMADEFREQUIREMENT("SchemaDefRequirement"); - - private static String[] symbols = new String[] {"SchemaDefRequirement"}; - private String docVal; - - private SchemaDefRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static SchemaDefRequirement_class fromDocumentVal(final String docVal) { - for(final SchemaDefRequirement_class val : SchemaDefRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", SchemaDefRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchema.java deleted file mode 100644 index 245f5eec..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchema.java +++ /dev/null @@ -1,77 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#SecondaryFileSchema
This interface is implemented by {@link SecondaryFileSchemaImpl}
- */ -public interface SecondaryFileSchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#SecondaryFileSchema/pattern
- *
- * Provides a pattern or expression specifying files or directories that - * should be included alongside the primary file. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getPattern(); - /** - * Getter for property https://w3id.org/cwl/cwl#SecondaryFileSchema/required
- *
- * An implementation must not fail workflow execution if `required` is - * set to `false` and the expected secondary file does not exist. - * Default value for `required` field is `true` for secondary files on - * input and `false` for secondary files on output. - * *
- */ - - Object getRequired(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchemaImpl.java deleted file mode 100644 index b22c20fd..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SecondaryFileSchemaImpl.java +++ /dev/null @@ -1,169 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#SecondaryFileSchema
- */ -public class SecondaryFileSchemaImpl extends SaveableImpl implements SecondaryFileSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Object pattern; - - /** - * Getter for property https://w3id.org/cwl/cwl#SecondaryFileSchema/pattern
- *
- * Provides a pattern or expression specifying files or directories that - * should be included alongside the primary file. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getPattern() { - return this.pattern; - } - - private Object required; - - /** - * Getter for property https://w3id.org/cwl/cwl#SecondaryFileSchema/required
- *
- * An implementation must not fail workflow execution if `required` is - * set to `false` and the expected secondary file does not exist. - * Default value for `required` field is `true` for secondary files on - * input and `false` for secondary files on output. - * *
- */ - - public Object getRequired() { - return this.required; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of SecondaryFileSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public SecondaryFileSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("SecondaryFileSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Object pattern; - try { - pattern = - LoaderInstances - .union_of_StringInstance_or_ExpressionLoader - .loadField(__doc.get("pattern"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - pattern = null; // won't be used but prevents compiler from complaining. - final String __message = "the `pattern` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object required; - - if (__doc.containsKey("required")) { - try { - required = - LoaderInstances - .union_of_NullInstance_or_BooleanInstance_or_ExpressionLoader - .loadField(__doc.get("required"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - required = null; // won't be used but prevents compiler from complaining. - final String __message = "the `required` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - required = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.pattern = (Object) pattern; - this.required = (Object) required; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("pattern", "required"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirement.java deleted file mode 100644 index 11f719a0..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirement.java +++ /dev/null @@ -1,43 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ShellCommandRequirement
This interface is implemented by {@link ShellCommandRequirementImpl}
- Modify the behavior of CommandLineTool to generate a single string - containing a shell command line. Each item in the argument list must be - joined into a string separated by single spaces and quoted to prevent - intepretation by the shell, unless `CommandLineBinding` for that argument - contains `shellQuote: false`. If `shellQuote: false` is specified, the - argument is joined into the command string without quoting, which allows - the use of shell metacharacters such as `|` for pipes. -
- */ -public interface ShellCommandRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#ShellCommandRequirement/class
- *
- * Always 'ShellCommandRequirement' *
- */ - - ShellCommandRequirement_class getClass_(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirementImpl.java deleted file mode 100644 index 53ebc7d3..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirementImpl.java +++ /dev/null @@ -1,112 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#ShellCommandRequirement
- Modify the behavior of CommandLineTool to generate a single string - containing a shell command line. Each item in the argument list must be - joined into a string separated by single spaces and quoted to prevent - intepretation by the shell, unless `CommandLineBinding` for that argument - contains `shellQuote: false`. If `shellQuote: false` is specified, the - argument is joined into the command string without quoting, which allows - the use of shell metacharacters such as `|` for pipes. -
- */ -public class ShellCommandRequirementImpl extends SaveableImpl implements ShellCommandRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private ShellCommandRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#ShellCommandRequirement/class
- *
- * Always 'ShellCommandRequirement' *
- */ - - public ShellCommandRequirement_class getClass_() { - return this.class_; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of ShellCommandRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ShellCommandRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ShellCommandRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - ShellCommandRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_ShellCommandRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (ShellCommandRequirement_class) class_; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirement_class.java deleted file mode 100644 index 29dea997..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ShellCommandRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum ShellCommandRequirement_class { - SHELLCOMMANDREQUIREMENT("ShellCommandRequirement"); - - private static String[] symbols = new String[] {"ShellCommandRequirement"}; - private String docVal; - - private ShellCommandRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static ShellCommandRequirement_class fromDocumentVal(final String docVal) { - for(final ShellCommandRequirement_class val : ShellCommandRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", ShellCommandRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Sink.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Sink.java deleted file mode 100644 index af30b22a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Sink.java +++ /dev/null @@ -1,46 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Sink
- */ -public interface Sink extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#source
- *
- * Specifies one or more workflow parameters that will provide input to - * the underlying step parameter. - * *
- */ - - Object getSource(); - /** - * Getter for property https://w3id.org/cwl/cwl#Sink/linkMerge
- *
- * The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". - * *
- */ - - java.util.Optional getLinkMerge(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwarePackage.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwarePackage.java deleted file mode 100644 index d30b9d69..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwarePackage.java +++ /dev/null @@ -1,95 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#SoftwarePackage
This interface is implemented by {@link SoftwarePackageImpl}
- */ -public interface SoftwarePackage extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/package
- *
- * The name of the software to be made available. If the name is - * common, inconsistent, or otherwise ambiguous it should be combined with - * one or more identifiers in the `specs` field. - * *
- */ - - String getPackage(); - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/version
- *
- * The (optional) versions of the software that are known to be - * compatible. - * *
- */ - - java.util.Optional> getVersion(); - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/specs
- *
- * One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s - * identifying resources for installing or enabling the software named in - * the `package` field. Implementations may provide resolvers which map - * these software identifer IRIs to some configuration action; or they can - * use only the name from the `package` field on a best effort basis. - * - * For example, the IRI https://packages.debian.org/bowtie could - * be resolved with `apt-get install bowtie`. The IRI - * https://anaconda.org/bioconda/bowtie could be resolved with `conda - * install -c bioconda bowtie`. - * - * IRIs can also be system independent and used to map to a specific - * software installation or selection mechanism. - * Using [RRID](https://www.identifiers.org/rrid/) as an example: - * https://identifiers.org/rrid/RRID:SCR_005476 - * could be fulfilled using the above mentioned Debian or bioconda - * package, a local installation managed by [Environement Modules](http://modules.sourceforge.net/), - * or any other mechanism the platform chooses. IRIs can also be from - * identifer sources that are discipline specific yet still system - * independent. As an example, the equivalent [ELIXIR Tools and Data - * Service Registry](https://bio.tools) IRI to the previous RRID example is - * https://bio.tools/tool/bowtie2/version/2.2.8. - * If supported by a given registry, implementations are encouraged to - * query these system independent sofware identifier IRIs directly for - * links to packaging systems. - * - * A site specific IRI can be listed as well. For example, an academic - * computing cluster using Environement Modules could list the IRI - * `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that - * `module load bowtie-tbb/1.1.2` should be executed to make available - * `bowtie` version 1.1.2 compiled with the TBB library prior to running - * the accompanying Workflow or CommandLineTool. Note that the example IRI - * is specific to a particular institution and computing environment as - * the Environment Modules system does not have a common namespace or - * standardized naming convention. - * - * This last example is the least portable and should only be used if - * mechanisms based off of the `package` field or more generic IRIs are - * unavailable or unsuitable. While harmless to other sites, site specific - * software IRIs should be left out of shared CWL descriptions to avoid - * clutter. - * *
- */ - - java.util.Optional> getSpecs(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwarePackageImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwarePackageImpl.java deleted file mode 100644 index fd5445fa..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwarePackageImpl.java +++ /dev/null @@ -1,210 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#SoftwarePackage
- */ -public class SoftwarePackageImpl extends SaveableImpl implements SoftwarePackage { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String package_; - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/package
- *
- * The name of the software to be made available. If the name is - * common, inconsistent, or otherwise ambiguous it should be combined with - * one or more identifiers in the `specs` field. - * *
- */ - - public String getPackage() { - return this.package_; - } - - private java.util.Optional> version; - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/version
- *
- * The (optional) versions of the software that are known to be - * compatible. - * *
- */ - - public java.util.Optional> getVersion() { - return this.version; - } - - private java.util.Optional> specs; - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/specs
- *
- * One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s - * identifying resources for installing or enabling the software named in - * the `package` field. Implementations may provide resolvers which map - * these software identifer IRIs to some configuration action; or they can - * use only the name from the `package` field on a best effort basis. - * - * For example, the IRI https://packages.debian.org/bowtie could - * be resolved with `apt-get install bowtie`. The IRI - * https://anaconda.org/bioconda/bowtie could be resolved with `conda - * install -c bioconda bowtie`. - * - * IRIs can also be system independent and used to map to a specific - * software installation or selection mechanism. - * Using [RRID](https://www.identifiers.org/rrid/) as an example: - * https://identifiers.org/rrid/RRID:SCR_005476 - * could be fulfilled using the above mentioned Debian or bioconda - * package, a local installation managed by [Environement Modules](http://modules.sourceforge.net/), - * or any other mechanism the platform chooses. IRIs can also be from - * identifer sources that are discipline specific yet still system - * independent. As an example, the equivalent [ELIXIR Tools and Data - * Service Registry](https://bio.tools) IRI to the previous RRID example is - * https://bio.tools/tool/bowtie2/version/2.2.8. - * If supported by a given registry, implementations are encouraged to - * query these system independent sofware identifier IRIs directly for - * links to packaging systems. - * - * A site specific IRI can be listed as well. For example, an academic - * computing cluster using Environement Modules could list the IRI - * `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that - * `module load bowtie-tbb/1.1.2` should be executed to make available - * `bowtie` version 1.1.2 compiled with the TBB library prior to running - * the accompanying Workflow or CommandLineTool. Note that the example IRI - * is specific to a particular institution and computing environment as - * the Environment Modules system does not have a common namespace or - * standardized naming convention. - * - * This last example is the least portable and should only be used if - * mechanisms based off of the `package` field or more generic IRIs are - * unavailable or unsuitable. While harmless to other sites, site specific - * software IRIs should be left out of shared CWL descriptions to avoid - * clutter. - * *
- */ - - public java.util.Optional> getSpecs() { - return this.specs; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of SoftwarePackageImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public SoftwarePackageImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("SoftwarePackageImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String package_; - try { - package_ = - LoaderInstances - .StringInstance - .loadField(__doc.get("package"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - package_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `package` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> version; - - if (__doc.containsKey("version")) { - try { - version = - LoaderInstances - .optional_array_of_StringInstance - .loadField(__doc.get("version"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - version = null; // won't be used but prevents compiler from complaining. - final String __message = "the `version` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - version = null; - } - java.util.Optional> specs; - - if (__doc.containsKey("specs")) { - try { - specs = - LoaderInstances - .uri_optional_array_of_StringInstance_False_False_None_True - .loadField(__doc.get("specs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - specs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `specs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - specs = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.package_ = (String) package_; - this.version = (java.util.Optional>) version; - this.specs = (java.util.Optional>) specs; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("package", "version", "specs"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirement.java deleted file mode 100644 index b2de49f1..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirement.java +++ /dev/null @@ -1,45 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#SoftwareRequirement
This interface is implemented by {@link SoftwareRequirementImpl}
- A list of software packages that should be configured in the environment of - the defined process. -
- */ -public interface SoftwareRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/class
- *
- * Always 'SoftwareRequirement' *
- */ - - SoftwareRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/packages
- *
- * The list of software to be configured. *
- */ - - java.util.List getPackages(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirementImpl.java deleted file mode 100644 index ffb0a220..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirementImpl.java +++ /dev/null @@ -1,131 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#SoftwareRequirement
- A list of software packages that should be configured in the environment of - the defined process. -
- */ -public class SoftwareRequirementImpl extends SaveableImpl implements SoftwareRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private SoftwareRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/class
- *
- * Always 'SoftwareRequirement' *
- */ - - public SoftwareRequirement_class getClass_() { - return this.class_; - } - - private java.util.List packages; - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/packages
- *
- * The list of software to be configured. *
- */ - - public java.util.List getPackages() { - return this.packages; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of SoftwareRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public SoftwareRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("SoftwareRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - SoftwareRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_SoftwareRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List packages; - try { - packages = - LoaderInstances - .idmap_packages_array_of_SoftwarePackage - .loadField(__doc.get("packages"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - packages = null; // won't be used but prevents compiler from complaining. - final String __message = "the `packages` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (SoftwareRequirement_class) class_; - this.packages = (java.util.List) packages; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "packages"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirement_class.java deleted file mode 100644 index ae0fa1e6..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SoftwareRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum SoftwareRequirement_class { - SOFTWAREREQUIREMENT("SoftwareRequirement"); - - private static String[] symbols = new String[] {"SoftwareRequirement"}; - private String docVal; - - private SoftwareRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static SoftwareRequirement_class fromDocumentVal(final String docVal) { - for(final SoftwareRequirement_class val : SoftwareRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", SoftwareRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirement.java deleted file mode 100644 index 073dd11b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirement.java +++ /dev/null @@ -1,38 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#StepInputExpressionRequirement
This interface is implemented by {@link StepInputExpressionRequirementImpl}
- Indicate that the workflow platform must support the `valueFrom` field - of [WorkflowStepInput](#WorkflowStepInput). -
- */ -public interface StepInputExpressionRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#StepInputExpressionRequirement/class
- *
- * Always 'StepInputExpressionRequirement' *
- */ - - StepInputExpressionRequirement_class getClass_(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirementImpl.java deleted file mode 100644 index 55ec06d0..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirementImpl.java +++ /dev/null @@ -1,107 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#StepInputExpressionRequirement
- Indicate that the workflow platform must support the `valueFrom` field - of [WorkflowStepInput](#WorkflowStepInput). -
- */ -public class StepInputExpressionRequirementImpl extends SaveableImpl implements StepInputExpressionRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private StepInputExpressionRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#StepInputExpressionRequirement/class
- *
- * Always 'StepInputExpressionRequirement' *
- */ - - public StepInputExpressionRequirement_class getClass_() { - return this.class_; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of StepInputExpressionRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public StepInputExpressionRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("StepInputExpressionRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - StepInputExpressionRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_StepInputExpressionRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (StepInputExpressionRequirement_class) class_; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirement_class.java deleted file mode 100644 index a6bf0b81..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/StepInputExpressionRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum StepInputExpressionRequirement_class { - STEPINPUTEXPRESSIONREQUIREMENT("StepInputExpressionRequirement"); - - private static String[] symbols = new String[] {"StepInputExpressionRequirement"}; - private String docVal; - - private StepInputExpressionRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static StepInputExpressionRequirement_class fromDocumentVal(final String docVal) { - for(final StepInputExpressionRequirement_class val : StepInputExpressionRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", StepInputExpressionRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirement.java deleted file mode 100644 index 56bd4437..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirement.java +++ /dev/null @@ -1,38 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement
This interface is implemented by {@link SubworkflowFeatureRequirementImpl}
- Indicates that the workflow platform must support nested workflows in - the `run` field of [WorkflowStep](#WorkflowStep). -
- */ -public interface SubworkflowFeatureRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement/class
- *
- * Always 'SubworkflowFeatureRequirement' *
- */ - - SubworkflowFeatureRequirement_class getClass_(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirementImpl.java deleted file mode 100644 index afbddd9d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirementImpl.java +++ /dev/null @@ -1,107 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement
- Indicates that the workflow platform must support nested workflows in - the `run` field of [WorkflowStep](#WorkflowStep). -
- */ -public class SubworkflowFeatureRequirementImpl extends SaveableImpl implements SubworkflowFeatureRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private SubworkflowFeatureRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement/class
- *
- * Always 'SubworkflowFeatureRequirement' *
- */ - - public SubworkflowFeatureRequirement_class getClass_() { - return this.class_; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of SubworkflowFeatureRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public SubworkflowFeatureRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("SubworkflowFeatureRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - SubworkflowFeatureRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_SubworkflowFeatureRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (SubworkflowFeatureRequirement_class) class_; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirement_class.java deleted file mode 100644 index 63d465dd..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/SubworkflowFeatureRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum SubworkflowFeatureRequirement_class { - SUBWORKFLOWFEATUREREQUIREMENT("SubworkflowFeatureRequirement"); - - private static String[] symbols = new String[] {"SubworkflowFeatureRequirement"}; - private String docVal; - - private SubworkflowFeatureRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static SubworkflowFeatureRequirement_class fromDocumentVal(final String docVal) { - for(final SubworkflowFeatureRequirement_class val : SubworkflowFeatureRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", SubworkflowFeatureRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimit.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimit.java deleted file mode 100644 index 51bda027..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimit.java +++ /dev/null @@ -1,52 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ToolTimeLimit
This interface is implemented by {@link ToolTimeLimitImpl}
- Set an upper limit on the execution time of a CommandLineTool. - A CommandLineTool whose execution duration exceeds the time - limit may be preemptively terminated and considered failed. - May also be used by batch systems to make scheduling decisions. - The execution duration excludes external operations, such as - staging of files, pulling a docker image etc, and only counts - wall-time for the execution of the command line itself. -
- */ -public interface ToolTimeLimit extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/class
- *
- * Always 'ToolTimeLimit' *
- */ - - ToolTimeLimit_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/timelimit
- *
- * The time limit, in seconds. A time limit of zero means no - * time limit. Negative time limits are an error. - * *
- */ - - Object getTimelimit(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimitImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimitImpl.java deleted file mode 100644 index 648c52d4..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimitImpl.java +++ /dev/null @@ -1,138 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#ToolTimeLimit
- Set an upper limit on the execution time of a CommandLineTool. - A CommandLineTool whose execution duration exceeds the time - limit may be preemptively terminated and considered failed. - May also be used by batch systems to make scheduling decisions. - The execution duration excludes external operations, such as - staging of files, pulling a docker image etc, and only counts - wall-time for the execution of the command line itself. -
- */ -public class ToolTimeLimitImpl extends SaveableImpl implements ToolTimeLimit { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private ToolTimeLimit_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/class
- *
- * Always 'ToolTimeLimit' *
- */ - - public ToolTimeLimit_class getClass_() { - return this.class_; - } - - private Object timelimit; - - /** - * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/timelimit
- *
- * The time limit, in seconds. A time limit of zero means no - * time limit. Negative time limits are an error. - * *
- */ - - public Object getTimelimit() { - return this.timelimit; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of ToolTimeLimitImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ToolTimeLimitImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ToolTimeLimitImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - ToolTimeLimit_class class_; - try { - class_ = - LoaderInstances - .uri_ToolTimeLimit_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object timelimit; - try { - timelimit = - LoaderInstances - .union_of_IntegerInstance_or_LongInstance_or_ExpressionLoader - .loadField(__doc.get("timelimit"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - timelimit = null; // won't be used but prevents compiler from complaining. - final String __message = "the `timelimit` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (ToolTimeLimit_class) class_; - this.timelimit = (Object) timelimit; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "timelimit"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimit_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimit_class.java deleted file mode 100644 index 078a8f0c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/ToolTimeLimit_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum ToolTimeLimit_class { - TOOLTIMELIMIT("ToolTimeLimit"); - - private static String[] symbols = new String[] {"ToolTimeLimit"}; - private String docVal; - - private ToolTimeLimit_class(final String docVal) { - this.docVal = docVal; - } - - public static ToolTimeLimit_class fromDocumentVal(final String docVal) { - for(final ToolTimeLimit_class val : ToolTimeLimit_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", ToolTimeLimit_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/UnionSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/UnionSchema.java deleted file mode 100644 index 52067ba2..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/UnionSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#UnionSchema
This interface is implemented by {@link UnionSchemaImpl}
- */ -public interface UnionSchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#names
- *
- * Defines the type of the union elements. *
- */ - - Object getNames(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `union` *
- */ - - Union_name getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/UnionSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/UnionSchemaImpl.java deleted file mode 100644 index ed701215..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/UnionSchemaImpl.java +++ /dev/null @@ -1,128 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/salad#UnionSchema
- */ -public class UnionSchemaImpl extends SaveableImpl implements UnionSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Object names; - - /** - * Getter for property https://w3id.org/cwl/salad#names
- *
- * Defines the type of the union elements. *
- */ - - public Object getNames() { - return this.names; - } - - private Union_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `union` *
- */ - - public Union_name getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of UnionSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public UnionSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("UnionSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Object names; - try { - names = - LoaderInstances - .uri_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("names"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - names = null; // won't be used but prevents compiler from complaining. - final String __message = "the `names` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Union_name type; - try { - type = - LoaderInstances - .typedsl_Union_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.names = (Object) names; - this.type = (Union_name) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("names", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Union_name.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Union_name.java deleted file mode 100644 index c7d160c6..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Union_name.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum Union_name { - UNION("union"); - - private static String[] symbols = new String[] {"union"}; - private String docVal; - - private Union_name(final String docVal) { - this.docVal = docVal; - } - - public static Union_name fromDocumentVal(final String docVal) { - for(final Union_name val : Union_name.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Union_name.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuse.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuse.java deleted file mode 100644 index 1f40837f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuse.java +++ /dev/null @@ -1,51 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#WorkReuse
This interface is implemented by {@link WorkReuseImpl}
- For implementations that support reusing output from past work (on - the assumption that same code and same input produce same - results), control whether to enable or disable the reuse behavior - for a particular tool or step (to accomodate situations where that - assumption is incorrect). A reused step is not executed but - instead returns the same output as the original execution. - - If `enableReuse` is not specified, correct tools should assume it - is enabled by default. -
- */ -public interface WorkReuse extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkReuse/class
- *
- * Always 'WorkReuse' *
- */ - - WorkReuse_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#WorkReuse/enableReuse
- - */ - - Object getEnableReuse(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuseImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuseImpl.java deleted file mode 100644 index 0c70d853..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuseImpl.java +++ /dev/null @@ -1,137 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkReuse
- For implementations that support reusing output from past work (on - the assumption that same code and same input produce same - results), control whether to enable or disable the reuse behavior - for a particular tool or step (to accomodate situations where that - assumption is incorrect). A reused step is not executed but - instead returns the same output as the original execution. - - If `enableReuse` is not specified, correct tools should assume it - is enabled by default. -
- */ -public class WorkReuseImpl extends SaveableImpl implements WorkReuse { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private WorkReuse_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkReuse/class
- *
- * Always 'WorkReuse' *
- */ - - public WorkReuse_class getClass_() { - return this.class_; - } - - private Object enableReuse; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkReuse/enableReuse
- - */ - - public Object getEnableReuse() { - return this.enableReuse; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of WorkReuseImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkReuseImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkReuseImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - WorkReuse_class class_; - try { - class_ = - LoaderInstances - .uri_WorkReuse_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object enableReuse; - try { - enableReuse = - LoaderInstances - .union_of_BooleanInstance_or_ExpressionLoader - .loadField(__doc.get("enableReuse"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - enableReuse = null; // won't be used but prevents compiler from complaining. - final String __message = "the `enableReuse` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (WorkReuse_class) class_; - this.enableReuse = (Object) enableReuse; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "enableReuse"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuse_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuse_class.java deleted file mode 100644 index 756e2a46..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkReuse_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum WorkReuse_class { - WORKREUSE("WorkReuse"); - - private static String[] symbols = new String[] {"WorkReuse"}; - private String docVal; - - private WorkReuse_class(final String docVal) { - this.docVal = docVal; - } - - public static WorkReuse_class fromDocumentVal(final String docVal) { - for(final WorkReuse_class val : WorkReuse_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", WorkReuse_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Workflow.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Workflow.java deleted file mode 100644 index 400b8e3b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Workflow.java +++ /dev/null @@ -1,172 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Workflow
This interface is implemented by {@link WorkflowImpl}
- A workflow describes a set of **steps** and the **dependencies** between - those steps. When a step produces output that will be consumed by a - second step, the first step is a dependency of the second step. - - When there is a dependency, the workflow engine must execute the preceding - step and wait for it to successfully produce output before executing the - dependent step. If two steps are defined in the workflow graph that - are not directly or indirectly dependent, these steps are **independent**, - and may execute in any order or execute concurrently. A workflow is - complete when all steps have been executed. - - Dependencies between parameters are expressed using the `source` field on - [workflow step input parameters](#WorkflowStepInput) and [workflow output - parameters](#WorkflowOutputParameter). - - The `source` field expresses the dependency of one parameter on another - such that when a value is associated with the parameter specified by - `source`, that value is propagated to the destination parameter. When all - data links inbound to a given step are fufilled, the step is ready to - execute. - - ## Workflow success and failure - - A completed step must result in one of `success`, `temporaryFailure` or - `permanentFailure` states. An implementation may choose to retry a step - execution which resulted in `temporaryFailure`. An implementation may - choose to either continue running other steps of a workflow, or terminate - immediately upon `permanentFailure`. - - * If any step of a workflow execution results in `permanentFailure`, then - the workflow status is `permanentFailure`. - - * If one or more steps result in `temporaryFailure` and all other steps - complete `success` or are not executed, then the workflow status is - `temporaryFailure`. - - * If all workflow steps are executed and complete with `success`, then the - workflow status is `success`. - - # Extensions - - [ScatterFeatureRequirement](#ScatterFeatureRequirement) and - [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are - available as standard [extensions](#Extensions_and_Metadata) to core - workflow semantics. -
- */ -public interface Workflow extends Process, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Workflow/class
- - */ - - Workflow_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - java.util.List getInputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - java.util.List getOutputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - java.util.Optional> getRequirements(); - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - java.util.Optional> getHints(); - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - java.util.Optional getCwlVersion(); - /** - * Getter for property https://w3id.org/cwl/cwl#Workflow/steps
- *
- * The individual steps that make up the workflow. Each step is executed when all of its - * input data links are fufilled. An implementation may choose to execute - * the steps in a different order than listed and/or execute steps - * concurrently, provided that dependencies between steps are met. - * *
- */ - - java.util.List getSteps(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowImpl.java deleted file mode 100644 index bdf7c0c6..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowImpl.java +++ /dev/null @@ -1,444 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#Workflow
- A workflow describes a set of **steps** and the **dependencies** between - those steps. When a step produces output that will be consumed by a - second step, the first step is a dependency of the second step. - - When there is a dependency, the workflow engine must execute the preceding - step and wait for it to successfully produce output before executing the - dependent step. If two steps are defined in the workflow graph that - are not directly or indirectly dependent, these steps are **independent**, - and may execute in any order or execute concurrently. A workflow is - complete when all steps have been executed. - - Dependencies between parameters are expressed using the `source` field on - [workflow step input parameters](#WorkflowStepInput) and [workflow output - parameters](#WorkflowOutputParameter). - - The `source` field expresses the dependency of one parameter on another - such that when a value is associated with the parameter specified by - `source`, that value is propagated to the destination parameter. When all - data links inbound to a given step are fufilled, the step is ready to - execute. - - ## Workflow success and failure - - A completed step must result in one of `success`, `temporaryFailure` or - `permanentFailure` states. An implementation may choose to retry a step - execution which resulted in `temporaryFailure`. An implementation may - choose to either continue running other steps of a workflow, or terminate - immediately upon `permanentFailure`. - - * If any step of a workflow execution results in `permanentFailure`, then - the workflow status is `permanentFailure`. - - * If one or more steps result in `temporaryFailure` and all other steps - complete `success` or are not executed, then the workflow status is - `temporaryFailure`. - - * If all workflow steps are executed and complete with `success`, then the - workflow status is `success`. - - # Extensions - - [ScatterFeatureRequirement](#ScatterFeatureRequirement) and - [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are - available as standard [extensions](#Extensions_and_Metadata) to core - workflow semantics. -
- */ -public class WorkflowImpl extends SaveableImpl implements Workflow { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private Workflow_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#Workflow/class
- - */ - - public Workflow_class getClass_() { - return this.class_; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.List inputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - public java.util.List getInputs() { - return this.inputs; - } - - private java.util.List outputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - public java.util.List getOutputs() { - return this.outputs; - } - - private java.util.Optional> requirements; - - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - public java.util.Optional> getRequirements() { - return this.requirements; - } - - private java.util.Optional> hints; - - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - public java.util.Optional> getHints() { - return this.hints; - } - - private java.util.Optional cwlVersion; - - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - public java.util.Optional getCwlVersion() { - return this.cwlVersion; - } - - private java.util.List steps; - - /** - * Getter for property https://w3id.org/cwl/cwl#Workflow/steps
- *
- * The individual steps that make up the workflow. Each step is executed when all of its - * input data links are fufilled. An implementation may choose to execute - * the steps in a different order than listed and/or execute steps - * concurrently, provided that dependencies between steps are met. - * *
- */ - - public java.util.List getSteps() { - return this.steps; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of WorkflowImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkflowImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkflowImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - Workflow_class class_; - try { - class_ = - LoaderInstances - .uri_Workflow_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.List inputs; - try { - inputs = - LoaderInstances - .idmap_inputs_array_of_WorkflowInputParameter - .loadField(__doc.get("inputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List outputs; - try { - outputs = - LoaderInstances - .idmap_outputs_array_of_WorkflowOutputParameter - .loadField(__doc.get("outputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> requirements; - - if (__doc.containsKey("requirements")) { - try { - requirements = - LoaderInstances - .idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement - .loadField(__doc.get("requirements"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - requirements = null; // won't be used but prevents compiler from complaining. - final String __message = "the `requirements` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - requirements = null; - } - java.util.Optional> hints; - - if (__doc.containsKey("hints")) { - try { - hints = - LoaderInstances - .idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance - .loadField(__doc.get("hints"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - hints = null; // won't be used but prevents compiler from complaining. - final String __message = "the `hints` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - hints = null; - } - java.util.Optional cwlVersion; - - if (__doc.containsKey("cwlVersion")) { - try { - cwlVersion = - LoaderInstances - .uri_optional_CWLVersion_False_True_None_None - .loadField(__doc.get("cwlVersion"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - cwlVersion = null; // won't be used but prevents compiler from complaining. - final String __message = "the `cwlVersion` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - cwlVersion = null; - } - java.util.List steps; - try { - steps = - LoaderInstances - .idmap_steps_array_of_WorkflowStep - .loadField(__doc.get("steps"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - steps = null; // won't be used but prevents compiler from complaining. - final String __message = "the `steps` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (java.util.Optional) id; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.inputs = (java.util.List) inputs; - this.outputs = (java.util.List) outputs; - this.requirements = (java.util.Optional>) requirements; - this.hints = (java.util.Optional>) hints; - this.cwlVersion = (java.util.Optional) cwlVersion; - this.class_ = (Workflow_class) class_; - this.steps = (java.util.List) steps; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id", "label", "doc", "inputs", "outputs", "requirements", "hints", "cwlVersion", "class", "steps"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameter.java deleted file mode 100644 index 90069300..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameter.java +++ /dev/null @@ -1,179 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowInputParameter
This interface is implemented by {@link WorkflowInputParameterImpl}
- */ -public interface WorkflowInputParameter extends InputParameter, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferrably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value to use for this parameter if the parameter is missing - * from the input object, or if the value of the parameter in the input - * object is `null`. Default values are applied before evaluating expressions - * (e.g. dependent `valueFrom` fields). - * *
- */ - - java.util.Optional getDefault(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowInputParameter/inputBinding
- *
- * Deprecated. Preserved for v1.0 backwards compatability. Will be removed in - * CWL v2.0. Use `WorkflowInputParameter.loadContents` instead. - * *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameterImpl.java deleted file mode 100644 index d6dba623..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowInputParameterImpl.java +++ /dev/null @@ -1,492 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowInputParameter
- */ -public class WorkflowInputParameterImpl extends SaveableImpl implements WorkflowInputParameter { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferrably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - private java.util.Optional default_; - - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value to use for this parameter if the parameter is missing - * from the input object, or if the value of the parameter in the input - * object is `null`. Default values are applied before evaluating expressions - * (e.g. dependent `valueFrom` fields). - * *
- */ - - public java.util.Optional getDefault() { - return this.default_; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowInputParameter/inputBinding
- *
- * Deprecated. Preserved for v1.0 backwards compatability. Will be removed in - * CWL v2.0. Use `WorkflowInputParameter.loadContents` instead. - * *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of WorkflowInputParameterImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkflowInputParameterImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkflowInputParameterImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - java.util.Optional default_; - - if (__doc.containsKey("default")) { - try { - default_ = - LoaderInstances - .optional_CWLObjectType - .loadField(__doc.get("default"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - default_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `default` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - default_ = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_InputBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.doc = (Object) doc; - this.id = (java.util.Optional) id; - this.format = (Object) format; - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - this.default_ = (java.util.Optional) default_; - this.type = (Object) type; - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("label", "secondaryFiles", "streamable", "doc", "id", "format", "loadContents", "loadListing", "default", "type", "inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameter.java deleted file mode 100644 index d42f0571..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameter.java +++ /dev/null @@ -1,152 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowOutputParameter
This interface is implemented by {@link WorkflowOutputParameterImpl}
- Describe an output parameter of a workflow. The parameter must be - connected to one or more parameters defined in the workflow that - will provide the value of the output parameter. It is legal to - connect a WorkflowInputParameter to a WorkflowOutputParameter. -
- */ -public interface WorkflowOutputParameter extends OutputParameter, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#outputSource
- *
- * Specifies one or more workflow parameters that supply the value of to - * the output parameter. - * *
- */ - - Object getOutputSource(); - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowOutputParameter/linkMerge
- *
- * The method to use to merge multiple sources into a single array. - * If not specified, the default method is "merge_nested". - * *
- */ - - java.util.Optional getLinkMerge(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - Object getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameterImpl.java deleted file mode 100644 index c4acce74..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowOutputParameterImpl.java +++ /dev/null @@ -1,419 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowOutputParameter
- Describe an output parameter of a workflow. The parameter must be - connected to one or more parameters defined in the workflow that - will provide the value of the output parameter. It is legal to - connect a WorkflowInputParameter to a WorkflowOutputParameter. -
- */ -public class WorkflowOutputParameterImpl extends SaveableImpl implements WorkflowOutputParameter { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private Object outputSource; - - /** - * Getter for property https://w3id.org/cwl/cwl#outputSource
- *
- * Specifies one or more workflow parameters that supply the value of to - * the output parameter. - * *
- */ - - public Object getOutputSource() { - return this.outputSource; - } - - private java.util.Optional linkMerge; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowOutputParameter/linkMerge
- *
- * The method to use to merge multiple sources into a single array. - * If not specified, the default method is "merge_nested". - * *
- */ - - public java.util.Optional getLinkMerge() { - return this.linkMerge; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - public Object getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of WorkflowOutputParameterImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkflowOutputParameterImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkflowOutputParameterImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - Object outputSource; - - if (__doc.containsKey("outputSource")) { - try { - outputSource = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_1_None - .loadField(__doc.get("outputSource"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputSource = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputSource` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - outputSource = null; - } - java.util.Optional linkMerge; - - if (__doc.containsKey("linkMerge")) { - try { - linkMerge = - LoaderInstances - .optional_LinkMergeMethod - .loadField(__doc.get("linkMerge"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - linkMerge = null; // won't be used but prevents compiler from complaining. - final String __message = "the `linkMerge` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - linkMerge = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.doc = (Object) doc; - this.id = (java.util.Optional) id; - this.format = (Object) format; - this.outputSource = (Object) outputSource; - this.linkMerge = (java.util.Optional) linkMerge; - this.type = (Object) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("label", "secondaryFiles", "streamable", "doc", "id", "format", "outputSource", "linkMerge", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStep.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStep.java deleted file mode 100644 index 47bde358..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStep.java +++ /dev/null @@ -1,172 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowStep
This interface is implemented by {@link WorkflowStepImpl}
- A workflow step is an executable element of a workflow. It specifies the - underlying process implementation (such as `CommandLineTool` or another - `Workflow`) in the `run` field and connects the input and output parameters - of the underlying process to workflow parameters. - - # Scatter/gather - - To use scatter/gather, - [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified - in the workflow or workflow step requirements. - - A "scatter" operation specifies that the associated workflow step or - subworkflow should execute separately over a list of input elements. Each - job making up a scatter operation is independent and may be executed - concurrently. - - The `scatter` field specifies one or more input parameters which will be - scattered. An input parameter may be listed more than once. The declared - type of each input parameter is implicitly becomes an array of items of the - input parameter type. If a parameter is listed more than once, it becomes - a nested array. As a result, upstream parameters which are connected to - scattered parameters must be arrays. - - All output parameter types are also implicitly wrapped in arrays. Each job - in the scatter results in an entry in the output array. - - If any scattered parameter runtime value is an empty array, all outputs are - set to empty arrays and no work is done for the step, according to - applicable scattering rules. - - If `scatter` declares more than one input parameter, `scatterMethod` - describes how to decompose the input into a discrete set of jobs. - - * **dotproduct** specifies that each of the input arrays are aligned and one - element taken from each array to construct each job. It is an error - if all input arrays are not the same length. - - * **nested_crossproduct** specifies the Cartesian product of the inputs, - producing a job for every combination of the scattered inputs. The - output must be nested arrays for each level of scattering, in the - order that the input arrays are listed in the `scatter` field. - - * **flat_crossproduct** specifies the Cartesian product of the inputs, - producing a job for every combination of the scattered inputs. The - output arrays must be flattened to a single level, but otherwise listed in the - order that the input arrays are listed in the `scatter` field. - - # Subworkflows - - To specify a nested workflow as part of a workflow step, - [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be - specified in the workflow or workflow step requirements. - - It is a fatal error if a workflow directly or indirectly invokes itself as - a subworkflow (recursive workflows are not allowed). -
- */ -public interface WorkflowStep extends Identified, Labeled, Documented, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#in
- *
- * Defines the input parameters of the workflow step. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used build a user - * interface for constructing the input object. - * *
- */ - - java.util.List getIn(); - /** - * Getter for property https://w3id.org/cwl/cwl#out
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - java.util.List getOut(); - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this workflow step. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - java.util.Optional> getRequirements(); - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this workflow step. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - java.util.Optional> getHints(); - /** - * Getter for property https://w3id.org/cwl/cwl#run
- *
- * Specifies the process to run. - * *
- */ - - Object getRun(); - /** - * Getter for property https://w3id.org/cwl/cwl#scatter
- - */ - - Object getScatter(); - /** - * Getter for property https://w3id.org/cwl/cwl#scatterMethod
- *
- * Required if `scatter` is an array of more than one element. - * *
- */ - - java.util.Optional getScatterMethod(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepImpl.java deleted file mode 100644 index 5f30f569..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepImpl.java +++ /dev/null @@ -1,450 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowStep
- A workflow step is an executable element of a workflow. It specifies the - underlying process implementation (such as `CommandLineTool` or another - `Workflow`) in the `run` field and connects the input and output parameters - of the underlying process to workflow parameters. - - # Scatter/gather - - To use scatter/gather, - [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified - in the workflow or workflow step requirements. - - A "scatter" operation specifies that the associated workflow step or - subworkflow should execute separately over a list of input elements. Each - job making up a scatter operation is independent and may be executed - concurrently. - - The `scatter` field specifies one or more input parameters which will be - scattered. An input parameter may be listed more than once. The declared - type of each input parameter is implicitly becomes an array of items of the - input parameter type. If a parameter is listed more than once, it becomes - a nested array. As a result, upstream parameters which are connected to - scattered parameters must be arrays. - - All output parameter types are also implicitly wrapped in arrays. Each job - in the scatter results in an entry in the output array. - - If any scattered parameter runtime value is an empty array, all outputs are - set to empty arrays and no work is done for the step, according to - applicable scattering rules. - - If `scatter` declares more than one input parameter, `scatterMethod` - describes how to decompose the input into a discrete set of jobs. - - * **dotproduct** specifies that each of the input arrays are aligned and one - element taken from each array to construct each job. It is an error - if all input arrays are not the same length. - - * **nested_crossproduct** specifies the Cartesian product of the inputs, - producing a job for every combination of the scattered inputs. The - output must be nested arrays for each level of scattering, in the - order that the input arrays are listed in the `scatter` field. - - * **flat_crossproduct** specifies the Cartesian product of the inputs, - producing a job for every combination of the scattered inputs. The - output arrays must be flattened to a single level, but otherwise listed in the - order that the input arrays are listed in the `scatter` field. - - # Subworkflows - - To specify a nested workflow as part of a workflow step, - [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be - specified in the workflow or workflow step requirements. - - It is a fatal error if a workflow directly or indirectly invokes itself as - a subworkflow (recursive workflows are not allowed). -
- */ -public class WorkflowStepImpl extends SaveableImpl implements WorkflowStep { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.List in; - - /** - * Getter for property https://w3id.org/cwl/cwl#in
- *
- * Defines the input parameters of the workflow step. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used build a user - * interface for constructing the input object. - * *
- */ - - public java.util.List getIn() { - return this.in; - } - - private java.util.List out; - - /** - * Getter for property https://w3id.org/cwl/cwl#out
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - public java.util.List getOut() { - return this.out; - } - - private java.util.Optional> requirements; - - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this workflow step. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - public java.util.Optional> getRequirements() { - return this.requirements; - } - - private java.util.Optional> hints; - - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this workflow step. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - public java.util.Optional> getHints() { - return this.hints; - } - - private Object run; - - /** - * Getter for property https://w3id.org/cwl/cwl#run
- *
- * Specifies the process to run. - * *
- */ - - public Object getRun() { - return this.run; - } - - private Object scatter; - - /** - * Getter for property https://w3id.org/cwl/cwl#scatter
- - */ - - public Object getScatter() { - return this.scatter; - } - - private java.util.Optional scatterMethod; - - /** - * Getter for property https://w3id.org/cwl/cwl#scatterMethod
- *
- * Required if `scatter` is an array of more than one element. - * *
- */ - - public java.util.Optional getScatterMethod() { - return this.scatterMethod; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of WorkflowStepImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkflowStepImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkflowStepImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.List in; - try { - in = - LoaderInstances - .idmap_in_array_of_WorkflowStepInput - .loadField(__doc.get("in"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - in = null; // won't be used but prevents compiler from complaining. - final String __message = "the `in` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List out; - try { - out = - LoaderInstances - .uri_array_of_union_of_StringInstance_or_WorkflowStepOutput_True_False_None_None - .loadField(__doc.get("out"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - out = null; // won't be used but prevents compiler from complaining. - final String __message = "the `out` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> requirements; - - if (__doc.containsKey("requirements")) { - try { - requirements = - LoaderInstances - .idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement - .loadField(__doc.get("requirements"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - requirements = null; // won't be used but prevents compiler from complaining. - final String __message = "the `requirements` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - requirements = null; - } - java.util.Optional> hints; - - if (__doc.containsKey("hints")) { - try { - hints = - LoaderInstances - .idmap_hints_optional_array_of_AnyInstance - .loadField(__doc.get("hints"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - hints = null; // won't be used but prevents compiler from complaining. - final String __message = "the `hints` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - hints = null; - } - Object run; - try { - run = - LoaderInstances - .uri_union_of_StringInstance_or_CommandLineTool_or_ExpressionTool_or_Workflow_False_False_None_None - .loadField(__doc.get("run"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - run = null; // won't be used but prevents compiler from complaining. - final String __message = "the `run` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object scatter; - - if (__doc.containsKey("scatter")) { - try { - scatter = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_0_None - .loadField(__doc.get("scatter"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - scatter = null; // won't be used but prevents compiler from complaining. - final String __message = "the `scatter` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - scatter = null; - } - java.util.Optional scatterMethod; - - if (__doc.containsKey("scatterMethod")) { - try { - scatterMethod = - LoaderInstances - .uri_optional_ScatterMethod_False_True_None_None - .loadField(__doc.get("scatterMethod"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - scatterMethod = null; // won't be used but prevents compiler from complaining. - final String __message = "the `scatterMethod` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - scatterMethod = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (java.util.Optional) id; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.in = (java.util.List) in; - this.out = (java.util.List) out; - this.requirements = (java.util.Optional>) requirements; - this.hints = (java.util.Optional>) hints; - this.run = (Object) run; - this.scatter = (Object) scatter; - this.scatterMethod = (java.util.Optional) scatterMethod; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id", "label", "doc", "in", "out", "requirements", "hints", "run", "scatter", "scatterMethod"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInput.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInput.java deleted file mode 100644 index 3f2bfd3b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInput.java +++ /dev/null @@ -1,171 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowStepInput
This interface is implemented by {@link WorkflowStepInputImpl}
- The input of a workflow step connects an upstream parameter (from the - workflow inputs, or the outputs of other workflows steps) with the input - parameters of the process specified by the `run` field. Only input parameters - declared by the target process will be passed through at runtime to the process - though additonal parameters may be specified (for use within `valueFrom` - expressions for instance) - unconnected or unused parameters do not represent an - error condition. - - ## Input object - - A WorkflowStepInput object must contain an `id` field in the form - `#fieldname` or `#prefix/fieldname`. When the `id` field contains a slash - `/` the field name consists of the characters following the final slash - (the prefix portion may contain one or more slashes to indicate scope). - This defines a field of the workflow step input object with the value of - the `source` parameter(s). - - ## Merging - - To merge multiple inbound data links, - [MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified - in the workflow or workflow step requirements. - - If the sink parameter is an array, or named in a [workflow - scatter](#WorkflowStep) operation, there may be multiple inbound data links - listed in the `source` field. The values from the input links are merged - depending on the method specified in the `linkMerge` field. If not - specified, the default method is "merge_nested". - - * **merge_nested** - - The input must be an array consisting of exactly one entry for each - input link. If "merge_nested" is specified with a single link, the value - from the link must be wrapped in a single-item list. - - * **merge_flattened** - - 1. The source and sink parameters must be compatible types, or the source - type must be compatible with single element from the "items" type of - the destination array parameter. - 2. Source parameters which are arrays are concatenated. - Source parameters which are single element types are appended as - single elements. -
- */ -public interface WorkflowStepInput extends Identified, Sink, LoadContents, Labeled, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#source
- *
- * Specifies one or more workflow parameters that will provide input to - * the underlying step parameter. - * *
- */ - - Object getSource(); - /** - * Getter for property https://w3id.org/cwl/cwl#Sink/linkMerge
- *
- * The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". - * *
- */ - - java.util.Optional getLinkMerge(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value for this parameter to use if either there is no - * `source` field, or the value produced by the `source` is `null`. The - * default must be applied prior to scattering or evaluating `valueFrom`. - * *
- */ - - java.util.Optional getDefault(); - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowStepInput/valueFrom
- *
- * To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must - * be specified in the workflow or workflow step requirements. - * - * If `valueFrom` is a constant string value, use this as the value for - * this input parameter. - * - * If `valueFrom` is a parameter reference or expression, it must be - * evaluated to yield the actual value to be assiged to the input field. - * - * The `self` value in the parameter reference or expression must be - * 1. `null` if there is no `source` field - * 2. the value of the parameter(s) specified in the `source` field when this - * workflow input parameter **is not** specified in this workflow step's `scatter` field. - * 3. an element of the parameter specified in the `source` field when this workflow input - * parameter **is** specified in this workflow step's `scatter` field. - * - * The value of `inputs` in the parameter reference or expression must be - * the input object to the workflow step after assigning the `source` - * values, applying `default`, and then scattering. The order of - * evaluating `valueFrom` among step input parameters is undefined and the - * result of evaluating `valueFrom` on a parameter must not be visible to - * evaluation of `valueFrom` on other parameters. - * *
- */ - - Object getValueFrom(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInputImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInputImpl.java deleted file mode 100644 index 882958b4..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepInputImpl.java +++ /dev/null @@ -1,421 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowStepInput
- The input of a workflow step connects an upstream parameter (from the - workflow inputs, or the outputs of other workflows steps) with the input - parameters of the process specified by the `run` field. Only input parameters - declared by the target process will be passed through at runtime to the process - though additonal parameters may be specified (for use within `valueFrom` - expressions for instance) - unconnected or unused parameters do not represent an - error condition. - - ## Input object - - A WorkflowStepInput object must contain an `id` field in the form - `#fieldname` or `#prefix/fieldname`. When the `id` field contains a slash - `/` the field name consists of the characters following the final slash - (the prefix portion may contain one or more slashes to indicate scope). - This defines a field of the workflow step input object with the value of - the `source` parameter(s). - - ## Merging - - To merge multiple inbound data links, - [MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified - in the workflow or workflow step requirements. - - If the sink parameter is an array, or named in a [workflow - scatter](#WorkflowStep) operation, there may be multiple inbound data links - listed in the `source` field. The values from the input links are merged - depending on the method specified in the `linkMerge` field. If not - specified, the default method is "merge_nested". - - * **merge_nested** - - The input must be an array consisting of exactly one entry for each - input link. If "merge_nested" is specified with a single link, the value - from the link must be wrapped in a single-item list. - - * **merge_flattened** - - 1. The source and sink parameters must be compatible types, or the source - type must be compatible with single element from the "items" type of - the destination array parameter. - 2. Source parameters which are arrays are concatenated. - Source parameters which are single element types are appended as - single elements. -
- */ -public class WorkflowStepInputImpl extends SaveableImpl implements WorkflowStepInput { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private Object source; - - /** - * Getter for property https://w3id.org/cwl/cwl#source
- *
- * Specifies one or more workflow parameters that will provide input to - * the underlying step parameter. - * *
- */ - - public Object getSource() { - return this.source; - } - - private java.util.Optional linkMerge; - - /** - * Getter for property https://w3id.org/cwl/cwl#Sink/linkMerge
- *
- * The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". - * *
- */ - - public java.util.Optional getLinkMerge() { - return this.linkMerge; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Read up to the first 64 KiB of text from the file and place it in the - * "contents" field of the file object for use by expressions. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private java.util.Optional default_; - - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value for this parameter to use if either there is no - * `source` field, or the value produced by the `source` is `null`. The - * default must be applied prior to scattering or evaluating `valueFrom`. - * *
- */ - - public java.util.Optional getDefault() { - return this.default_; - } - - private Object valueFrom; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowStepInput/valueFrom
- *
- * To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must - * be specified in the workflow or workflow step requirements. - * - * If `valueFrom` is a constant string value, use this as the value for - * this input parameter. - * - * If `valueFrom` is a parameter reference or expression, it must be - * evaluated to yield the actual value to be assiged to the input field. - * - * The `self` value in the parameter reference or expression must be - * 1. `null` if there is no `source` field - * 2. the value of the parameter(s) specified in the `source` field when this - * workflow input parameter **is not** specified in this workflow step's `scatter` field. - * 3. an element of the parameter specified in the `source` field when this workflow input - * parameter **is** specified in this workflow step's `scatter` field. - * - * The value of `inputs` in the parameter reference or expression must be - * the input object to the workflow step after assigning the `source` - * values, applying `default`, and then scattering. The order of - * evaluating `valueFrom` among step input parameters is undefined and the - * result of evaluating `valueFrom` on a parameter must not be visible to - * evaluation of `valueFrom` on other parameters. - * *
- */ - - public Object getValueFrom() { - return this.valueFrom; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of WorkflowStepInputImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkflowStepInputImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkflowStepInputImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - Object source; - - if (__doc.containsKey("source")) { - try { - source = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_2_None - .loadField(__doc.get("source"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - source = null; // won't be used but prevents compiler from complaining. - final String __message = "the `source` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - source = null; - } - java.util.Optional linkMerge; - - if (__doc.containsKey("linkMerge")) { - try { - linkMerge = - LoaderInstances - .optional_LinkMergeMethod - .loadField(__doc.get("linkMerge"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - linkMerge = null; // won't be used but prevents compiler from complaining. - final String __message = "the `linkMerge` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - linkMerge = null; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - java.util.Optional default_; - - if (__doc.containsKey("default")) { - try { - default_ = - LoaderInstances - .optional_CWLObjectType - .loadField(__doc.get("default"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - default_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `default` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - default_ = null; - } - Object valueFrom; - - if (__doc.containsKey("valueFrom")) { - try { - valueFrom = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("valueFrom"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - valueFrom = null; // won't be used but prevents compiler from complaining. - final String __message = "the `valueFrom` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - valueFrom = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (java.util.Optional) id; - this.source = (Object) source; - this.linkMerge = (java.util.Optional) linkMerge; - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - this.label = (java.util.Optional) label; - this.default_ = (java.util.Optional) default_; - this.valueFrom = (Object) valueFrom; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id", "source", "linkMerge", "loadContents", "loadListing", "label", "default", "valueFrom"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepOutput.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepOutput.java deleted file mode 100644 index f0762883..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepOutput.java +++ /dev/null @@ -1,44 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowStepOutput
This interface is implemented by {@link WorkflowStepOutputImpl}
- Associate an output parameter of the underlying process with a workflow - parameter. The workflow parameter (given in the `id` field) be may be used - as a `source` to connect with input parameters of other workflow steps, or - with an output parameter of the process. - - A unique identifier for this workflow output parameter. This is - the identifier to use in the `source` field of `WorkflowStepInput` - to connect the output value to downstream parameters. -
- */ -public interface WorkflowStepOutput extends Identified, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - java.util.Optional getId(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepOutputImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepOutputImpl.java deleted file mode 100644 index cf8bb936..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepOutputImpl.java +++ /dev/null @@ -1,133 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowStepOutput
- Associate an output parameter of the underlying process with a workflow - parameter. The workflow parameter (given in the `id` field) be may be used - as a `source` to connect with input parameters of other workflow steps, or - with an output parameter of the process. - - A unique identifier for this workflow output parameter. This is - the identifier to use in the `source` field of `WorkflowStepInput` - to connect the output value to downstream parameters. -
- */ -public class WorkflowStepOutputImpl extends SaveableImpl implements WorkflowStepOutput { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Identified/id
- *
- * The unique identifier for this object. *
- */ - - public java.util.Optional getId() { - return this.id; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of WorkflowStepOutputImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkflowStepOutputImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkflowStepOutputImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (java.util.Optional) id; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Workflow_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/Workflow_class.java deleted file mode 100644 index 17a1ead3..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/Workflow_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum Workflow_class { - WORKFLOW("Workflow"); - - private static String[] symbols = new String[] {"Workflow"}; - private String docVal; - - private Workflow_class(final String docVal) { - this.docVal = docVal; - } - - public static Workflow_class fromDocumentVal(final String docVal) { - for(final Workflow_class val : Workflow_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Workflow_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/package.html b/src/main/java/org/commonwl/cwlsdk/cwl1_1/package.html deleted file mode 100644 index 1478017f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/package.html +++ /dev/null @@ -1,4 +0,0 @@ - -Package for the auto-generated Java objects corresponding generated by Schema Salad -for https://w3id.org/cwl/cwl#. - diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/stderr.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/stderr.java deleted file mode 100644 index dcde2ceb..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/stderr.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum stderr { - STDERR("stderr"); - - private static String[] symbols = new String[] {"stderr"}; - private String docVal; - - private stderr(final String docVal) { - this.docVal = docVal; - } - - public static stderr fromDocumentVal(final String docVal) { - for(final stderr val : stderr.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", stderr.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/stdin.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/stdin.java deleted file mode 100644 index dd99c871..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/stdin.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum stdin { - STDIN("stdin"); - - private static String[] symbols = new String[] {"stdin"}; - private String docVal; - - private stdin(final String docVal) { - this.docVal = docVal; - } - - public static stdin fromDocumentVal(final String docVal) { - for(final stdin val : stdin.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", stdin.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/stdout.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/stdout.java deleted file mode 100644 index 04743421..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/stdout.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_1; - -import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException; - -public enum stdout { - STDOUT("stdout"); - - private static String[] symbols = new String[] {"stdout"}; - private String docVal; - - private stdout(final String docVal) { - this.docVal = docVal; - } - - public static stdout fromDocumentVal(final String docVal) { - for(final stdout val : stdout.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", stdout.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/AnyLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/AnyLoader.java deleted file mode 100644 index b6158c12..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/AnyLoader.java +++ /dev/null @@ -1,15 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -public class AnyLoader implements Loader { - - public Object load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - if (doc == null) { - throw new ValidationException("Expected non-null"); - } - return doc; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/ArrayLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/ArrayLoader.java deleted file mode 100644 index 47f2f247..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/ArrayLoader.java +++ /dev/null @@ -1,43 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.ArrayList; -import java.util.List; - -public class ArrayLoader implements Loader> { - private final Loader itemLoader; - - public ArrayLoader(Loader itemLoader) { - this.itemLoader = itemLoader; - } - - public List load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - final List docList = (List) Loader.validateOfJavaType(List.class, doc); - final List r = new ArrayList(); - final List loaders = new ArrayList(); - loaders.add(this); - loaders.add(this.itemLoader); - final UnionLoader unionLoader = new UnionLoader(loaders); - final List errors = new ArrayList(); - for (final Object el : docList) { - try { - final Object loadedField = unionLoader.loadField(el, baseUri, loadingOptions); - final boolean flatten = !"@list".equals(loadingOptions.container); - if (flatten && loadedField instanceof List) { - r.addAll((List) loadedField); - } else { - r.add((T) loadedField); - } - } catch (final ValidationException e) { - errors.add(e); - } - } - if (!errors.isEmpty()) { - throw new ValidationException("", errors); - } - return r; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/ConstantMaps.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/ConstantMaps.java deleted file mode 100644 index 73c60751..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/ConstantMaps.java +++ /dev/null @@ -1,271 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.HashMap; - -public class ConstantMaps { - // declare as HashMap for clone(). - public static final HashMap vocab = new HashMap(); - public static final HashMap rvocab = new HashMap(); - - static { - vocab.put("Any", "https://w3id.org/cwl/salad#Any"); - vocab.put("ArraySchema", "https://w3id.org/cwl/salad#ArraySchema"); - vocab.put("CWLArraySchema", "https://w3id.org/cwl/cwl#CWLArraySchema"); - vocab.put("CWLInputFile", "https://w3id.org/cwl/cwl#CWLInputFile"); - vocab.put("CWLObjectType", "https://w3id.org/cwl/cwl#CWLObjectType"); - vocab.put("CWLRecordField", "https://w3id.org/cwl/cwl#CWLRecordField"); - vocab.put("CWLRecordSchema", "https://w3id.org/cwl/cwl#CWLRecordSchema"); - vocab.put("CWLType", "https://w3id.org/cwl/cwl#CWLType"); - vocab.put("CWLVersion", "https://w3id.org/cwl/cwl#CWLVersion"); - vocab.put("CommandInputArraySchema", "https://w3id.org/cwl/cwl#CommandInputArraySchema"); - vocab.put("CommandInputEnumSchema", "https://w3id.org/cwl/cwl#CommandInputEnumSchema"); - vocab.put("CommandInputParameter", "https://w3id.org/cwl/cwl#CommandInputParameter"); - vocab.put("CommandInputRecordField", "https://w3id.org/cwl/cwl#CommandInputRecordField"); - vocab.put("CommandInputRecordSchema", "https://w3id.org/cwl/cwl#CommandInputRecordSchema"); - vocab.put("CommandInputSchema", "https://w3id.org/cwl/cwl#CommandInputSchema"); - vocab.put("CommandLineBindable", "https://w3id.org/cwl/cwl#CommandLineBindable"); - vocab.put("CommandLineBinding", "https://w3id.org/cwl/cwl#CommandLineBinding"); - vocab.put("CommandLineTool", "CommandLineTool"); - vocab.put("CommandOutputArraySchema", "https://w3id.org/cwl/cwl#CommandOutputArraySchema"); - vocab.put("CommandOutputBinding", "https://w3id.org/cwl/cwl#CommandOutputBinding"); - vocab.put("CommandOutputEnumSchema", "https://w3id.org/cwl/cwl#CommandOutputEnumSchema"); - vocab.put("CommandOutputParameter", "https://w3id.org/cwl/cwl#CommandOutputParameter"); - vocab.put("CommandOutputRecordField", "https://w3id.org/cwl/cwl#CommandOutputRecordField"); - vocab.put("CommandOutputRecordSchema", "https://w3id.org/cwl/cwl#CommandOutputRecordSchema"); - vocab.put("Directory", "Directory"); - vocab.put("Dirent", "https://w3id.org/cwl/cwl#Dirent"); - vocab.put("DockerRequirement", "DockerRequirement"); - vocab.put("Documented", "https://w3id.org/cwl/salad#Documented"); - vocab.put("EnumSchema", "https://w3id.org/cwl/salad#EnumSchema"); - vocab.put("EnvVarRequirement", "EnvVarRequirement"); - vocab.put("EnvironmentDef", "https://w3id.org/cwl/cwl#EnvironmentDef"); - vocab.put("Expression", "https://w3id.org/cwl/cwl#Expression"); - vocab.put("ExpressionPlaceholder", "https://w3id.org/cwl/cwl#ExpressionPlaceholder"); - vocab.put("ExpressionTool", "ExpressionTool"); - vocab.put("ExpressionToolOutputParameter", "https://w3id.org/cwl/cwl#ExpressionToolOutputParameter"); - vocab.put("FieldBase", "https://w3id.org/cwl/cwl#FieldBase"); - vocab.put("File", "File"); - vocab.put("IOSchema", "https://w3id.org/cwl/cwl#IOSchema"); - vocab.put("Identified", "https://w3id.org/cwl/cwl#Identified"); - vocab.put("InitialWorkDirRequirement", "InitialWorkDirRequirement"); - vocab.put("InlineJavascriptRequirement", "InlineJavascriptRequirement"); - vocab.put("InplaceUpdateRequirement", "InplaceUpdateRequirement"); - vocab.put("InputArraySchema", "https://w3id.org/cwl/cwl#InputArraySchema"); - vocab.put("InputBinding", "https://w3id.org/cwl/cwl#InputBinding"); - vocab.put("InputEnumSchema", "https://w3id.org/cwl/cwl#InputEnumSchema"); - vocab.put("InputFormat", "https://w3id.org/cwl/cwl#InputFormat"); - vocab.put("InputParameter", "https://w3id.org/cwl/cwl#InputParameter"); - vocab.put("InputRecordField", "https://w3id.org/cwl/cwl#InputRecordField"); - vocab.put("InputRecordSchema", "https://w3id.org/cwl/cwl#InputRecordSchema"); - vocab.put("InputSchema", "https://w3id.org/cwl/cwl#InputSchema"); - vocab.put("Labeled", "https://w3id.org/cwl/cwl#Labeled"); - vocab.put("LinkMergeMethod", "https://w3id.org/cwl/cwl#LinkMergeMethod"); - vocab.put("LoadContents", "https://w3id.org/cwl/cwl#LoadContents"); - vocab.put("LoadListingEnum", "https://w3id.org/cwl/cwl#LoadListingEnum"); - vocab.put("LoadListingRequirement", "LoadListingRequirement"); - vocab.put("MapSchema", "https://w3id.org/cwl/salad#MapSchema"); - vocab.put("MultipleInputFeatureRequirement", "MultipleInputFeatureRequirement"); - vocab.put("NetworkAccess", "NetworkAccess"); - vocab.put("OutputArraySchema", "https://w3id.org/cwl/cwl#OutputArraySchema"); - vocab.put("OutputEnumSchema", "https://w3id.org/cwl/cwl#OutputEnumSchema"); - vocab.put("OutputFormat", "https://w3id.org/cwl/cwl#OutputFormat"); - vocab.put("OutputParameter", "https://w3id.org/cwl/cwl#OutputParameter"); - vocab.put("OutputRecordField", "https://w3id.org/cwl/cwl#OutputRecordField"); - vocab.put("OutputRecordSchema", "https://w3id.org/cwl/cwl#OutputRecordSchema"); - vocab.put("OutputSchema", "https://w3id.org/cwl/cwl#OutputSchema"); - vocab.put("Parameter", "https://w3id.org/cwl/cwl#Parameter"); - vocab.put("PrimitiveType", "https://w3id.org/cwl/salad#PrimitiveType"); - vocab.put("Process", "https://w3id.org/cwl/cwl#Process"); - vocab.put("ProcessRequirement", "https://w3id.org/cwl/cwl#ProcessRequirement"); - vocab.put("RecordField", "https://w3id.org/cwl/salad#RecordField"); - vocab.put("RecordSchema", "https://w3id.org/cwl/salad#RecordSchema"); - vocab.put("ResourceRequirement", "ResourceRequirement"); - vocab.put("ScatterFeatureRequirement", "ScatterFeatureRequirement"); - vocab.put("ScatterMethod", "https://w3id.org/cwl/cwl#ScatterMethod"); - vocab.put("SchemaDefRequirement", "SchemaDefRequirement"); - vocab.put("SecondaryFileSchema", "https://w3id.org/cwl/cwl#SecondaryFileSchema"); - vocab.put("ShellCommandRequirement", "ShellCommandRequirement"); - vocab.put("Sink", "https://w3id.org/cwl/cwl#Sink"); - vocab.put("SoftwarePackage", "https://w3id.org/cwl/cwl#SoftwarePackage"); - vocab.put("SoftwareRequirement", "SoftwareRequirement"); - vocab.put("StepInputExpressionRequirement", "StepInputExpressionRequirement"); - vocab.put("SubworkflowFeatureRequirement", "SubworkflowFeatureRequirement"); - vocab.put("ToolTimeLimit", "ToolTimeLimit"); - vocab.put("UnionSchema", "https://w3id.org/cwl/salad#UnionSchema"); - vocab.put("WorkReuse", "WorkReuse"); - vocab.put("Workflow", "Workflow"); - vocab.put("WorkflowInputParameter", "https://w3id.org/cwl/cwl#WorkflowInputParameter"); - vocab.put("WorkflowOutputParameter", "https://w3id.org/cwl/cwl#WorkflowOutputParameter"); - vocab.put("WorkflowStep", "https://w3id.org/cwl/cwl#WorkflowStep"); - vocab.put("WorkflowStepInput", "https://w3id.org/cwl/cwl#WorkflowStepInput"); - vocab.put("WorkflowStepOutput", "https://w3id.org/cwl/cwl#WorkflowStepOutput"); - vocab.put("array", "array"); - vocab.put("boolean", "http://www.w3.org/2001/XMLSchema#boolean"); - vocab.put("deep_listing", "https://w3id.org/cwl/cwl#LoadListingEnum/deep_listing"); - vocab.put("dotproduct", "https://w3id.org/cwl/cwl#ScatterMethod/dotproduct"); - vocab.put("double", "http://www.w3.org/2001/XMLSchema#double"); - vocab.put("draft-2", "https://w3id.org/cwl/cwl#draft-2"); - vocab.put("draft-3", "https://w3id.org/cwl/cwl#draft-3"); - vocab.put("draft-3.dev1", "https://w3id.org/cwl/cwl#draft-3.dev1"); - vocab.put("draft-3.dev2", "https://w3id.org/cwl/cwl#draft-3.dev2"); - vocab.put("draft-3.dev3", "https://w3id.org/cwl/cwl#draft-3.dev3"); - vocab.put("draft-3.dev4", "https://w3id.org/cwl/cwl#draft-3.dev4"); - vocab.put("draft-3.dev5", "https://w3id.org/cwl/cwl#draft-3.dev5"); - vocab.put("draft-4.dev1", "https://w3id.org/cwl/cwl#draft-4.dev1"); - vocab.put("draft-4.dev2", "https://w3id.org/cwl/cwl#draft-4.dev2"); - vocab.put("draft-4.dev3", "https://w3id.org/cwl/cwl#draft-4.dev3"); - vocab.put("enum", "enum"); - vocab.put("flat_crossproduct", "https://w3id.org/cwl/cwl#ScatterMethod/flat_crossproduct"); - vocab.put("float", "http://www.w3.org/2001/XMLSchema#float"); - vocab.put("int", "http://www.w3.org/2001/XMLSchema#int"); - vocab.put("long", "http://www.w3.org/2001/XMLSchema#long"); - vocab.put("map", "map"); - vocab.put("merge_flattened", "https://w3id.org/cwl/cwl#LinkMergeMethod/merge_flattened"); - vocab.put("merge_nested", "https://w3id.org/cwl/cwl#LinkMergeMethod/merge_nested"); - vocab.put("nested_crossproduct", "https://w3id.org/cwl/cwl#ScatterMethod/nested_crossproduct"); - vocab.put("no_listing", "https://w3id.org/cwl/cwl#LoadListingEnum/no_listing"); - vocab.put("null", "https://w3id.org/cwl/salad#null"); - vocab.put("record", "record"); - vocab.put("shallow_listing", "https://w3id.org/cwl/cwl#LoadListingEnum/shallow_listing"); - vocab.put("stderr", "https://w3id.org/cwl/cwl#stderr"); - vocab.put("stdin", "https://w3id.org/cwl/cwl#stdin"); - vocab.put("stdout", "https://w3id.org/cwl/cwl#stdout"); - vocab.put("string", "http://www.w3.org/2001/XMLSchema#string"); - vocab.put("union", "union"); - vocab.put("v1.0", "https://w3id.org/cwl/cwl#v1.0"); - vocab.put("v1.0.dev4", "https://w3id.org/cwl/cwl#v1.0.dev4"); - vocab.put("v1.1", "https://w3id.org/cwl/cwl#v1.1"); - vocab.put("v1.1.0-dev1", "https://w3id.org/cwl/cwl#v1.1.0-dev1"); - - - rvocab.put("https://w3id.org/cwl/salad#Any", "Any"); - rvocab.put("https://w3id.org/cwl/salad#ArraySchema", "ArraySchema"); - rvocab.put("https://w3id.org/cwl/cwl#CWLArraySchema", "CWLArraySchema"); - rvocab.put("https://w3id.org/cwl/cwl#CWLInputFile", "CWLInputFile"); - rvocab.put("https://w3id.org/cwl/cwl#CWLObjectType", "CWLObjectType"); - rvocab.put("https://w3id.org/cwl/cwl#CWLRecordField", "CWLRecordField"); - rvocab.put("https://w3id.org/cwl/cwl#CWLRecordSchema", "CWLRecordSchema"); - rvocab.put("https://w3id.org/cwl/cwl#CWLType", "CWLType"); - rvocab.put("https://w3id.org/cwl/cwl#CWLVersion", "CWLVersion"); - rvocab.put("https://w3id.org/cwl/cwl#CommandInputArraySchema", "CommandInputArraySchema"); - rvocab.put("https://w3id.org/cwl/cwl#CommandInputEnumSchema", "CommandInputEnumSchema"); - rvocab.put("https://w3id.org/cwl/cwl#CommandInputParameter", "CommandInputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#CommandInputRecordField", "CommandInputRecordField"); - rvocab.put("https://w3id.org/cwl/cwl#CommandInputRecordSchema", "CommandInputRecordSchema"); - rvocab.put("https://w3id.org/cwl/cwl#CommandInputSchema", "CommandInputSchema"); - rvocab.put("https://w3id.org/cwl/cwl#CommandLineBindable", "CommandLineBindable"); - rvocab.put("https://w3id.org/cwl/cwl#CommandLineBinding", "CommandLineBinding"); - rvocab.put("CommandLineTool", "CommandLineTool"); - rvocab.put("https://w3id.org/cwl/cwl#CommandOutputArraySchema", "CommandOutputArraySchema"); - rvocab.put("https://w3id.org/cwl/cwl#CommandOutputBinding", "CommandOutputBinding"); - rvocab.put("https://w3id.org/cwl/cwl#CommandOutputEnumSchema", "CommandOutputEnumSchema"); - rvocab.put("https://w3id.org/cwl/cwl#CommandOutputParameter", "CommandOutputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#CommandOutputRecordField", "CommandOutputRecordField"); - rvocab.put("https://w3id.org/cwl/cwl#CommandOutputRecordSchema", "CommandOutputRecordSchema"); - rvocab.put("Directory", "Directory"); - rvocab.put("https://w3id.org/cwl/cwl#Dirent", "Dirent"); - rvocab.put("DockerRequirement", "DockerRequirement"); - rvocab.put("https://w3id.org/cwl/salad#Documented", "Documented"); - rvocab.put("https://w3id.org/cwl/salad#EnumSchema", "EnumSchema"); - rvocab.put("EnvVarRequirement", "EnvVarRequirement"); - rvocab.put("https://w3id.org/cwl/cwl#EnvironmentDef", "EnvironmentDef"); - rvocab.put("https://w3id.org/cwl/cwl#Expression", "Expression"); - rvocab.put("https://w3id.org/cwl/cwl#ExpressionPlaceholder", "ExpressionPlaceholder"); - rvocab.put("ExpressionTool", "ExpressionTool"); - rvocab.put("https://w3id.org/cwl/cwl#ExpressionToolOutputParameter", "ExpressionToolOutputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#FieldBase", "FieldBase"); - rvocab.put("File", "File"); - rvocab.put("https://w3id.org/cwl/cwl#IOSchema", "IOSchema"); - rvocab.put("https://w3id.org/cwl/cwl#Identified", "Identified"); - rvocab.put("InitialWorkDirRequirement", "InitialWorkDirRequirement"); - rvocab.put("InlineJavascriptRequirement", "InlineJavascriptRequirement"); - rvocab.put("InplaceUpdateRequirement", "InplaceUpdateRequirement"); - rvocab.put("https://w3id.org/cwl/cwl#InputArraySchema", "InputArraySchema"); - rvocab.put("https://w3id.org/cwl/cwl#InputBinding", "InputBinding"); - rvocab.put("https://w3id.org/cwl/cwl#InputEnumSchema", "InputEnumSchema"); - rvocab.put("https://w3id.org/cwl/cwl#InputFormat", "InputFormat"); - rvocab.put("https://w3id.org/cwl/cwl#InputParameter", "InputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#InputRecordField", "InputRecordField"); - rvocab.put("https://w3id.org/cwl/cwl#InputRecordSchema", "InputRecordSchema"); - rvocab.put("https://w3id.org/cwl/cwl#InputSchema", "InputSchema"); - rvocab.put("https://w3id.org/cwl/cwl#Labeled", "Labeled"); - rvocab.put("https://w3id.org/cwl/cwl#LinkMergeMethod", "LinkMergeMethod"); - rvocab.put("https://w3id.org/cwl/cwl#LoadContents", "LoadContents"); - rvocab.put("https://w3id.org/cwl/cwl#LoadListingEnum", "LoadListingEnum"); - rvocab.put("LoadListingRequirement", "LoadListingRequirement"); - rvocab.put("https://w3id.org/cwl/salad#MapSchema", "MapSchema"); - rvocab.put("MultipleInputFeatureRequirement", "MultipleInputFeatureRequirement"); - rvocab.put("NetworkAccess", "NetworkAccess"); - rvocab.put("https://w3id.org/cwl/cwl#OutputArraySchema", "OutputArraySchema"); - rvocab.put("https://w3id.org/cwl/cwl#OutputEnumSchema", "OutputEnumSchema"); - rvocab.put("https://w3id.org/cwl/cwl#OutputFormat", "OutputFormat"); - rvocab.put("https://w3id.org/cwl/cwl#OutputParameter", "OutputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#OutputRecordField", "OutputRecordField"); - rvocab.put("https://w3id.org/cwl/cwl#OutputRecordSchema", "OutputRecordSchema"); - rvocab.put("https://w3id.org/cwl/cwl#OutputSchema", "OutputSchema"); - rvocab.put("https://w3id.org/cwl/cwl#Parameter", "Parameter"); - rvocab.put("https://w3id.org/cwl/salad#PrimitiveType", "PrimitiveType"); - rvocab.put("https://w3id.org/cwl/cwl#Process", "Process"); - rvocab.put("https://w3id.org/cwl/cwl#ProcessRequirement", "ProcessRequirement"); - rvocab.put("https://w3id.org/cwl/salad#RecordField", "RecordField"); - rvocab.put("https://w3id.org/cwl/salad#RecordSchema", "RecordSchema"); - rvocab.put("ResourceRequirement", "ResourceRequirement"); - rvocab.put("ScatterFeatureRequirement", "ScatterFeatureRequirement"); - rvocab.put("https://w3id.org/cwl/cwl#ScatterMethod", "ScatterMethod"); - rvocab.put("SchemaDefRequirement", "SchemaDefRequirement"); - rvocab.put("https://w3id.org/cwl/cwl#SecondaryFileSchema", "SecondaryFileSchema"); - rvocab.put("ShellCommandRequirement", "ShellCommandRequirement"); - rvocab.put("https://w3id.org/cwl/cwl#Sink", "Sink"); - rvocab.put("https://w3id.org/cwl/cwl#SoftwarePackage", "SoftwarePackage"); - rvocab.put("SoftwareRequirement", "SoftwareRequirement"); - rvocab.put("StepInputExpressionRequirement", "StepInputExpressionRequirement"); - rvocab.put("SubworkflowFeatureRequirement", "SubworkflowFeatureRequirement"); - rvocab.put("ToolTimeLimit", "ToolTimeLimit"); - rvocab.put("https://w3id.org/cwl/salad#UnionSchema", "UnionSchema"); - rvocab.put("WorkReuse", "WorkReuse"); - rvocab.put("Workflow", "Workflow"); - rvocab.put("https://w3id.org/cwl/cwl#WorkflowInputParameter", "WorkflowInputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#WorkflowOutputParameter", "WorkflowOutputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#WorkflowStep", "WorkflowStep"); - rvocab.put("https://w3id.org/cwl/cwl#WorkflowStepInput", "WorkflowStepInput"); - rvocab.put("https://w3id.org/cwl/cwl#WorkflowStepOutput", "WorkflowStepOutput"); - rvocab.put("array", "array"); - rvocab.put("http://www.w3.org/2001/XMLSchema#boolean", "boolean"); - rvocab.put("https://w3id.org/cwl/cwl#LoadListingEnum/deep_listing", "deep_listing"); - rvocab.put("https://w3id.org/cwl/cwl#ScatterMethod/dotproduct", "dotproduct"); - rvocab.put("http://www.w3.org/2001/XMLSchema#double", "double"); - rvocab.put("https://w3id.org/cwl/cwl#draft-2", "draft-2"); - rvocab.put("https://w3id.org/cwl/cwl#draft-3", "draft-3"); - rvocab.put("https://w3id.org/cwl/cwl#draft-3.dev1", "draft-3.dev1"); - rvocab.put("https://w3id.org/cwl/cwl#draft-3.dev2", "draft-3.dev2"); - rvocab.put("https://w3id.org/cwl/cwl#draft-3.dev3", "draft-3.dev3"); - rvocab.put("https://w3id.org/cwl/cwl#draft-3.dev4", "draft-3.dev4"); - rvocab.put("https://w3id.org/cwl/cwl#draft-3.dev5", "draft-3.dev5"); - rvocab.put("https://w3id.org/cwl/cwl#draft-4.dev1", "draft-4.dev1"); - rvocab.put("https://w3id.org/cwl/cwl#draft-4.dev2", "draft-4.dev2"); - rvocab.put("https://w3id.org/cwl/cwl#draft-4.dev3", "draft-4.dev3"); - rvocab.put("enum", "enum"); - rvocab.put("https://w3id.org/cwl/cwl#ScatterMethod/flat_crossproduct", "flat_crossproduct"); - rvocab.put("http://www.w3.org/2001/XMLSchema#float", "float"); - rvocab.put("http://www.w3.org/2001/XMLSchema#int", "int"); - rvocab.put("http://www.w3.org/2001/XMLSchema#long", "long"); - rvocab.put("map", "map"); - rvocab.put("https://w3id.org/cwl/cwl#LinkMergeMethod/merge_flattened", "merge_flattened"); - rvocab.put("https://w3id.org/cwl/cwl#LinkMergeMethod/merge_nested", "merge_nested"); - rvocab.put("https://w3id.org/cwl/cwl#ScatterMethod/nested_crossproduct", "nested_crossproduct"); - rvocab.put("https://w3id.org/cwl/cwl#LoadListingEnum/no_listing", "no_listing"); - rvocab.put("https://w3id.org/cwl/salad#null", "null"); - rvocab.put("record", "record"); - rvocab.put("https://w3id.org/cwl/cwl#LoadListingEnum/shallow_listing", "shallow_listing"); - rvocab.put("https://w3id.org/cwl/cwl#stderr", "stderr"); - rvocab.put("https://w3id.org/cwl/cwl#stdin", "stdin"); - rvocab.put("https://w3id.org/cwl/cwl#stdout", "stdout"); - rvocab.put("http://www.w3.org/2001/XMLSchema#string", "string"); - rvocab.put("union", "union"); - rvocab.put("https://w3id.org/cwl/cwl#v1.0", "v1.0"); - rvocab.put("https://w3id.org/cwl/cwl#v1.0.dev4", "v1.0.dev4"); - rvocab.put("https://w3id.org/cwl/cwl#v1.1", "v1.1"); - rvocab.put("https://w3id.org/cwl/cwl#v1.1.0-dev1", "v1.1.0-dev1"); - - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/DefaultFetcher.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/DefaultFetcher.java deleted file mode 100644 index 3c706d77..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/DefaultFetcher.java +++ /dev/null @@ -1,48 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.io.IOException; -import java.net.URI; -import java.util.Arrays; -import java.util.Scanner; - -public class DefaultFetcher implements Fetcher { - - public String urlJoin(final String baseUrl, final String url) { - if (url.startsWith("_:")) { - return url; - } - - final URI baseUri = Uris.toUri(baseUrl); - final URI uri = Uris.toUri(url); - if (baseUri.getScheme() != null - && !baseUri.getScheme().equals("file") - && "file".equals(uri.getScheme())) { - throw new ValidationException( - String.format( - "Not resolving potential remote exploit %s from base %s".format(url, baseUrl))); - } - String result = baseUri.resolve(uri).toString(); - if (result.startsWith("file:")) { - // Well this is gross - needed for http as well? - result = "file://" + result.substring("file:".length()); - } - return result; - } - - public String fetchText(final String url) { - final URI uri = Uris.toUri(url); - final String scheme = uri.getScheme(); - if (Arrays.asList("http", "https", "file").contains(scheme)) { - Scanner scanner; - try { - scanner = new Scanner(uri.toURL().openStream(), "UTF-8").useDelimiter("\\A"); - } catch (IOException e) { - throw new ValidationException("Error fetching %s: %s.".format(url, e)); - } - String result = scanner.next(); - scanner.close(); - return result; - } - throw new ValidationException("Unsupported scheme in URL: %s".format(url)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/EnumLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/EnumLoader.java deleted file mode 100644 index 524025b4..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/EnumLoader.java +++ /dev/null @@ -1,33 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.lang.reflect.Method; -import java.lang.ReflectiveOperationException; -import java.util.Arrays; -import java.util.List; - -public class EnumLoader implements Loader{ - private final Class symbolEnumClass; - - public EnumLoader(final Class symbolEnumClass) { - this.symbolEnumClass = symbolEnumClass; - } - - public T load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - final String docString = Loader.validateOfJavaType(String.class, doc); - try { - final Method m = symbolEnumClass.getMethod("fromDocumentVal", String.class); - final T val = (T) m.invoke(null, docString); - return val; - } catch (final ReflectiveOperationException e) { - final Throwable cause = e.getCause(); - if (cause instanceof RuntimeException) { - throw (RuntimeException) cause; - } - throw new RuntimeException(e); - } - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/ExpressionLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/ExpressionLoader.java deleted file mode 100644 index c30a127e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/ExpressionLoader.java +++ /dev/null @@ -1,19 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -public class ExpressionLoader implements Loader { - - public ExpressionLoader() { - } - - public String load( - final Object doc_, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - if (doc_ instanceof String) { - return (String) doc_; - } else { - throw new ValidationException("Expected a string."); - } - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Fetcher.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Fetcher.java deleted file mode 100644 index f21df68c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Fetcher.java +++ /dev/null @@ -1,8 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -public interface Fetcher { - - public abstract String urlJoin(final String baseUrl, final String url); - - public abstract String fetchText(final String url); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/IdMapLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/IdMapLoader.java deleted file mode 100644 index c9a163ca..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/IdMapLoader.java +++ /dev/null @@ -1,51 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.TreeSet; - -public class IdMapLoader implements Loader { - private final Loader innerLoader; - private final String mapSubject; - private final String mapPredicate; - - public IdMapLoader( - final Loader innerLoader, final String mapSubject, final String mapPredicate) { - this.innerLoader = innerLoader; - this.mapSubject = mapSubject; - this.mapPredicate = mapPredicate; - } - - public T load( - final Object doc_, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - Object doc = doc_; - if (doc instanceof Map) { - final Map docMap = (Map) doc; - final List asList = new ArrayList(); - for (final String key : docMap.keySet()) { - final Object el = docMap.get(key); - if (el instanceof Map) { - final Map v2 = new HashMap((Map) el); - v2.put(this.mapSubject, key); - asList.add(v2); - } else { - if (this.mapPredicate != null) { - final Map v3 = new HashMap(); - v3.put(this.mapPredicate, el); - v3.put(this.mapSubject, key); - asList.add(v3); - } else { - throw new ValidationException("No mapPredicate"); - } - } - } - doc = asList; - } - return this.innerLoader.load(doc, baseUri, loadingOptions); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Loader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Loader.java deleted file mode 100644 index 2e49adab..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Loader.java +++ /dev/null @@ -1,125 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -public interface Loader { - - T load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot); - - default T load(final Object doc, final String baseUri, final LoadingOptions loadingOptions) { - return load(doc, baseUri, loadingOptions, null); - } - - default T documentLoad( - final String doc, final String baseUri, final LoadingOptions loadingOptions) { - return load(doc, baseUri, loadingOptions); - } - - default T documentLoad( - final Map doc_, final String baseUri_, final LoadingOptions loadingOptions_) { - Map doc = doc_; - LoadingOptions loadingOptions = loadingOptions_; - if (doc.containsKey("$namespaces")) { - final Map namespaces = (Map) doc.get("$namespaces"); - loadingOptions = - new LoadingOptionsBuilder().copiedFrom(loadingOptions).setNamespaces(namespaces).build(); - doc = copyWithoutKey(doc, "$namespaces"); - } - String baseUri = baseUri_; - if (doc.containsKey("$base")) { - baseUri = (String) doc.get("$base"); - } - if (doc.containsKey("$graph")) { - return load(doc.get("$graph"), baseUri, loadingOptions); - } else { - return load(doc, baseUri, loadingOptions, baseUri); - } - } - - default T documentLoad( - final List doc, final String baseUri, final LoadingOptions loadingOptions) { - return load(doc, baseUri, loadingOptions); - } - - default T documentLoadByUrl(final String url, final LoadingOptions loadingOptions) { - if (loadingOptions.idx.containsKey(url)) { - Object result = loadingOptions.idx.get(url); - if (result instanceof String) { - return documentLoad((String) result, url, loadingOptions); - } else if (result instanceof Map) { - return documentLoad((Map) result, url, loadingOptions); - } - return load(result, url, loadingOptions); - } - - final String text = loadingOptions.fetcher.fetchText(url); - try { - Map resultMap = YamlUtils.mapFromString(text); - loadingOptions.idx.put(url, resultMap); - final LoadingOptionsBuilder urlLoadingOptions = - new LoadingOptionsBuilder().copiedFrom(loadingOptions).setFileUri(url); - return documentLoad(resultMap, url, urlLoadingOptions.build()); - } catch (ClassCastException e) { - List resultList = YamlUtils.listFromString(text); - loadingOptions.idx.put(url, resultList); - final LoadingOptionsBuilder urlLoadingOptions = - new LoadingOptionsBuilder().copiedFrom(loadingOptions).setFileUri(url); - return documentLoad(resultList, url, urlLoadingOptions.build()); - } - } - - default T loadField( - final Object val_, final String baseUri, final LoadingOptions loadingOptions) { - Object val = val_; - if (val instanceof Map) { - Map valMap = (Map) val; - if (valMap.containsKey("$import")) { - if (loadingOptions.fileUri == null) { - throw new ValidationException("Cannot load $import without fileuri"); - } - return documentLoadByUrl( - loadingOptions.fetcher.urlJoin(loadingOptions.fileUri, (String) valMap.get("$import")), - loadingOptions); - } else if (valMap.containsKey("$include")) { - if (loadingOptions.fileUri == null) { - throw new ValidationException("Cannot load $import without fileuri"); - } - val = - loadingOptions.fetcher.fetchText( - loadingOptions.fetcher.urlJoin( - loadingOptions.fileUri, (String) valMap.get("$include"))); - } - } - return load(val, baseUri, loadingOptions); - } - - default Map copyWithoutKey(final Map doc, final String key) { - final Map result = new HashMap(); - for (final Map.Entry entry : doc.entrySet()) { - if (!entry.getKey().equals(key)) { - result.put(entry.getKey(), entry.getValue()); - } - } - return result; - } - - static T validateOfJavaType(final Class clazz, final Object doc) { - if (!clazz.isInstance(doc)) { - String className = "null"; - if (doc != null) { - className = doc.getClass().getName(); - } - final String message = - String.format( - "Expected object with Java type of %s but got %s", clazz.getName(), className); - throw new ValidationException(message); - } - return (T) doc; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/LoaderInstances.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/LoaderInstances.java deleted file mode 100644 index f030f0c0..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/LoaderInstances.java +++ /dev/null @@ -1,319 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.List; -import org.commonwl.cwlsdk.cwl1_1.*; - -public class LoaderInstances { - public static Loader StringInstance = new PrimitiveLoader(String.class); - public static Loader IntegerInstance = new PrimitiveLoader(Integer.class); - public static Loader LongInstance = new PrimitiveLoader(Long.class); - public static Loader DoubleInstance = new PrimitiveLoader(Double.class); - public static Loader BooleanInstance = new PrimitiveLoader(Boolean.class); - public static Loader NullInstance = new NullLoader(); - public static Loader AnyInstance = new AnyLoader(); - public static Loader Documented = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.Documented.class, null, null); - public static Loader PrimitiveType = new EnumLoader(PrimitiveType.class); - public static Loader Any = new EnumLoader(Any.class); - public static Loader RecordField = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.RecordFieldImpl.class, null, null); - public static Loader RecordSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.RecordSchemaImpl.class, null, null); - public static Loader EnumSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.EnumSchemaImpl.class, null, null); - public static Loader ArraySchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.ArraySchemaImpl.class, null, null); - public static Loader MapSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.MapSchemaImpl.class, null, null); - public static Loader UnionSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.UnionSchemaImpl.class, null, null); - public static Loader CWLType = new EnumLoader(CWLType.class); - public static Loader CWLArraySchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CWLArraySchemaImpl.class, null, null); - public static Loader CWLRecordField = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CWLRecordFieldImpl.class, null, null); - public static Loader CWLRecordSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CWLRecordSchemaImpl.class, null, null); - public static Loader File = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.FileImpl.class, null, null); - public static Loader Directory = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.DirectoryImpl.class, null, null); - public static Loader CWLObjectType = new UnionLoader(new Loader[] {}); - public static Loader> optional_CWLObjectType = new OptionalLoader(CWLObjectType); - public static Loader>> array_of_optional_CWLObjectType = new ArrayLoader(optional_CWLObjectType); - public static Loader>> map_of_optional_CWLObjectType = new MapLoader(optional_CWLObjectType, null, null); - public static Loader InlineJavascriptRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.InlineJavascriptRequirementImpl.class, null, null); - public static Loader SchemaDefRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.SchemaDefRequirementImpl.class, null, null); - public static Loader LoadListingRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.LoadListingRequirementImpl.class, null, null); - public static Loader DockerRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.DockerRequirementImpl.class, null, null); - public static Loader SoftwareRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.SoftwareRequirementImpl.class, null, null); - public static Loader InitialWorkDirRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.InitialWorkDirRequirementImpl.class, null, null); - public static Loader EnvVarRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.EnvVarRequirementImpl.class, null, null); - public static Loader ShellCommandRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.ShellCommandRequirementImpl.class, null, null); - public static Loader ResourceRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.ResourceRequirementImpl.class, null, null); - public static Loader WorkReuse = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.WorkReuseImpl.class, null, null); - public static Loader NetworkAccess = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.NetworkAccessImpl.class, null, null); - public static Loader InplaceUpdateRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.InplaceUpdateRequirementImpl.class, null, null); - public static Loader ToolTimeLimit = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.ToolTimeLimitImpl.class, null, null); - public static Loader SubworkflowFeatureRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.SubworkflowFeatureRequirementImpl.class, null, null); - public static Loader ScatterFeatureRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.ScatterFeatureRequirementImpl.class, null, null); - public static Loader MultipleInputFeatureRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.MultipleInputFeatureRequirementImpl.class, null, null); - public static Loader StepInputExpressionRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.StepInputExpressionRequirementImpl.class, null, null); - public static Loader union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement = new UnionLoader(new Loader[] { InlineJavascriptRequirement, SchemaDefRequirement, LoadListingRequirement, DockerRequirement, SoftwareRequirement, InitialWorkDirRequirement, EnvVarRequirement, ShellCommandRequirement, ResourceRequirement, WorkReuse, NetworkAccess, InplaceUpdateRequirement, ToolTimeLimit, SubworkflowFeatureRequirement, ScatterFeatureRequirement, MultipleInputFeatureRequirement, StepInputExpressionRequirement }); - public static Loader> array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement = new ArrayLoader(union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement); - public static Loader union_of_NullInstance_or_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_CWLObjectType = new UnionLoader(new Loader[] { NullInstance, array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement, CWLObjectType }); - public static Loader> map_of_union_of_NullInstance_or_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_CWLObjectType = new MapLoader(union_of_NullInstance_or_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_CWLObjectType, "@list", true); - public static Loader CWLVersion = new EnumLoader(CWLVersion.class); - public static Loader Labeled = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.Labeled.class, null, null); - public static Loader Identified = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.Identified.class, null, null); - public static Loader LoadListingEnum = new EnumLoader(LoadListingEnum.class); - public static Loader LoadContents = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.LoadContents.class, null, null); - public static Loader FieldBase = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.FieldBase.class, null, null); - public static Loader InputFormat = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.InputFormat.class, null, null); - public static Loader OutputFormat = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.OutputFormat.class, null, null); - public static Loader Parameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.Parameter.class, null, null); - public static Loader Expression = new EnumLoader(Expression.class); - public static Loader InputBinding = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.InputBindingImpl.class, null, null); - public static Loader IOSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.IOSchema.class, null, null); - public static Loader InputSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.InputSchema.class, null, null); - public static Loader OutputSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.OutputSchema.class, null, null); - public static Loader InputRecordField = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.InputRecordFieldImpl.class, null, null); - public static Loader InputRecordSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.InputRecordSchemaImpl.class, null, null); - public static Loader InputEnumSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.InputEnumSchemaImpl.class, null, null); - public static Loader InputArraySchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.InputArraySchemaImpl.class, null, null); - public static Loader OutputRecordField = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.OutputRecordFieldImpl.class, null, null); - public static Loader OutputRecordSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.OutputRecordSchemaImpl.class, null, null); - public static Loader OutputEnumSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.OutputEnumSchemaImpl.class, null, null); - public static Loader OutputArraySchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.OutputArraySchemaImpl.class, null, null); - public static Loader InputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.InputParameter.class, null, null); - public static Loader OutputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.OutputParameter.class, null, null); - public static Loader ProcessRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.ProcessRequirement.class, null, null); - public static Loader Process = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.Process.class, null, null); - public static Loader CommandInputSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandInputSchema.class, null, null); - public static Loader SecondaryFileSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.SecondaryFileSchemaImpl.class, null, null); - public static Loader EnvironmentDef = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.EnvironmentDefImpl.class, null, null); - public static Loader CommandLineBinding = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandLineBindingImpl.class, null, null); - public static Loader CommandOutputBinding = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandOutputBindingImpl.class, null, null); - public static Loader CommandLineBindable = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandLineBindableImpl.class, null, null); - public static Loader CommandInputRecordField = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandInputRecordFieldImpl.class, null, null); - public static Loader CommandInputRecordSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandInputRecordSchemaImpl.class, null, null); - public static Loader CommandInputEnumSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandInputEnumSchemaImpl.class, null, null); - public static Loader CommandInputArraySchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandInputArraySchemaImpl.class, null, null); - public static Loader CommandOutputRecordField = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandOutputRecordFieldImpl.class, null, null); - public static Loader CommandOutputRecordSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandOutputRecordSchemaImpl.class, null, null); - public static Loader CommandOutputEnumSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandOutputEnumSchemaImpl.class, null, null); - public static Loader CommandOutputArraySchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandOutputArraySchemaImpl.class, null, null); - public static Loader CommandInputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandInputParameterImpl.class, null, null); - public static Loader CommandOutputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandOutputParameterImpl.class, null, null); - public static Loader stdin = new EnumLoader(stdin.class); - public static Loader stdout = new EnumLoader(stdout.class); - public static Loader stderr = new EnumLoader(stderr.class); - public static Loader CommandLineTool = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.CommandLineToolImpl.class, null, null); - public static Loader SoftwarePackage = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.SoftwarePackageImpl.class, null, null); - public static Loader Dirent = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.DirentImpl.class, null, null); - public static Loader ExpressionToolOutputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.ExpressionToolOutputParameterImpl.class, null, null); - public static Loader WorkflowInputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.WorkflowInputParameterImpl.class, null, null); - public static Loader ExpressionTool = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.ExpressionToolImpl.class, null, null); - public static Loader LinkMergeMethod = new EnumLoader(LinkMergeMethod.class); - public static Loader WorkflowOutputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.WorkflowOutputParameterImpl.class, null, null); - public static Loader Sink = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.Sink.class, null, null); - public static Loader WorkflowStepInput = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.WorkflowStepInputImpl.class, null, null); - public static Loader WorkflowStepOutput = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.WorkflowStepOutputImpl.class, null, null); - public static Loader ScatterMethod = new EnumLoader(ScatterMethod.class); - public static Loader WorkflowStep = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.WorkflowStepImpl.class, null, null); - public static Loader Workflow = new RecordLoader(org.commonwl.cwlsdk.cwl1_1.WorkflowImpl.class, null, null); - public static Loader> array_of_StringInstance = new ArrayLoader(StringInstance); - public static Loader union_of_NullInstance_or_StringInstance_or_array_of_StringInstance = new UnionLoader(new Loader[] { NullInstance, StringInstance, array_of_StringInstance }); - public static Loader uri_StringInstance_True_False_None_None = new UriLoader(StringInstance, true, false, null, null); - public static Loader union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance = new UnionLoader(new Loader[] { PrimitiveType, RecordSchema, EnumSchema, ArraySchema, MapSchema, UnionSchema, StringInstance }); - public static Loader> array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance = new ArrayLoader(union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance); - public static Loader union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance = new UnionLoader(new Loader[] { PrimitiveType, RecordSchema, EnumSchema, ArraySchema, MapSchema, UnionSchema, StringInstance, array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance }); - public static Loader typedsl_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_2 = new TypeDslLoader(union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance, 2); - public static Loader> array_of_RecordField = new ArrayLoader(RecordField); - public static Loader>> optional_array_of_RecordField = new OptionalLoader(array_of_RecordField); - public static Loader>> idmap_fields_optional_array_of_RecordField = new IdMapLoader(optional_array_of_RecordField, "name", "type"); - public static Loader Record_name = new EnumLoader(Record_name.class); - public static Loader typedsl_Record_name_2 = new TypeDslLoader(Record_name, 2); - public static Loader> optional_StringInstance = new OptionalLoader(StringInstance); - public static Loader> uri_optional_StringInstance_True_False_None_None = new UriLoader(optional_StringInstance, true, false, null, null); - public static Loader> uri_array_of_StringInstance_True_False_None_None = new UriLoader(array_of_StringInstance, true, false, null, null); - public static Loader Enum_name = new EnumLoader(Enum_name.class); - public static Loader typedsl_Enum_name_2 = new TypeDslLoader(Enum_name, 2); - public static Loader uri_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_False_True_2_None = new UriLoader(union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance, false, true, 2, null); - public static Loader Array_name = new EnumLoader(Array_name.class); - public static Loader typedsl_Array_name_2 = new TypeDslLoader(Array_name, 2); - public static Loader Map_name = new EnumLoader(Map_name.class); - public static Loader typedsl_Map_name_2 = new TypeDslLoader(Map_name, 2); - public static Loader Union_name = new EnumLoader(Union_name.class); - public static Loader typedsl_Union_name_2 = new TypeDslLoader(Union_name, 2); - public static Loader union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance = new UnionLoader(new Loader[] { PrimitiveType, CWLRecordSchema, EnumSchema, CWLArraySchema, StringInstance }); - public static Loader> array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance = new ArrayLoader(union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance); - public static Loader union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance = new UnionLoader(new Loader[] { PrimitiveType, CWLRecordSchema, EnumSchema, CWLArraySchema, StringInstance, array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance }); - public static Loader uri_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_False_True_2_None = new UriLoader(union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance, false, true, 2, null); - public static Loader typedsl_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance, 2); - public static Loader> array_of_CWLRecordField = new ArrayLoader(CWLRecordField); - public static Loader>> optional_array_of_CWLRecordField = new OptionalLoader(array_of_CWLRecordField); - public static Loader>> idmap_fields_optional_array_of_CWLRecordField = new IdMapLoader(optional_array_of_CWLRecordField, "name", "type"); - public static Loader File_class = new EnumLoader(File_class.class); - public static Loader uri_File_class_False_True_None_None = new UriLoader(File_class, false, true, null, null); - public static Loader> uri_optional_StringInstance_False_False_None_None = new UriLoader(optional_StringInstance, false, false, null, null); - public static Loader union_of_NullInstance_or_IntegerInstance_or_LongInstance = new UnionLoader(new Loader[] { NullInstance, IntegerInstance, LongInstance }); - public static Loader union_of_File_or_Directory = new UnionLoader(new Loader[] { File, Directory }); - public static Loader> array_of_union_of_File_or_Directory = new ArrayLoader(union_of_File_or_Directory); - public static Loader>> optional_array_of_union_of_File_or_Directory = new OptionalLoader(array_of_union_of_File_or_Directory); - public static Loader>> secondaryfilesdsl_optional_array_of_union_of_File_or_Directory = new SecondaryFilesDslLoader(optional_array_of_union_of_File_or_Directory); - public static Loader> uri_optional_StringInstance_True_False_None_True = new UriLoader(optional_StringInstance, true, false, null, true); - public static Loader Directory_class = new EnumLoader(Directory_class.class); - public static Loader uri_Directory_class_False_True_None_None = new UriLoader(Directory_class, false, true, null, null); - public static Loader> optional_BooleanInstance = new OptionalLoader(BooleanInstance); - public static Loader> optional_LoadListingEnum = new OptionalLoader(LoadListingEnum); - public static Loader> array_of_SecondaryFileSchema = new ArrayLoader(SecondaryFileSchema); - public static Loader union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema = new UnionLoader(new Loader[] { NullInstance, SecondaryFileSchema, array_of_SecondaryFileSchema }); - public static Loader secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema = new SecondaryFilesDslLoader(union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema); - public static Loader ExpressionLoader = new ExpressionLoader(); - public static Loader union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { NullInstance, StringInstance, array_of_StringInstance, ExpressionLoader }); - public static Loader uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader_True_False_None_True = new UriLoader(union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader, true, false, null, true); - public static Loader union_of_NullInstance_or_StringInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { NullInstance, StringInstance, ExpressionLoader }); - public static Loader uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True = new UriLoader(union_of_NullInstance_or_StringInstance_or_ExpressionLoader, true, false, null, true); - public static Loader union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, InputRecordSchema, InputEnumSchema, InputArraySchema, StringInstance }); - public static Loader> array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance = new ArrayLoader(union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance); - public static Loader union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, InputRecordSchema, InputEnumSchema, InputArraySchema, StringInstance, array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance }); - public static Loader typedsl_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance, 2); - public static Loader> array_of_InputRecordField = new ArrayLoader(InputRecordField); - public static Loader>> optional_array_of_InputRecordField = new OptionalLoader(array_of_InputRecordField); - public static Loader>> idmap_fields_optional_array_of_InputRecordField = new IdMapLoader(optional_array_of_InputRecordField, "name", "type"); - public static Loader uri_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_False_True_2_None = new UriLoader(union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance, false, true, 2, null); - public static Loader union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, OutputRecordSchema, OutputEnumSchema, OutputArraySchema, StringInstance }); - public static Loader> array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance = new ArrayLoader(union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance); - public static Loader union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, OutputRecordSchema, OutputEnumSchema, OutputArraySchema, StringInstance, array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance }); - public static Loader typedsl_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance, 2); - public static Loader> array_of_OutputRecordField = new ArrayLoader(OutputRecordField); - public static Loader>> optional_array_of_OutputRecordField = new OptionalLoader(array_of_OutputRecordField); - public static Loader>> idmap_fields_optional_array_of_OutputRecordField = new IdMapLoader(optional_array_of_OutputRecordField, "name", "type"); - public static Loader uri_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_False_True_2_None = new UriLoader(union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance, false, true, 2, null); - public static Loader union_of_CommandInputParameter_or_WorkflowInputParameter = new UnionLoader(new Loader[] { CommandInputParameter, WorkflowInputParameter }); - public static Loader> array_of_union_of_CommandInputParameter_or_WorkflowInputParameter = new ArrayLoader(union_of_CommandInputParameter_or_WorkflowInputParameter); - public static Loader> idmap_inputs_array_of_union_of_CommandInputParameter_or_WorkflowInputParameter = new IdMapLoader(array_of_union_of_CommandInputParameter_or_WorkflowInputParameter, "id", "type"); - public static Loader union_of_CommandOutputParameter_or_ExpressionToolOutputParameter_or_WorkflowOutputParameter = new UnionLoader(new Loader[] { CommandOutputParameter, ExpressionToolOutputParameter, WorkflowOutputParameter }); - public static Loader> array_of_union_of_CommandOutputParameter_or_ExpressionToolOutputParameter_or_WorkflowOutputParameter = new ArrayLoader(union_of_CommandOutputParameter_or_ExpressionToolOutputParameter_or_WorkflowOutputParameter); - public static Loader> idmap_outputs_array_of_union_of_CommandOutputParameter_or_ExpressionToolOutputParameter_or_WorkflowOutputParameter = new IdMapLoader(array_of_union_of_CommandOutputParameter_or_ExpressionToolOutputParameter_or_WorkflowOutputParameter, "id", "type"); - public static Loader>> optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement = new OptionalLoader(array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement); - public static Loader>> idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement = new IdMapLoader(optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement, "class", "None"); - public static Loader union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance = new UnionLoader(new Loader[] { InlineJavascriptRequirement, SchemaDefRequirement, LoadListingRequirement, DockerRequirement, SoftwareRequirement, InitialWorkDirRequirement, EnvVarRequirement, ShellCommandRequirement, ResourceRequirement, WorkReuse, NetworkAccess, InplaceUpdateRequirement, ToolTimeLimit, SubworkflowFeatureRequirement, ScatterFeatureRequirement, MultipleInputFeatureRequirement, StepInputExpressionRequirement, AnyInstance }); - public static Loader> array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance = new ArrayLoader(union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance); - public static Loader>> optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance = new OptionalLoader(array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance); - public static Loader>> idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance = new IdMapLoader(optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance, "class", "None"); - public static Loader> optional_CWLVersion = new OptionalLoader(CWLVersion); - public static Loader> uri_optional_CWLVersion_False_True_None_None = new UriLoader(optional_CWLVersion, false, true, null, null); - public static Loader InlineJavascriptRequirement_class = new EnumLoader(InlineJavascriptRequirement_class.class); - public static Loader uri_InlineJavascriptRequirement_class_False_True_None_None = new UriLoader(InlineJavascriptRequirement_class, false, true, null, null); - public static Loader>> optional_array_of_StringInstance = new OptionalLoader(array_of_StringInstance); - public static Loader SchemaDefRequirement_class = new EnumLoader(SchemaDefRequirement_class.class); - public static Loader uri_SchemaDefRequirement_class_False_True_None_None = new UriLoader(SchemaDefRequirement_class, false, true, null, null); - public static Loader union_of_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema = new UnionLoader(new Loader[] { CommandInputRecordSchema, CommandInputEnumSchema, CommandInputArraySchema }); - public static Loader> array_of_union_of_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema = new ArrayLoader(union_of_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema); - public static Loader union_of_StringInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { StringInstance, ExpressionLoader }); - public static Loader union_of_NullInstance_or_BooleanInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { NullInstance, BooleanInstance, ExpressionLoader }); - public static Loader LoadListingRequirement_class = new EnumLoader(LoadListingRequirement_class.class); - public static Loader uri_LoadListingRequirement_class_False_True_None_None = new UriLoader(LoadListingRequirement_class, false, true, null, null); - public static Loader union_of_NullInstance_or_IntegerInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { NullInstance, IntegerInstance, ExpressionLoader }); - public static Loader union_of_NullInstance_or_StringInstance_or_ExpressionLoader_or_array_of_StringInstance = new UnionLoader(new Loader[] { NullInstance, StringInstance, ExpressionLoader, array_of_StringInstance }); - public static Loader> optional_ExpressionLoader = new OptionalLoader(ExpressionLoader); - public static Loader> optional_CommandLineBinding = new OptionalLoader(CommandLineBinding); - public static Loader union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, CommandInputRecordSchema, CommandInputEnumSchema, CommandInputArraySchema, StringInstance }); - public static Loader> array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance = new ArrayLoader(union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance); - public static Loader union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, CommandInputRecordSchema, CommandInputEnumSchema, CommandInputArraySchema, StringInstance, array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance }); - public static Loader typedsl_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance, 2); - public static Loader> array_of_CommandInputRecordField = new ArrayLoader(CommandInputRecordField); - public static Loader>> optional_array_of_CommandInputRecordField = new OptionalLoader(array_of_CommandInputRecordField); - public static Loader>> idmap_fields_optional_array_of_CommandInputRecordField = new IdMapLoader(optional_array_of_CommandInputRecordField, "name", "type"); - public static Loader uri_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_False_True_2_None = new UriLoader(union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance, false, true, 2, null); - public static Loader union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, CommandOutputRecordSchema, CommandOutputEnumSchema, CommandOutputArraySchema, StringInstance }); - public static Loader> array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance = new ArrayLoader(union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance); - public static Loader union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, CommandOutputRecordSchema, CommandOutputEnumSchema, CommandOutputArraySchema, StringInstance, array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance }); - public static Loader typedsl_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance, 2); - public static Loader> optional_CommandOutputBinding = new OptionalLoader(CommandOutputBinding); - public static Loader> array_of_CommandOutputRecordField = new ArrayLoader(CommandOutputRecordField); - public static Loader>> optional_array_of_CommandOutputRecordField = new OptionalLoader(array_of_CommandOutputRecordField); - public static Loader>> idmap_fields_optional_array_of_CommandOutputRecordField = new IdMapLoader(optional_array_of_CommandOutputRecordField, "name", "type"); - public static Loader uri_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_False_True_2_None = new UriLoader(union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance, false, true, 2, null); - public static Loader union_of_CWLType_or_stdin_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, stdin, CommandInputRecordSchema, CommandInputEnumSchema, CommandInputArraySchema, StringInstance, array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance }); - public static Loader typedsl_union_of_CWLType_or_stdin_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_CWLType_or_stdin_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance, 2); - public static Loader union_of_CWLType_or_stdout_or_stderr_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, stdout, stderr, CommandOutputRecordSchema, CommandOutputEnumSchema, CommandOutputArraySchema, StringInstance, array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance }); - public static Loader typedsl_union_of_CWLType_or_stdout_or_stderr_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_CWLType_or_stdout_or_stderr_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance, 2); - public static Loader CommandLineTool_class = new EnumLoader(CommandLineTool_class.class); - public static Loader uri_CommandLineTool_class_False_True_None_None = new UriLoader(CommandLineTool_class, false, true, null, null); - public static Loader> array_of_CommandInputParameter = new ArrayLoader(CommandInputParameter); - public static Loader> idmap_inputs_array_of_CommandInputParameter = new IdMapLoader(array_of_CommandInputParameter, "id", "type"); - public static Loader> array_of_CommandOutputParameter = new ArrayLoader(CommandOutputParameter); - public static Loader> idmap_outputs_array_of_CommandOutputParameter = new IdMapLoader(array_of_CommandOutputParameter, "id", "type"); - public static Loader union_of_StringInstance_or_ExpressionLoader_or_CommandLineBinding = new UnionLoader(new Loader[] { StringInstance, ExpressionLoader, CommandLineBinding }); - public static Loader> array_of_union_of_StringInstance_or_ExpressionLoader_or_CommandLineBinding = new ArrayLoader(union_of_StringInstance_or_ExpressionLoader_or_CommandLineBinding); - public static Loader>> optional_array_of_union_of_StringInstance_or_ExpressionLoader_or_CommandLineBinding = new OptionalLoader(array_of_union_of_StringInstance_or_ExpressionLoader_or_CommandLineBinding); - public static Loader> array_of_IntegerInstance = new ArrayLoader(IntegerInstance); - public static Loader>> optional_array_of_IntegerInstance = new OptionalLoader(array_of_IntegerInstance); - public static Loader DockerRequirement_class = new EnumLoader(DockerRequirement_class.class); - public static Loader uri_DockerRequirement_class_False_True_None_None = new UriLoader(DockerRequirement_class, false, true, null, null); - public static Loader SoftwareRequirement_class = new EnumLoader(SoftwareRequirement_class.class); - public static Loader uri_SoftwareRequirement_class_False_True_None_None = new UriLoader(SoftwareRequirement_class, false, true, null, null); - public static Loader> array_of_SoftwarePackage = new ArrayLoader(SoftwarePackage); - public static Loader> idmap_packages_array_of_SoftwarePackage = new IdMapLoader(array_of_SoftwarePackage, "package", "specs"); - public static Loader>> uri_optional_array_of_StringInstance_False_False_None_True = new UriLoader(optional_array_of_StringInstance, false, false, null, true); - public static Loader InitialWorkDirRequirement_class = new EnumLoader(InitialWorkDirRequirement_class.class); - public static Loader uri_InitialWorkDirRequirement_class_False_True_None_None = new UriLoader(InitialWorkDirRequirement_class, false, true, null, null); - public static Loader union_of_NullInstance_or_File_or_array_of_union_of_File_or_Directory_or_Directory_or_Dirent_or_ExpressionLoader = new UnionLoader(new Loader[] { NullInstance, File, array_of_union_of_File_or_Directory, Directory, Dirent, ExpressionLoader }); - public static Loader> array_of_union_of_NullInstance_or_File_or_array_of_union_of_File_or_Directory_or_Directory_or_Dirent_or_ExpressionLoader = new ArrayLoader(union_of_NullInstance_or_File_or_array_of_union_of_File_or_Directory_or_Directory_or_Dirent_or_ExpressionLoader); - public static Loader union_of_array_of_union_of_NullInstance_or_File_or_array_of_union_of_File_or_Directory_or_Directory_or_Dirent_or_ExpressionLoader_or_ExpressionLoader = new UnionLoader(new Loader[] { array_of_union_of_NullInstance_or_File_or_array_of_union_of_File_or_Directory_or_Directory_or_Dirent_or_ExpressionLoader, ExpressionLoader }); - public static Loader EnvVarRequirement_class = new EnumLoader(EnvVarRequirement_class.class); - public static Loader uri_EnvVarRequirement_class_False_True_None_None = new UriLoader(EnvVarRequirement_class, false, true, null, null); - public static Loader> array_of_EnvironmentDef = new ArrayLoader(EnvironmentDef); - public static Loader> idmap_envDef_array_of_EnvironmentDef = new IdMapLoader(array_of_EnvironmentDef, "envName", "envValue"); - public static Loader ShellCommandRequirement_class = new EnumLoader(ShellCommandRequirement_class.class); - public static Loader uri_ShellCommandRequirement_class_False_True_None_None = new UriLoader(ShellCommandRequirement_class, false, true, null, null); - public static Loader ResourceRequirement_class = new EnumLoader(ResourceRequirement_class.class); - public static Loader uri_ResourceRequirement_class_False_True_None_None = new UriLoader(ResourceRequirement_class, false, true, null, null); - public static Loader union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { NullInstance, IntegerInstance, LongInstance, ExpressionLoader }); - public static Loader WorkReuse_class = new EnumLoader(WorkReuse_class.class); - public static Loader uri_WorkReuse_class_False_True_None_None = new UriLoader(WorkReuse_class, false, true, null, null); - public static Loader union_of_BooleanInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { BooleanInstance, ExpressionLoader }); - public static Loader NetworkAccess_class = new EnumLoader(NetworkAccess_class.class); - public static Loader uri_NetworkAccess_class_False_True_None_None = new UriLoader(NetworkAccess_class, false, true, null, null); - public static Loader InplaceUpdateRequirement_class = new EnumLoader(InplaceUpdateRequirement_class.class); - public static Loader uri_InplaceUpdateRequirement_class_False_True_None_None = new UriLoader(InplaceUpdateRequirement_class, false, true, null, null); - public static Loader ToolTimeLimit_class = new EnumLoader(ToolTimeLimit_class.class); - public static Loader uri_ToolTimeLimit_class_False_True_None_None = new UriLoader(ToolTimeLimit_class, false, true, null, null); - public static Loader union_of_IntegerInstance_or_LongInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { IntegerInstance, LongInstance, ExpressionLoader }); - public static Loader> optional_InputBinding = new OptionalLoader(InputBinding); - public static Loader ExpressionTool_class = new EnumLoader(ExpressionTool_class.class); - public static Loader uri_ExpressionTool_class_False_True_None_None = new UriLoader(ExpressionTool_class, false, true, null, null); - public static Loader> array_of_WorkflowInputParameter = new ArrayLoader(WorkflowInputParameter); - public static Loader> idmap_inputs_array_of_WorkflowInputParameter = new IdMapLoader(array_of_WorkflowInputParameter, "id", "type"); - public static Loader> array_of_ExpressionToolOutputParameter = new ArrayLoader(ExpressionToolOutputParameter); - public static Loader> idmap_outputs_array_of_ExpressionToolOutputParameter = new IdMapLoader(array_of_ExpressionToolOutputParameter, "id", "type"); - public static Loader uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_1_None = new UriLoader(union_of_NullInstance_or_StringInstance_or_array_of_StringInstance, false, false, 1, null); - public static Loader> optional_LinkMergeMethod = new OptionalLoader(LinkMergeMethod); - public static Loader uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_2_None = new UriLoader(union_of_NullInstance_or_StringInstance_or_array_of_StringInstance, false, false, 2, null); - public static Loader> array_of_WorkflowStepInput = new ArrayLoader(WorkflowStepInput); - public static Loader> idmap_in_array_of_WorkflowStepInput = new IdMapLoader(array_of_WorkflowStepInput, "id", "source"); - public static Loader union_of_StringInstance_or_WorkflowStepOutput = new UnionLoader(new Loader[] { StringInstance, WorkflowStepOutput }); - public static Loader> array_of_union_of_StringInstance_or_WorkflowStepOutput = new ArrayLoader(union_of_StringInstance_or_WorkflowStepOutput); - public static Loader> uri_array_of_union_of_StringInstance_or_WorkflowStepOutput_True_False_None_None = new UriLoader(array_of_union_of_StringInstance_or_WorkflowStepOutput, true, false, null, null); - public static Loader> array_of_AnyInstance = new ArrayLoader(AnyInstance); - public static Loader>> optional_array_of_AnyInstance = new OptionalLoader(array_of_AnyInstance); - public static Loader>> idmap_hints_optional_array_of_AnyInstance = new IdMapLoader(optional_array_of_AnyInstance, "class", "None"); - public static Loader union_of_StringInstance_or_CommandLineTool_or_ExpressionTool_or_Workflow = new UnionLoader(new Loader[] { StringInstance, CommandLineTool, ExpressionTool, Workflow }); - public static Loader uri_union_of_StringInstance_or_CommandLineTool_or_ExpressionTool_or_Workflow_False_False_None_None = new UriLoader(union_of_StringInstance_or_CommandLineTool_or_ExpressionTool_or_Workflow, false, false, null, null); - public static Loader uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_0_None = new UriLoader(union_of_NullInstance_or_StringInstance_or_array_of_StringInstance, false, false, 0, null); - public static Loader> optional_ScatterMethod = new OptionalLoader(ScatterMethod); - public static Loader> uri_optional_ScatterMethod_False_True_None_None = new UriLoader(optional_ScatterMethod, false, true, null, null); - public static Loader Workflow_class = new EnumLoader(Workflow_class.class); - public static Loader uri_Workflow_class_False_True_None_None = new UriLoader(Workflow_class, false, true, null, null); - public static Loader> array_of_WorkflowOutputParameter = new ArrayLoader(WorkflowOutputParameter); - public static Loader> idmap_outputs_array_of_WorkflowOutputParameter = new IdMapLoader(array_of_WorkflowOutputParameter, "id", "type"); - public static Loader> array_of_WorkflowStep = new ArrayLoader(WorkflowStep); - public static Loader> idmap_steps_array_of_WorkflowStep = new IdMapLoader(array_of_WorkflowStep, "id", "None"); - public static Loader SubworkflowFeatureRequirement_class = new EnumLoader(SubworkflowFeatureRequirement_class.class); - public static Loader uri_SubworkflowFeatureRequirement_class_False_True_None_None = new UriLoader(SubworkflowFeatureRequirement_class, false, true, null, null); - public static Loader ScatterFeatureRequirement_class = new EnumLoader(ScatterFeatureRequirement_class.class); - public static Loader uri_ScatterFeatureRequirement_class_False_True_None_None = new UriLoader(ScatterFeatureRequirement_class, false, true, null, null); - public static Loader MultipleInputFeatureRequirement_class = new EnumLoader(MultipleInputFeatureRequirement_class.class); - public static Loader uri_MultipleInputFeatureRequirement_class_False_True_None_None = new UriLoader(MultipleInputFeatureRequirement_class, false, true, null, null); - public static Loader StepInputExpressionRequirement_class = new EnumLoader(StepInputExpressionRequirement_class.class); - public static Loader uri_StepInputExpressionRequirement_class_False_True_None_None = new UriLoader(StepInputExpressionRequirement_class, false, true, null, null); - public static Loader union_of_CommandLineTool_or_ExpressionTool_or_Workflow = new UnionLoader(new Loader[] { CommandLineTool, ExpressionTool, Workflow }); - public static Loader> array_of_union_of_CommandLineTool_or_ExpressionTool_or_Workflow = new ArrayLoader(union_of_CommandLineTool_or_ExpressionTool_or_Workflow); - public static Loader union_of_CommandLineTool_or_ExpressionTool_or_Workflow_or_array_of_union_of_CommandLineTool_or_ExpressionTool_or_Workflow = new UnionLoader(new Loader[] { CommandLineTool, ExpressionTool, Workflow, array_of_union_of_CommandLineTool_or_ExpressionTool_or_Workflow }); - - static { - ((UnionLoader) CWLObjectType).addLoaders(new Loader[] { BooleanInstance, IntegerInstance, LongInstance, DoubleInstance, DoubleInstance, StringInstance, File, Directory, array_of_optional_CWLObjectType, map_of_optional_CWLObjectType }); - } - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/LoadingOptions.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/LoadingOptions.java deleted file mode 100644 index 28642a6d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/LoadingOptions.java +++ /dev/null @@ -1,129 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.net.URI; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Map; - -public class LoadingOptions { - Fetcher fetcher; - String fileUri; - Map namespaces; - List schemas; - Boolean noLinkCheck; - String container; - Map idx; - Map vocab; - Map rvocab; - - LoadingOptions( - final Fetcher fetcher, - final String fileUri, - final Map namespaces, - final List schemas, - final Boolean noLinkCheck, - final String container, - final Map idx) { - this.fetcher = fetcher; - this.fileUri = fileUri; - this.namespaces = namespaces; - this.schemas = schemas; - this.noLinkCheck = noLinkCheck; - this.container = container; - this.idx = idx; - - if (namespaces != null) { - this.vocab = (Map) ConstantMaps.vocab.clone(); - this.rvocab = (Map) ConstantMaps.rvocab.clone(); - for (Map.Entry namespaceEntry : namespaces.entrySet()) { - this.vocab.put(namespaceEntry.getKey(), namespaceEntry.getValue()); - this.rvocab.put(namespaceEntry.getValue(), namespaceEntry.getKey()); - } - } else { - this.vocab = (Map) ConstantMaps.vocab; - this.rvocab = (Map) ConstantMaps.rvocab; - } - } - - public String expandUrl( - String url_, - final String baseUrl, - final boolean scopedId, - final boolean vocabTerm, - final Integer scopedRef) { - // NOT CONVERTING this - doesn't match type declaration - // if not isinstance(url, str): - // return url - String url = url_; - if (url.equals("@id") || url.equals("@type")) { - return url; - } - - if (vocabTerm && this.vocab.containsKey(url)) { - return url; - } - - if (!this.vocab.isEmpty() && url.contains(":")) { - String prefix = url.split(":")[0]; - if (this.vocab.containsKey(prefix)) { - url = this.vocab.get(prefix) + url.substring(prefix.length() + 1); - } - } - - Uris.UriSplit split = Uris.split(url); - final String scheme = split.scheme; - final boolean hasFragment = stringHasContent(split.fragment); - if (scheme != null - && ((scheme.length() > 0 - && (scheme.equals("http") || scheme.equals("https") || scheme.equals("file"))) - || url.startsWith("$(") - || url.startsWith("${"))) { - // pass - } else if (scopedId && !hasFragment) { - final Uris.UriSplit splitbase = Uris.split(baseUrl); - final String frg; - if (stringHasContent(splitbase.fragment)) { - frg = splitbase.fragment + "/" + split.path; - } else { - frg = split.path; - } - String pt; - if (!splitbase.path.equals("")) { - pt = splitbase.path; - } else { - pt = "/"; - } - url = Uris.unsplit(splitbase.scheme, splitbase.netloc, pt, splitbase.query, frg); - } else if (scopedRef != null && !hasFragment) { - final Uris.UriSplit splitbase = Uris.split(baseUrl); - final ArrayList sp = new ArrayList(Arrays.asList(splitbase.fragment.split("/"))); - int n = scopedRef; - while (n > 0 && sp.size() > 0) { - sp.remove(sp.size()-1); - n -= 1; - } - sp.add(url); - final String fragment = String.join("/", sp); - url = Uris.unsplit(splitbase.scheme, splitbase.netloc, splitbase.path, splitbase.query, fragment); - } else { - url = this.fetcher.urlJoin(baseUrl, url); - } - - if (vocabTerm) { - split = Uris.split(url); - if (stringHasContent(split.scheme)) { - if (this.rvocab.containsKey(url)) { - return this.rvocab.get(url); - } - } else { - throw new ValidationException("Term '{}' not in vocabulary".format(url)); - } - } - return url; - } - - static boolean stringHasContent(final String s) { - return s != null && s.length() > 0; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/LoadingOptionsBuilder.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/LoadingOptionsBuilder.java deleted file mode 100644 index a8a20f8a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/LoadingOptionsBuilder.java +++ /dev/null @@ -1,82 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Optional; - -public class LoadingOptionsBuilder { - private Optional fetcher = Optional.empty(); - private Optional fileUri = Optional.empty(); - private Optional> namespaces = Optional.empty(); - private Optional> schemas = Optional.empty(); - private Optional copyFrom = Optional.empty(); - private Optional noLinkCheck = Optional.empty(); - private Optional container = Optional.empty(); - - public LoadingOptionsBuilder() {} - - public LoadingOptionsBuilder setFetcher(final Fetcher fetcher) { - this.fetcher = Optional.of(fetcher); - return this; - } - - public LoadingOptionsBuilder copiedFrom(final LoadingOptions copyFrom) { - this.copyFrom = Optional.of(copyFrom); - return this; - } - - public LoadingOptionsBuilder setFileUri(final String fileUri) { - this.fileUri = Optional.of(fileUri); - return this; - } - - public LoadingOptionsBuilder setNamespaces(final Map namespaces) { - this.namespaces = Optional.of(namespaces); - return this; - } - - public LoadingOptionsBuilder setNoLinkCheck(final Boolean noLinkCheck) { - this.noLinkCheck = Optional.of(noLinkCheck); - return this; - } - - public LoadingOptionsBuilder setContainer(final String container) { - this.container = Optional.of(container); - return this; - } - - public LoadingOptions build() { - Fetcher fetcher = this.fetcher.orElse(null); - String fileUri = this.fileUri.orElse(null); - List schemas = this.schemas.orElse(null); - Map namespaces = this.namespaces.orElse(null); - Boolean noLinkCheck = this.noLinkCheck.orElse(null); - String container = this.container.orElse(null); - Map idx = new HashMap(); - if (this.copyFrom.isPresent()) { - final LoadingOptions copyFrom = this.copyFrom.get(); - idx = copyFrom.idx; - if (fetcher == null) { - fetcher = copyFrom.fetcher; - } - if (fileUri == null) { - fileUri = copyFrom.fileUri; - } - if (namespaces == null) { - namespaces = copyFrom.namespaces; - schemas = copyFrom.schemas; // Bug in Python codegen? - } - if (noLinkCheck == null) { - noLinkCheck = copyFrom.noLinkCheck; - } - if (container == null) { - container = copyFrom.container; - } - } - if (fetcher == null) { - fetcher = new DefaultFetcher(); - } - return new LoadingOptions(fetcher, fileUri, namespaces, schemas, noLinkCheck, container, idx); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/MapLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/MapLoader.java deleted file mode 100644 index 05a4901f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/MapLoader.java +++ /dev/null @@ -1,51 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -public class MapLoader implements Loader> { - private final Loader valueLoader; - private final String container; - private final Boolean noLinkCheck; - - public MapLoader(Loader valueLoader, final String container, final Boolean noLinkCheck) { - this.valueLoader = valueLoader; - this.container = container; - this.noLinkCheck = noLinkCheck; - } - - public Map load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - final Map docMap = (Map) Loader.validateOfJavaType(Map.class, doc); - LoadingOptions innerLoadingOptions = loadingOptions; - if (this.container != null || this.noLinkCheck != null) { - LoadingOptionsBuilder builder = new LoadingOptionsBuilder().copiedFrom(loadingOptions); - if (this.container != null) { - builder.setContainer(this.container); - } - if (this.noLinkCheck != null) { - builder.setNoLinkCheck(this.noLinkCheck); - } - innerLoadingOptions = builder.build(); - } - final Map r = new HashMap(); - final List errors = new ArrayList(); - for (final Map.Entry entry : docMap.entrySet()) { - try { - final Object loadedField = this.valueLoader.loadField(entry.getValue(), baseUri, innerLoadingOptions); - r.put(entry.getKey(), (T) loadedField); - } catch (final ValidationException e) { - errors.add(e); - } - } - if (!errors.isEmpty()) { - throw new ValidationException("", errors); - } - return r; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/NullLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/NullLoader.java deleted file mode 100644 index 24cd8ae7..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/NullLoader.java +++ /dev/null @@ -1,15 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -public class NullLoader implements Loader { - - public Object load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - if (doc != null) { - throw new ValidationException("Expected null"); - } - return doc; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/OneOrListOf.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/OneOrListOf.java deleted file mode 100644 index 90d6d46e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/OneOrListOf.java +++ /dev/null @@ -1,48 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.List; -import java.util.Optional; - -public class OneOrListOf { - private Optional object; - private Optional> objects; - - private OneOrListOf(final T object, final List objects) { - this.object = Optional.ofNullable(object); - this.objects = Optional.ofNullable(objects); - } - - public static OneOrListOf oneOf(T object) { - return new OneOrListOf(object, null); - } - - public static OneOrListOf listOf(List objects) { - assert objects != null; - return new OneOrListOf(null, objects); - } - - public boolean isOne() { - return this.getOneOptional().isPresent(); - } - - public boolean isList() { - return this.getListOptional().isPresent(); - } - - public Optional getOneOptional() { - return this.object; - } - - public Optional> getListOptional() { - return this.objects; - } - - public T getOne() { - return this.getOneOptional().get(); - } - - public List getList() { - return this.getListOptional().get(); - } - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/OneOrListOfLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/OneOrListOfLoader.java deleted file mode 100644 index 9ef54778..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/OneOrListOfLoader.java +++ /dev/null @@ -1,35 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.ArrayList; -import java.util.List; -import java.util.Optional; - - -public class OneOrListOfLoader implements Loader> { - private final Loader oneLoader; - private final Loader> listLoader; - - public OneOrListOfLoader(Loader oneLoader, Loader> listLoader) { - this.oneLoader = oneLoader; - this.listLoader = listLoader; - } - - public OneOrListOf load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - final List errors = new ArrayList(); - try { - return OneOrListOf.oneOf(this.oneLoader.load(doc, baseUri, loadingOptions, docRoot)); - } catch (ValidationException e) { - errors.add(e); - } - try { - return OneOrListOf.listOf(this.listLoader.load(doc, baseUri, loadingOptions, docRoot)); - } catch (ValidationException e) { - errors.add(e); - } - throw new ValidationException("Failed to one or list of of type", errors); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/OptionalLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/OptionalLoader.java deleted file mode 100644 index 347d171e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/OptionalLoader.java +++ /dev/null @@ -1,23 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.Optional; - - -public class OptionalLoader implements Loader> { - private final Loader itemLoader; - - public OptionalLoader(Loader itemLoader) { - this.itemLoader = itemLoader; - } - - public Optional load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - if(doc == null) { - return Optional.empty(); - } - return Optional.of(itemLoader.load(doc, baseUri, loadingOptions, docRoot)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/PrimitiveLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/PrimitiveLoader.java deleted file mode 100644 index 108b9756..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/PrimitiveLoader.java +++ /dev/null @@ -1,17 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -public class PrimitiveLoader implements Loader { - private Class clazz; - - public PrimitiveLoader(Class clazz) { - this.clazz = clazz; - } - - public T load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - return Loader.validateOfJavaType(this.clazz, doc); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/RecordLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/RecordLoader.java deleted file mode 100644 index 7cc2184e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/RecordLoader.java +++ /dev/null @@ -1,51 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.lang.reflect.Constructor; -import java.lang.reflect.InvocationTargetException; - -public class RecordLoader implements Loader { - private final Class saveableClass; - private final String container; - private final Boolean noLinkCheck; - - public RecordLoader(final Class saveableClass, final String container, final Boolean noLinkCheck) { - this.saveableClass = saveableClass; - this.container = container; - this.noLinkCheck = noLinkCheck; - } - - public T load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - Loader.validateOfJavaType(java.util.Map.class, doc); - try { - final Constructor constructor = - this.saveableClass.getConstructor( - new Class[] {Object.class, String.class, LoadingOptions.class, String.class}); - LoadingOptions innerLoadingOptions = loadingOptions; - if (this.container != null || this.noLinkCheck != null) { - LoadingOptionsBuilder builder = new LoadingOptionsBuilder().copiedFrom(loadingOptions); - if (this.container != null) { - builder.setContainer(this.container); - } - if (this.noLinkCheck != null) { - builder.setNoLinkCheck(this.noLinkCheck); - } - innerLoadingOptions = builder.build(); - } - final T ret = constructor.newInstance(doc, baseUri, innerLoadingOptions, docRoot); - return ret; - } catch (InvocationTargetException e) { - final Throwable cause = e.getCause(); - if (cause instanceof RuntimeException) { - throw (RuntimeException) cause; - } - throw new RuntimeException(e.getCause()); - } catch (ReflectiveOperationException e) { - throw new RuntimeException(e); - } - } - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/RootLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/RootLoader.java deleted file mode 100644 index 2bdc5bba..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/RootLoader.java +++ /dev/null @@ -1,105 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.io.File; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.Map; - -public class RootLoader { - public static Object loadDocument( - final Map doc, final String baseUri_, final LoadingOptions loadingOptions_) { - final String baseUri = ensureBaseUri(baseUri_); - LoadingOptions loadingOptions = loadingOptions_; - if (loadingOptions == null) { - loadingOptions = new LoadingOptionsBuilder().setFileUri(baseUri).build(); - } - return LoaderInstances.union_of_CommandLineTool_or_ExpressionTool_or_Workflow_or_array_of_union_of_CommandLineTool_or_ExpressionTool_or_Workflow.documentLoad(doc, baseUri, loadingOptions); - } - - public static Object loadDocument( - final Map doc, final String baseUri) { - return loadDocument(doc, baseUri, null); - } - - public static Object loadDocument(final Map doc) { - return loadDocument(doc, ensureBaseUri(null)); - } - - public static Object loadDocument(final Path path) { - return loadDocument(readPath(path), path.toUri().toString()); - } - - public static Object loadDocument(final Path path, String baseUri) { - return loadDocument(readPath(path), baseUri); - } - - public static Object loadDocument( - final Path path, LoadingOptions loadingOptions) { - return loadDocument(readPath(path), loadingOptions); - } - - public static Object loadDocument( -final Path path, String baseUri, LoadingOptions loadingOptions) { - return loadDocument(readPath(path), baseUri, loadingOptions); - } - - public static Object loadDocument(final File file) { - return loadDocument(file.toPath()); - } - - public static Object loadDocument(final File file, String baseUri) { - return loadDocument(file.toPath(), baseUri); - } - - public static Object loadDocument(final File file, LoadingOptions loadingOptions) { - return loadDocument(file.toPath(), loadingOptions); - } - - public static Object loadDocument( - final File file, String baseUri, LoadingOptions loadingOptions) { - return loadDocument(file.toPath(), baseUri, loadingOptions); - } - - public static Object loadDocument(final String doc) { - return loadDocument(doc, ensureBaseUri(null)); - } - - public static Object loadDocument(final String doc, final LoadingOptions loadingOptions) { - return loadDocument(doc, ensureBaseUri(null), loadingOptions); - } - - public static Object loadDocument(final String doc, final String uri) { - return loadDocument(doc, uri, null); - } - - public static Object loadDocument( - final String doc, final String uri_, final LoadingOptions loadingOptions_) { - final String uri = ensureBaseUri(uri_); - LoadingOptions loadingOptions = loadingOptions_; - if (loadingOptions == null) { - loadingOptions = new LoadingOptionsBuilder().setFileUri(uri).build(); - } - final Map result = YamlUtils.mapFromString(doc); - loadingOptions.idx.put(uri, result); - return loadDocument(result, uri, loadingOptions); - } - - static String readPath(final Path path) { - try { - return new String(Files.readAllBytes(path), "UTF8"); - } catch (final IOException e) { - throw new RuntimeException(e); - } - } - - static String ensureBaseUri(final String baseUri_) { - String baseUri = baseUri_; - if(baseUri == null) { - baseUri = Uris.fileUri(Paths.get(".").toAbsolutePath().normalize().toString()) + "/"; - } - return baseUri; - } - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Saveable.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Saveable.java deleted file mode 100644 index e25365c9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Saveable.java +++ /dev/null @@ -1,6 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -public interface Saveable { - // TODO: implement writable interface - // public abstract void save(boolean top, String baseUrl, boolean relativeUris); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/SaveableImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/SaveableImpl.java deleted file mode 100644 index 24361e62..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/SaveableImpl.java +++ /dev/null @@ -1,5 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -public class SaveableImpl implements Saveable { - public SaveableImpl(Object doc, String baseUri, LoadingOptions loadingOptions, String docRoot) {} -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/SecondaryFilesDslLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/SecondaryFilesDslLoader.java deleted file mode 100644 index 0837f62c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/SecondaryFilesDslLoader.java +++ /dev/null @@ -1,86 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -public class SecondaryFilesDslLoader implements Loader { - private final Loader innerLoader; - - public SecondaryFilesDslLoader(final Loader innerLoader) { - this.innerLoader = innerLoader; - } - - - public T load( - final Object doc_, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - Object doc = doc_; - List> r = new ArrayList>(); - if (doc instanceof List) { - final List docList = (List) doc; - for (final Object d : docList) { - Map entry = new HashMap(); - if (d instanceof String) { - String dString = (String) d; - if (dString.endsWith("?")) { - entry.put("pattern", dString.substring(0, dString.length()-1)); - entry.put("required", false); - } else { - entry.put("pattern", dString); - } - r.add(entry); - } else if (d instanceof Map) { - @SuppressWarnings("unchecked") - Map dMap = new HashMap((Map) d); - if (dMap.containsKey("pattern")) { - entry.put("pattern", dMap.remove("pattern")); - } else { - throw new ValidationException("Missing 'pattern' in secondaryFiles specification entry."); - } - if (dMap.containsKey("required")) { - entry.put("required", dMap.remove("required")); - } - if (dMap.size() > 0) { - throw new ValidationException("Unallowed values in secondaryFiles specification entry."); - } - r.add(entry); - } else { - throw new ValidationException("Expected a string or sequence of (strings or mappings)."); - } - } - } else if (doc instanceof Map) { - Map entry = new HashMap(); - @SuppressWarnings("unchecked") - Map dMap = new HashMap((Map) doc); - if (dMap.containsKey("pattern")) { - entry.put("pattern", dMap.remove("pattern")); - } else { - throw new ValidationException("Missing 'pattern' in secondaryFiles specification entry."); - } - if (dMap.containsKey("required")) { - entry.put("required", dMap.remove("required")); - } - if (dMap.size() > 0) { - throw new ValidationException("Unallowed values in secondaryFiles specification entry."); - } - r.add(entry); - } else if (doc instanceof String) { - String dString = (String) doc; - Map entry = new HashMap(); - if (dString.endsWith("?")) { - entry.put("pattern", dString.substring(0, dString.length()-1)); - entry.put("required", false); - } else { - entry.put("pattern", dString); - } - r.add(entry); - } else { - throw new ValidationException("Expected a string or sequence of (strings or mappings)."); - } - return this.innerLoader.load(r, baseUri, loadingOptions, docRoot); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/TypeDslLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/TypeDslLoader.java deleted file mode 100644 index 6caec158..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/TypeDslLoader.java +++ /dev/null @@ -1,81 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.regex.Matcher; -import java.util.regex.Pattern; - -public class TypeDslLoader implements Loader { - private final Loader innerLoader; - private final Integer refScope; - private static final Pattern TYPE_DSL_REGEX = Pattern.compile("^([^\\[?]+)(\\[\\])?(\\?)?$"); - - public TypeDslLoader(final Loader innerLoader, final Integer refScope) { - this.innerLoader = innerLoader; - this.refScope = refScope; - } - - private Object resolve( - final String doc_, final String baseUri, final LoadingOptions loadingOptions) { - final Matcher m = TYPE_DSL_REGEX.matcher(doc_); - if (m.matches()) { - final String first = - loadingOptions.expandUrl(m.group(1), baseUri, false, true, this.refScope); - Object second = null; - Object third = null; - if (m.group(2) != null && m.group(2).length() > 0) { - HashMap resolvedMap = new HashMap(); - resolvedMap.put("type", "array"); - resolvedMap.put("items", first); - second = resolvedMap; - } - if (m.group(3) != null && m.group(3).length() > 0) { - third = Arrays.asList("null", second != null ? second : first); - } - if (third != null) { - return third; - } else { - return second != null ? second : first; - } - } else { - return doc_; - } - } - - public T load( - final Object doc_, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - Object doc = doc_; - if (doc instanceof List) { - final List docList = (List) doc; - final List r = new ArrayList(); - for (final Object d : docList) { - if (d instanceof String) { - Object resolved = this.resolve((String) d, baseUri, loadingOptions); - if (resolved instanceof List) { - List resolvedList = (List) resolved; - for (Object i : resolvedList) { - if (!r.contains(i)) { - r.add(i); - } - } - } else { - if (!r.contains(resolved)) { - r.add(resolved); - } - } - } else { - r.add(d); - } - } - doc = docList; - } else if (doc instanceof String) { - doc = this.resolve((String) doc, baseUri, loadingOptions); - } - return this.innerLoader.load(doc, baseUri, loadingOptions); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/UnionLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/UnionLoader.java deleted file mode 100644 index b7516ce0..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/UnionLoader.java +++ /dev/null @@ -1,41 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - -public class UnionLoader implements Loader { - private final ArrayList alternates; - - public UnionLoader(List alternates) { - this.alternates = new ArrayList(alternates); - } - - public UnionLoader(Loader[] alternates) { - this(Arrays.asList(alternates)); - } - - public void addLoaders(List loaders) { - this.alternates.addAll(loaders); - } - - public void addLoaders(Loader[] loaders) { - this.addLoaders(Arrays.asList(loaders)); - } - - public Object load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - final List errors = new ArrayList(); - for (final Loader loader : this.alternates) { - try { - return loader.load(doc, baseUri, loadingOptions, docRoot); - } catch (ValidationException e) { - errors.add(e); - } - } - throw new ValidationException("Failed to match union type", errors); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/UriLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/UriLoader.java deleted file mode 100644 index 4ddbbb63..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/UriLoader.java +++ /dev/null @@ -1,59 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.ArrayList; -import java.util.List; - -public class UriLoader implements Loader { - private final Loader innerLoader; - private final boolean scopedId; - private final boolean vocabTerm; - private final Integer scopedRef; - private final Boolean noLinkCheck; - - public UriLoader( - final Loader innerLoader, - final boolean scopedId, - final boolean vocabTerm, - final Integer scopedRef, - final Boolean noLinkCheck) { - this.innerLoader = innerLoader; - this.scopedId = scopedId; - this.vocabTerm = vocabTerm; - this.scopedRef = scopedRef; - this.noLinkCheck = noLinkCheck; - } - - private Object expandUrl( - final Object object, final String baseUri, final LoadingOptions loadingOptions) { - if (object instanceof String) { - return loadingOptions.expandUrl( - (String) object, baseUri, this.scopedId, this.vocabTerm, this.scopedRef); - } else { - return object; - } - } - - public T load( - final Object doc_, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - LoadingOptions innerLoadingOptions = loadingOptions; - if (this.noLinkCheck != null) { - innerLoadingOptions = new LoadingOptionsBuilder().copiedFrom(loadingOptions).setNoLinkCheck(this.noLinkCheck).build(); - } - Object doc = doc_; - if (doc instanceof List) { - List docList = (List) doc; - List docWithExpansion = new ArrayList(); - for (final Object el : docList) { - docWithExpansion.add(this.expandUrl(el, baseUri, innerLoadingOptions)); - } - doc = docWithExpansion; - } - if (doc instanceof String) { - doc = this.expandUrl(doc, baseUri, innerLoadingOptions); - } - return this.innerLoader.load(doc, baseUri, innerLoadingOptions); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Uris.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Uris.java deleted file mode 100644 index 5a0279ef..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Uris.java +++ /dev/null @@ -1,129 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.io.UnsupportedEncodingException; -import java.net.URI; -import java.net.URISyntaxException; -import java.nio.charset.StandardCharsets; - -public class Uris { - - // Emulate Python's urlsplit. - public static class UriSplit { - String scheme; - String netloc; - String path; - String query; - String fragment; - - public UriSplit(String scheme, String netloc, String path, String query, String fragment) { - this.scheme = scheme; - this.netloc = netloc; - this.path = path; - this.query = query; - this.fragment = fragment; - } - - public String toString() { - return String.format("UriSplit[%s,%s,%s,%s,%s]", this.scheme, this.netloc, this.path, this.query, - this.fragment); - } - - } - - public static String fileUri(final String path) { - return fileUri(path, false); - } - - public static String fileUri(final String path, final boolean splitFrag) { - if (path.equals("file://")) { - return path; - } - String frag; - String urlPath; - if (splitFrag) { - final String[] pathsp = path.split("#", 2); - // is quoting this? - urlPath = Uris.quote(pathsp[0]); - if (pathsp.length == 2) { - frag = "#" + Uris.quote(pathsp[1]); - } else { - frag = ""; - urlPath = Uris.quote(path); - } - } else { - urlPath = Uris.quote(path); - frag = ""; - } - if (urlPath.startsWith("//")) { - return "file:" + urlPath + frag; - } else { - return "file://" + urlPath + frag; - } - } - - public static UriSplit split(final String uriString) { - try { - final URI uri = new URI(uriString); - return new Uris.UriSplit(uri.getScheme(), uri.getAuthority(), uri.getPath(), uri.getQuery(), - uri.getFragment()); - } catch (URISyntaxException e) { - return new Uris.UriSplit(null, null, uriString, null, null); - } - } - - public static String unsplit(final String scheme, final String netloc, final String path, final String query, - final String fragment) { - try { - return new URI(scheme, netloc, path, query, fragment).toString(); - } catch (URISyntaxException e) { - if (scheme == null && path.startsWith("_:")) { - String uri = path; - if (fragment != null && fragment.length() > 0) { - uri += "#" + fragment; - } - return fragment; - } - throw new RuntimeException(e); - } - } - - public static URI toUri(final String url) { - try { - return new URI(url); - } catch (URISyntaxException e) { - throw new RuntimeException(e); - } - } - - public static String quote(final String uri) { - try { - return java.net.URLDecoder.decode(uri, StandardCharsets.UTF_8.name()); - } catch (UnsupportedEncodingException e) { - throw new RuntimeException(e); - } - } - - public static String unquote(final String uri) { - try { - return java.net.URLEncoder.encode(uri, StandardCharsets.UTF_8.name()); - } catch (UnsupportedEncodingException e) { - throw new RuntimeException(e); - } - } - - public static String shortname(final String input_id) { - try { - final URI uri = new URI(input_id); - final String fragment = uri.getFragment(); - if (fragment != null) { - String[] fragment_elements = fragment.split("/"); - return fragment_elements[fragment_elements.length - 1]; - } else { - String[] path_elements = uri.getPath().split("/"); - return path_elements[path_elements.length - 1]; - } - } catch (URISyntaxException e) { - return input_id; - } - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/ValidationException.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/ValidationException.java deleted file mode 100644 index a1f6c44b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/ValidationException.java +++ /dev/null @@ -1,80 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - -public class ValidationException extends RuntimeException { - private final List children; - private String bullet = ""; - private String currentMessage; - - public ValidationException(final String message) { - this(message, (List) null); - } - - public ValidationException(final String message, final ValidationException child) { - this(message, Arrays.asList(child)); - } - - public ValidationException(final String message, final List children_) { - super(message); - this.currentMessage = message; - final List children = new ArrayList(); - if (children_ != null) { - for (final ValidationException child : children_) { - children.addAll(child.simplify()); - } - } - this.children = children; - } - - public ValidationException withBullet(final String bullet) { - this.bullet = bullet; - return this; - } - - public List simplify() { - if (getMessage().length() > 0) { - return Arrays.asList(this); - } else { - return this.children; - } - } - - public String summary(final int level, final boolean withBullet) { - final int indentPerLevel = 2; - final String spaces = new String(new char[level * indentPerLevel]).replace("\0", " "); - final String bullet; - if (this.bullet.length() > 0 && withBullet) { - bullet = this.bullet; - } else { - bullet = ""; - } - return spaces + bullet + this.currentMessage; - } - - public String prettyStr(final Integer level_) { - Integer level = level_; - if (level == null) { - level = 0; - } - final List parts = new ArrayList(); - int nextLevel; - if (this.currentMessage != null && this.currentMessage.length() > 0) { - parts.add(this.summary(level, true)); - nextLevel = level + 1; - } else { - nextLevel = level; - } - for (final ValidationException child : this.children) { - parts.add(child.prettyStr(nextLevel)); - } - final String ret = String.join("\n", parts); - return ret; - } - - public String getMessage() { - return this.prettyStr(null); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Validator.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Validator.java deleted file mode 100644 index 7b71142d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/Validator.java +++ /dev/null @@ -1,24 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.io.File; -import org.snakeyaml.engine.v2.api.Dump; -import org.snakeyaml.engine.v2.api.DumpSettings; -import org.snakeyaml.engine.v2.common.ScalarStyle; - -import com.fasterxml.jackson.annotation.JsonInclude.Include; -import com.fasterxml.jackson.databind.ObjectMapper; - -public class Validator { - public static void main(final String[] args) throws Exception { - if (args.length != 1) { - throw new Exception("No argument supplied to validate."); - } - // TODO: allow URLs and such. - final File uri = new File(args[0]); - Object doc = RootLoader.loadDocument(uri); - ObjectMapper mapper = new ObjectMapper(); - mapper.setSerializationInclusion(Include.NON_NULL).writerWithDefaultPrettyPrinter().writeValue(System.out, doc); - System.out.println(); - - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/YamlUtils.java b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/YamlUtils.java deleted file mode 100644 index 94781bc7..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/YamlUtils.java +++ /dev/null @@ -1,31 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Objects; -import java.util.regex.Pattern; - -import org.snakeyaml.engine.v2.api.Load; -import org.snakeyaml.engine.v2.api.LoadSettings; -import org.snakeyaml.engine.v2.nodes.Tag; -import org.snakeyaml.engine.v2.resolver.ScalarResolver; -import org.snakeyaml.engine.v2.schema.CoreSchema; - -public class YamlUtils { - - public static Map mapFromString(final String text) { - LoadSettings settings = LoadSettings.builder().setSchema(new CoreSchema()).build(); - Load load = new Load(settings); - final Map result = (Map) load.loadFromString(text); - return result; - } - - public static List listFromString(final String text) { - LoadSettings settings = LoadSettings.builder().setSchema(new CoreSchema()).build(); - Load load = new Load(settings); - final List result = (List) load.loadFromString(text); - return result; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/package.html b/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/package.html deleted file mode 100644 index 317b1d96..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_1/utils/package.html +++ /dev/null @@ -1,3 +0,0 @@ - -This package contains utilities for working the SchemaSalad generated code for the org.commonwl.cwlsdk.cwl1_1 package. - diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Any.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Any.java deleted file mode 100644 index 95d5748b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Any.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum Any { - ANY("Any"); - - private static String[] symbols = new String[] {"Any"}; - private String docVal; - - private Any(final String docVal) { - this.docVal = docVal; - } - - public static Any fromDocumentVal(final String docVal) { - for(final Any val : Any.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Any.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ArraySchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ArraySchema.java deleted file mode 100644 index 229ef6d9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ArraySchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#ArraySchema
This interface is implemented by {@link ArraySchemaImpl}
- */ -public interface ArraySchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - Object getItems(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - Array_name getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ArraySchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ArraySchemaImpl.java deleted file mode 100644 index c2c62502..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ArraySchemaImpl.java +++ /dev/null @@ -1,128 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/salad#ArraySchema
- */ -public class ArraySchemaImpl extends SaveableImpl implements ArraySchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Object items; - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - public Object getItems() { - return this.items; - } - - private Array_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - public Array_name getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of ArraySchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ArraySchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ArraySchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Object items; - try { - items = - LoaderInstances - .uri_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("items"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - items = null; // won't be used but prevents compiler from complaining. - final String __message = "the `items` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Array_name type; - try { - type = - LoaderInstances - .typedsl_Array_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.items = (Object) items; - this.type = (Array_name) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("items", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Array_name.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Array_name.java deleted file mode 100644 index 68142666..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Array_name.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum Array_name { - ARRAY("array"); - - private static String[] symbols = new String[] {"array"}; - private String docVal; - - private Array_name(final String docVal) { - this.docVal = docVal; - } - - public static Array_name fromDocumentVal(final String docVal) { - for(final Array_name val : Array_name.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Array_name.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CUDARequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CUDARequirement.java deleted file mode 100644 index f923a069..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CUDARequirement.java +++ /dev/null @@ -1,91 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for http://commonwl.org/cwltool#CUDARequirement
This interface is implemented by {@link CUDARequirementImpl}
- Require support for NVIDA CUDA (GPU hardware acceleration). -
- */ -public interface CUDARequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property http://commonwl.org/cwltool#CUDARequirement/class
- *
- * cwltool:CUDARequirement *
- */ - - String getClass_(); - /** - * Getter for property http://commonwl.org/cwltool#CUDARequirement/cudaComputeCapability
- *
- * CUDA hardware capability required to run the software, in X.Y - * format. - * - * * If this is a single value, it defines only the minimum - * compute capability. GPUs with higher capability are also - * accepted. - * - * * If it is an array value, then only select GPUs with compute - * capabilities that explicitly appear in the array. - * *
- */ - - Object getCudaComputeCapability(); - /** - * Getter for property http://commonwl.org/cwltool#CUDARequirement/cudaDeviceCountMax
- *
- * Maximum number of GPU devices to request. If not specified, - * same as `cudaDeviceCountMin`. - * *
- */ - - Object getCudaDeviceCountMax(); - /** - * Getter for property http://commonwl.org/cwltool#CUDARequirement/cudaDeviceCountMin
- *
- * Minimum number of GPU devices to request. If not specified, - * same as `cudaDeviceCountMax`. If neither are specified, - * default 1. - * *
- */ - - Object getCudaDeviceCountMin(); - /** - * Getter for property http://commonwl.org/cwltool#CUDARequirement/cudaVersionMin
- *
- * Minimum CUDA version to run the software, in X.Y format. This - * corresponds to a CUDA SDK release. When running directly on - * the host (not in a container) the host must have a compatible - * CUDA SDK (matching the exact version, or, starting with CUDA - * 11.3, matching major version). When run in a container, the - * container image should provide the CUDA runtime, and the host - * driver is injected into the container. In this case, because - * CUDA drivers are backwards compatible, it is possible to - * use an older SDK with a newer driver across major versions. - * - * See https://docs.nvidia.com/deploy/cuda-compatibility/ for - * details. - * *
- */ - - String getCudaVersionMin(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CUDARequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CUDARequirementImpl.java deleted file mode 100644 index a130743c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CUDARequirementImpl.java +++ /dev/null @@ -1,240 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for http://commonwl.org/cwltool#CUDARequirement
- Require support for NVIDA CUDA (GPU hardware acceleration). -
- */ -public class CUDARequirementImpl extends SaveableImpl implements CUDARequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String class_; - - /** - * Getter for property http://commonwl.org/cwltool#CUDARequirement/class
- *
- * cwltool:CUDARequirement *
- */ - - public String getClass_() { - return this.class_; - } - - private Object cudaComputeCapability; - - /** - * Getter for property http://commonwl.org/cwltool#CUDARequirement/cudaComputeCapability
- *
- * CUDA hardware capability required to run the software, in X.Y - * format. - * - * * If this is a single value, it defines only the minimum - * compute capability. GPUs with higher capability are also - * accepted. - * - * * If it is an array value, then only select GPUs with compute - * capabilities that explicitly appear in the array. - * *
- */ - - public Object getCudaComputeCapability() { - return this.cudaComputeCapability; - } - - private Object cudaDeviceCountMax; - - /** - * Getter for property http://commonwl.org/cwltool#CUDARequirement/cudaDeviceCountMax
- *
- * Maximum number of GPU devices to request. If not specified, - * same as `cudaDeviceCountMin`. - * *
- */ - - public Object getCudaDeviceCountMax() { - return this.cudaDeviceCountMax; - } - - private Object cudaDeviceCountMin; - - /** - * Getter for property http://commonwl.org/cwltool#CUDARequirement/cudaDeviceCountMin
- *
- * Minimum number of GPU devices to request. If not specified, - * same as `cudaDeviceCountMax`. If neither are specified, - * default 1. - * *
- */ - - public Object getCudaDeviceCountMin() { - return this.cudaDeviceCountMin; - } - - private String cudaVersionMin; - - /** - * Getter for property http://commonwl.org/cwltool#CUDARequirement/cudaVersionMin
- *
- * Minimum CUDA version to run the software, in X.Y format. This - * corresponds to a CUDA SDK release. When running directly on - * the host (not in a container) the host must have a compatible - * CUDA SDK (matching the exact version, or, starting with CUDA - * 11.3, matching major version). When run in a container, the - * container image should provide the CUDA runtime, and the host - * driver is injected into the container. In this case, because - * CUDA drivers are backwards compatible, it is possible to - * use an older SDK with a newer driver across major versions. - * - * See https://docs.nvidia.com/deploy/cuda-compatibility/ for - * details. - * *
- */ - - public String getCudaVersionMin() { - return this.cudaVersionMin; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CUDARequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CUDARequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CUDARequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String class_; - try { - class_ = - LoaderInstances - .uri_StringInstance_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object cudaComputeCapability; - try { - cudaComputeCapability = - LoaderInstances - .union_of_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("cudaComputeCapability"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - cudaComputeCapability = null; // won't be used but prevents compiler from complaining. - final String __message = "the `cudaComputeCapability` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object cudaDeviceCountMax; - - if (__doc.containsKey("cudaDeviceCountMax")) { - try { - cudaDeviceCountMax = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_ExpressionLoader - .loadField(__doc.get("cudaDeviceCountMax"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - cudaDeviceCountMax = null; // won't be used but prevents compiler from complaining. - final String __message = "the `cudaDeviceCountMax` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - cudaDeviceCountMax = null; - } - Object cudaDeviceCountMin; - - if (__doc.containsKey("cudaDeviceCountMin")) { - try { - cudaDeviceCountMin = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_ExpressionLoader - .loadField(__doc.get("cudaDeviceCountMin"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - cudaDeviceCountMin = null; // won't be used but prevents compiler from complaining. - final String __message = "the `cudaDeviceCountMin` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - cudaDeviceCountMin = null; - } - String cudaVersionMin; - try { - cudaVersionMin = - LoaderInstances - .StringInstance - .loadField(__doc.get("cudaVersionMin"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - cudaVersionMin = null; // won't be used but prevents compiler from complaining. - final String __message = "the `cudaVersionMin` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (String) class_; - this.cudaComputeCapability = (Object) cudaComputeCapability; - this.cudaDeviceCountMax = (Object) cudaDeviceCountMax; - this.cudaDeviceCountMin = (Object) cudaDeviceCountMin; - this.cudaVersionMin = (String) cudaVersionMin; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "cudaComputeCapability", "cudaDeviceCountMax", "cudaDeviceCountMin", "cudaVersionMin"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLArraySchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLArraySchema.java deleted file mode 100644 index 77edf95f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLArraySchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CWLArraySchema
This interface is implemented by {@link CWLArraySchemaImpl}
- */ -public interface CWLArraySchema extends ArraySchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - Object getItems(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - Array_name getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLArraySchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLArraySchemaImpl.java deleted file mode 100644 index e642c62d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLArraySchemaImpl.java +++ /dev/null @@ -1,128 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CWLArraySchema
- */ -public class CWLArraySchemaImpl extends SaveableImpl implements CWLArraySchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Object items; - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - public Object getItems() { - return this.items; - } - - private Array_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - public Array_name getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CWLArraySchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CWLArraySchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CWLArraySchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Object items; - try { - items = - LoaderInstances - .uri_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("items"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - items = null; // won't be used but prevents compiler from complaining. - final String __message = "the `items` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Array_name type; - try { - type = - LoaderInstances - .typedsl_Array_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.items = (Object) items; - this.type = (Array_name) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("items", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLRecordField.java deleted file mode 100644 index 5962f3ea..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLRecordField.java +++ /dev/null @@ -1,51 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CWLRecordField
This interface is implemented by {@link CWLRecordFieldImpl}
- */ -public interface CWLRecordField extends RecordField, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - String getName(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - Object getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLRecordFieldImpl.java deleted file mode 100644 index 94185e74..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLRecordFieldImpl.java +++ /dev/null @@ -1,175 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CWLRecordField
- */ -public class CWLRecordFieldImpl extends SaveableImpl implements CWLRecordField { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String name; - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - public String getName() { - return this.name; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - public Object getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CWLRecordFieldImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CWLRecordFieldImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CWLRecordFieldImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - if (name == null) { - if (__docRoot != null) { - name = __docRoot; - } else { - throw new ValidationException("Missing name"); - } - } - __baseUri = (String) name; - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.doc = (Object) doc; - this.name = (String) name; - this.type = (Object) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("doc", "name", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLRecordSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLRecordSchema.java deleted file mode 100644 index a5d80cba..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLRecordSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CWLRecordSchema
This interface is implemented by {@link CWLRecordSchemaImpl}
- */ -public interface CWLRecordSchema extends RecordSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - java.util.Optional> getFields(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - Record_name getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLRecordSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLRecordSchemaImpl.java deleted file mode 100644 index 899c33de..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLRecordSchemaImpl.java +++ /dev/null @@ -1,134 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CWLRecordSchema
- */ -public class CWLRecordSchemaImpl extends SaveableImpl implements CWLRecordSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional> fields; - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - public java.util.Optional> getFields() { - return this.fields; - } - - private Record_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - public Record_name getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CWLRecordSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CWLRecordSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CWLRecordSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional> fields; - - if (__doc.containsKey("fields")) { - try { - fields = - LoaderInstances - .idmap_fields_optional_array_of_CWLRecordField - .loadField(__doc.get("fields"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - fields = null; // won't be used but prevents compiler from complaining. - final String __message = "the `fields` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - fields = null; - } - Record_name type; - try { - type = - LoaderInstances - .typedsl_Record_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.fields = (java.util.Optional>) fields; - this.type = (Record_name) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("fields", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLType.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLType.java deleted file mode 100644 index b7e3f5dd..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLType.java +++ /dev/null @@ -1,45 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum CWLType { - NULL("null"), - BOOLEAN("boolean"), - INT("int"), - LONG("long"), - FLOAT("float"), - DOUBLE("double"), - STRING("string"), - FILE("File"), - DIRECTORY("Directory"); - - private static String[] symbols = new String[] {"null", "boolean", "int", "long", "float", "double", "string", "File", "Directory"}; - private String docVal; - - private CWLType(final String docVal) { - this.docVal = docVal; - } - - public static CWLType fromDocumentVal(final String docVal) { - for(final CWLType val : CWLType.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", CWLType.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLVersion.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLVersion.java deleted file mode 100644 index d901cf8b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CWLVersion.java +++ /dev/null @@ -1,56 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum CWLVersion { - DRAFT_2("draft-2"), - DRAFT_3_DEV1("draft-3.dev1"), - DRAFT_3_DEV2("draft-3.dev2"), - DRAFT_3_DEV3("draft-3.dev3"), - DRAFT_3_DEV4("draft-3.dev4"), - DRAFT_3_DEV5("draft-3.dev5"), - DRAFT_3("draft-3"), - DRAFT_4_DEV1("draft-4.dev1"), - DRAFT_4_DEV2("draft-4.dev2"), - DRAFT_4_DEV3("draft-4.dev3"), - V1_0_DEV4("v1.0.dev4"), - V1_0("v1.0"), - V1_1_0_DEV1("v1.1.0-dev1"), - V1_1("v1.1"), - V1_2_0_DEV1("v1.2.0-dev1"), - V1_2_0_DEV2("v1.2.0-dev2"), - V1_2_0_DEV3("v1.2.0-dev3"), - V1_2_0_DEV4("v1.2.0-dev4"), - V1_2_0_DEV5("v1.2.0-dev5"), - V1_2("v1.2"); - - private static String[] symbols = new String[] {"draft-2", "draft-3.dev1", "draft-3.dev2", "draft-3.dev3", "draft-3.dev4", "draft-3.dev5", "draft-3", "draft-4.dev1", "draft-4.dev2", "draft-4.dev3", "v1.0.dev4", "v1.0", "v1.1.0-dev1", "v1.1", "v1.2.0-dev1", "v1.2.0-dev2", "v1.2.0-dev3", "v1.2.0-dev4", "v1.2.0-dev5", "v1.2"}; - private String docVal; - - private CWLVersion(final String docVal) { - this.docVal = docVal; - } - - public static CWLVersion fromDocumentVal(final String docVal) { - for(final CWLVersion val : CWLVersion.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", CWLVersion.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputArraySchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputArraySchema.java deleted file mode 100644 index 912c3906..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputArraySchema.java +++ /dev/null @@ -1,70 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputArraySchema
This interface is implemented by {@link CommandInputArraySchemaImpl}
- */ -public interface CommandInputArraySchema extends InputArraySchema, CommandInputSchema, CommandLineBindable, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - Object getItems(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - Array_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputArraySchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputArraySchemaImpl.java deleted file mode 100644 index df99f642..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputArraySchemaImpl.java +++ /dev/null @@ -1,262 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputArraySchema
- */ -public class CommandInputArraySchemaImpl extends SaveableImpl implements CommandInputArraySchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private Object items; - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - public Object getItems() { - return this.items; - } - - private Array_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - public Array_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandInputArraySchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandInputArraySchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandInputArraySchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - Object items; - try { - items = - LoaderInstances - .uri_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("items"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - items = null; // won't be used but prevents compiler from complaining. - final String __message = "the `items` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Array_name type; - try { - type = - LoaderInstances - .typedsl_Array_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_CommandLineBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.items = (Object) items; - this.type = (Array_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("items", "type", "label", "doc", "name", "inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputEnumSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputEnumSchema.java deleted file mode 100644 index a5f1dc6d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputEnumSchema.java +++ /dev/null @@ -1,70 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputEnumSchema
This interface is implemented by {@link CommandInputEnumSchemaImpl}
- */ -public interface CommandInputEnumSchema extends InputEnumSchema, CommandInputSchema, CommandLineBindable, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - java.util.List getSymbols(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - Enum_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputEnumSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputEnumSchemaImpl.java deleted file mode 100644 index 55e7b4b7..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputEnumSchemaImpl.java +++ /dev/null @@ -1,262 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputEnumSchema
- */ -public class CommandInputEnumSchemaImpl extends SaveableImpl implements CommandInputEnumSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.List symbols; - - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - public java.util.List getSymbols() { - return this.symbols; - } - - private Enum_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - public Enum_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandInputEnumSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandInputEnumSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandInputEnumSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.List symbols; - try { - symbols = - LoaderInstances - .uri_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("symbols"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - symbols = null; // won't be used but prevents compiler from complaining. - final String __message = "the `symbols` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Enum_name type; - try { - type = - LoaderInstances - .typedsl_Enum_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_CommandLineBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.name = (java.util.Optional) name; - this.symbols = (java.util.List) symbols; - this.type = (Enum_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("name", "symbols", "type", "label", "doc", "inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameter.java deleted file mode 100644 index ead0d54d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameter.java +++ /dev/null @@ -1,184 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputParameter
This interface is implemented by {@link CommandInputParameterImpl}
- An input parameter for a CommandLineTool.
- */ -public interface CommandInputParameter extends InputParameter, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - String getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value to use for this parameter if the parameter is missing - * from the input object, or if the value of the parameter in the input - * object is `null`. Default values are applied before evaluating expressions - * (e.g. dependent `valueFrom` fields). - * *
- */ - - java.util.Optional getDefault(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandInputParameter/inputBinding
- *
- * Describes how to turn the input parameters of a process into - * command line arguments. - * *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameterImpl.java deleted file mode 100644 index ad6601f5..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputParameterImpl.java +++ /dev/null @@ -1,492 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputParameter
- An input parameter for a CommandLineTool.
- */ -public class CommandInputParameterImpl extends SaveableImpl implements CommandInputParameter { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - public String getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - private java.util.Optional default_; - - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value to use for this parameter if the parameter is missing - * from the input object, or if the value of the parameter in the input - * object is `null`. Default values are applied before evaluating expressions - * (e.g. dependent `valueFrom` fields). - * *
- */ - - public java.util.Optional getDefault() { - return this.default_; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandInputParameter/inputBinding
- *
- * Describes how to turn the input parameters of a process into - * command line arguments. - * *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandInputParameterImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandInputParameterImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandInputParameterImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - if (id == null) { - if (__docRoot != null) { - id = __docRoot; - } else { - throw new ValidationException("Missing id"); - } - } - __baseUri = (String) id; - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - java.util.Optional default_; - - if (__doc.containsKey("default")) { - try { - default_ = - LoaderInstances - .optional_CWLObjectType - .loadField(__doc.get("default"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - default_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `default` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - default_ = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_stdin_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_CommandLineBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.doc = (Object) doc; - this.id = (String) id; - this.format = (Object) format; - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - this.default_ = (java.util.Optional) default_; - this.type = (Object) type; - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("label", "secondaryFiles", "streamable", "doc", "id", "format", "loadContents", "loadListing", "default", "type", "inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordField.java deleted file mode 100644 index 8c8c37b7..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordField.java +++ /dev/null @@ -1,171 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputRecordField
This interface is implemented by {@link CommandInputRecordFieldImpl}
- */ -public interface CommandInputRecordField extends InputRecordField, CommandLineBindable, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - String getName(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordFieldImpl.java deleted file mode 100644 index 77d7cdb1..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordFieldImpl.java +++ /dev/null @@ -1,456 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordField
- */ -public class CommandInputRecordFieldImpl extends SaveableImpl implements CommandInputRecordField { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String name; - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - public String getName() { - return this.name; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandInputRecordFieldImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandInputRecordFieldImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandInputRecordFieldImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - if (name == null) { - if (__docRoot != null) { - name = __docRoot; - } else { - throw new ValidationException("Missing name"); - } - } - __baseUri = (String) name; - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_CommandLineBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.doc = (Object) doc; - this.name = (String) name; - this.type = (Object) type; - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.format = (Object) format; - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("doc", "name", "type", "label", "secondaryFiles", "streamable", "format", "loadContents", "loadListing", "inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordSchema.java deleted file mode 100644 index ea5d2de5..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordSchema.java +++ /dev/null @@ -1,70 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputRecordSchema
This interface is implemented by {@link CommandInputRecordSchemaImpl}
- */ -public interface CommandInputRecordSchema extends InputRecordSchema, CommandInputSchema, CommandLineBindable, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - java.util.Optional> getFields(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - Record_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordSchemaImpl.java deleted file mode 100644 index b460918f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputRecordSchemaImpl.java +++ /dev/null @@ -1,268 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordSchema
- */ -public class CommandInputRecordSchemaImpl extends SaveableImpl implements CommandInputRecordSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.Optional> fields; - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - public java.util.Optional> getFields() { - return this.fields; - } - - private Record_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - public Record_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandInputRecordSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandInputRecordSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandInputRecordSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.Optional> fields; - - if (__doc.containsKey("fields")) { - try { - fields = - LoaderInstances - .idmap_fields_optional_array_of_CommandInputRecordField - .loadField(__doc.get("fields"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - fields = null; // won't be used but prevents compiler from complaining. - final String __message = "the `fields` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - fields = null; - } - Record_name type; - try { - type = - LoaderInstances - .typedsl_Record_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_CommandLineBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.fields = (java.util.Optional>) fields; - this.type = (Record_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("fields", "type", "label", "doc", "name", "inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputSchema.java deleted file mode 100644 index 5312a084..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandInputSchema.java +++ /dev/null @@ -1,28 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputSchema
- */ -public interface CommandInputSchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBindable.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBindable.java deleted file mode 100644 index 56f5ea14..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBindable.java +++ /dev/null @@ -1,35 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineBindable
- */ -public interface CommandLineBindable extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBindable/inputBinding
- *
- * Describes how to turn this object into command line arguments. *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBinding.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBinding.java deleted file mode 100644 index 9e96b3fd..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBinding.java +++ /dev/null @@ -1,150 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineBinding
This interface is implemented by {@link CommandLineBindingImpl}
- - When listed under `inputBinding` in the input schema, the term - "value" refers to the corresponding value in the input object. For - binding objects listed in `CommandLineTool.arguments`, the term "value" - refers to the effective value after evaluating `valueFrom`. - - The binding behavior when building the command line depends on the data - type of the value. If there is a mismatch between the type described by - the input schema and the effective value, such as resulting from an - expression evaluation, an implementation must use the data type of the - effective value. - - - **string**: Add `prefix` and the string to the command line. - - - **number**: Add `prefix` and decimal representation to command line. - - - **boolean**: If true, add `prefix` to the command line. If false, add - nothing. - - - **File**: Add `prefix` and the value of - [`File.path`](#File) to the command line. - - - **Directory**: Add `prefix` and the value of - [`Directory.path`](#Directory) to the command line. - - - **array**: If `itemSeparator` is specified, add `prefix` and the join - the array into a single string with `itemSeparator` separating the - items. Otherwise, first add `prefix`, then recursively process - individual elements. - If the array is empty, it does not add anything to command line. - - - **object**: Add `prefix` only, and recursively add object fields for - which `inputBinding` is specified. - - - **null**: Add nothing. -
- */ -public interface CommandLineBinding extends InputBinding, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#InputBinding/loadContents
- *
- * Use of `loadContents` in `InputBinding` is deprecated. - * Preserved for v1.0 backwards compatibility. Will be removed in - * CWL v2.0. Use `InputParameter.loadContents` instead. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/position
- *
- * The sorting key. Default position is 0. If a [CWL Parameter Reference](#Parameter_references) - * or [CWL Expression](#Expressions_(Optional)) is used and if the - * inputBinding is associated with an input parameter, then the value of - * `self` will be the value of the input parameter. Input parameter - * defaults (as specified by the `InputParameter.default` field) must be - * applied before evaluating the expression. Expressions must return a - * single value of type int or a null. - * *
- */ - - Object getPosition(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/prefix
- *
- * Command line prefix to add before the value. *
- */ - - java.util.Optional getPrefix(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/separate
- *
- * If true (default), then the prefix and value must be added as separate - * command line arguments; if false, prefix and value must be concatenated - * into a single command line argument. - * *
- */ - - java.util.Optional getSeparate(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/itemSeparator
- *
- * Join the array elements into a single string with the elements - * separated by `itemSeparator`. - * *
- */ - - java.util.Optional getItemSeparator(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/valueFrom
- *
- * If `valueFrom` is a constant string value, use this as the value and - * apply the binding rules above. - * - * If `valueFrom` is an expression, evaluate the expression to yield the - * actual value to use to build the command line and apply the binding - * rules above. If the inputBinding is associated with an input - * parameter, the value of `self` in the expression will be the value of - * the input parameter. Input parameter defaults (as specified by the - * `InputParameter.default` field) must be applied before evaluating the - * expression. - * - * If the value of the associated input parameter is `null`, `valueFrom` is - * not evaluated and nothing is added to the command line. - * - * When a binding is part of the `CommandLineTool.arguments` field, - * the `valueFrom` field is required. - * *
- */ - - Object getValueFrom(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/shellQuote
- *
- * If `ShellCommandRequirement` is in the requirements for the current command, - * this controls whether the value is quoted on the command line (default is true). - * Use `shellQuote: false` to inject metacharacters for operations such as pipes. - * - * If `shellQuote` is true or not provided, the implementation must not - * permit interpretation of any shell metacharacters or directives. - * *
- */ - - java.util.Optional getShellQuote(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBindingImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBindingImpl.java deleted file mode 100644 index 12f98f9c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineBindingImpl.java +++ /dev/null @@ -1,363 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandLineBinding
- - When listed under `inputBinding` in the input schema, the term - "value" refers to the corresponding value in the input object. For - binding objects listed in `CommandLineTool.arguments`, the term "value" - refers to the effective value after evaluating `valueFrom`. - - The binding behavior when building the command line depends on the data - type of the value. If there is a mismatch between the type described by - the input schema and the effective value, such as resulting from an - expression evaluation, an implementation must use the data type of the - effective value. - - - **string**: Add `prefix` and the string to the command line. - - - **number**: Add `prefix` and decimal representation to command line. - - - **boolean**: If true, add `prefix` to the command line. If false, add - nothing. - - - **File**: Add `prefix` and the value of - [`File.path`](#File) to the command line. - - - **Directory**: Add `prefix` and the value of - [`Directory.path`](#Directory) to the command line. - - - **array**: If `itemSeparator` is specified, add `prefix` and the join - the array into a single string with `itemSeparator` separating the - items. Otherwise, first add `prefix`, then recursively process - individual elements. - If the array is empty, it does not add anything to command line. - - - **object**: Add `prefix` only, and recursively add object fields for - which `inputBinding` is specified. - - - **null**: Add nothing. -
- */ -public class CommandLineBindingImpl extends SaveableImpl implements CommandLineBinding { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#InputBinding/loadContents
- *
- * Use of `loadContents` in `InputBinding` is deprecated. - * Preserved for v1.0 backwards compatibility. Will be removed in - * CWL v2.0. Use `InputParameter.loadContents` instead. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private Object position; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/position
- *
- * The sorting key. Default position is 0. If a [CWL Parameter Reference](#Parameter_references) - * or [CWL Expression](#Expressions_(Optional)) is used and if the - * inputBinding is associated with an input parameter, then the value of - * `self` will be the value of the input parameter. Input parameter - * defaults (as specified by the `InputParameter.default` field) must be - * applied before evaluating the expression. Expressions must return a - * single value of type int or a null. - * *
- */ - - public Object getPosition() { - return this.position; - } - - private java.util.Optional prefix; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/prefix
- *
- * Command line prefix to add before the value. *
- */ - - public java.util.Optional getPrefix() { - return this.prefix; - } - - private java.util.Optional separate; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/separate
- *
- * If true (default), then the prefix and value must be added as separate - * command line arguments; if false, prefix and value must be concatenated - * into a single command line argument. - * *
- */ - - public java.util.Optional getSeparate() { - return this.separate; - } - - private java.util.Optional itemSeparator; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/itemSeparator
- *
- * Join the array elements into a single string with the elements - * separated by `itemSeparator`. - * *
- */ - - public java.util.Optional getItemSeparator() { - return this.itemSeparator; - } - - private Object valueFrom; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/valueFrom
- *
- * If `valueFrom` is a constant string value, use this as the value and - * apply the binding rules above. - * - * If `valueFrom` is an expression, evaluate the expression to yield the - * actual value to use to build the command line and apply the binding - * rules above. If the inputBinding is associated with an input - * parameter, the value of `self` in the expression will be the value of - * the input parameter. Input parameter defaults (as specified by the - * `InputParameter.default` field) must be applied before evaluating the - * expression. - * - * If the value of the associated input parameter is `null`, `valueFrom` is - * not evaluated and nothing is added to the command line. - * - * When a binding is part of the `CommandLineTool.arguments` field, - * the `valueFrom` field is required. - * *
- */ - - public Object getValueFrom() { - return this.valueFrom; - } - - private java.util.Optional shellQuote; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineBinding/shellQuote
- *
- * If `ShellCommandRequirement` is in the requirements for the current command, - * this controls whether the value is quoted on the command line (default is true). - * Use `shellQuote: false` to inject metacharacters for operations such as pipes. - * - * If `shellQuote` is true or not provided, the implementation must not - * permit interpretation of any shell metacharacters or directives. - * *
- */ - - public java.util.Optional getShellQuote() { - return this.shellQuote; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandLineBindingImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandLineBindingImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandLineBindingImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - Object position; - - if (__doc.containsKey("position")) { - try { - position = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_ExpressionLoader - .loadField(__doc.get("position"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - position = null; // won't be used but prevents compiler from complaining. - final String __message = "the `position` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - position = null; - } - java.util.Optional prefix; - - if (__doc.containsKey("prefix")) { - try { - prefix = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("prefix"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - prefix = null; // won't be used but prevents compiler from complaining. - final String __message = "the `prefix` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - prefix = null; - } - java.util.Optional separate; - - if (__doc.containsKey("separate")) { - try { - separate = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("separate"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - separate = null; // won't be used but prevents compiler from complaining. - final String __message = "the `separate` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - separate = null; - } - java.util.Optional itemSeparator; - - if (__doc.containsKey("itemSeparator")) { - try { - itemSeparator = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("itemSeparator"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - itemSeparator = null; // won't be used but prevents compiler from complaining. - final String __message = "the `itemSeparator` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - itemSeparator = null; - } - Object valueFrom; - - if (__doc.containsKey("valueFrom")) { - try { - valueFrom = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("valueFrom"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - valueFrom = null; // won't be used but prevents compiler from complaining. - final String __message = "the `valueFrom` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - valueFrom = null; - } - java.util.Optional shellQuote; - - if (__doc.containsKey("shellQuote")) { - try { - shellQuote = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("shellQuote"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - shellQuote = null; // won't be used but prevents compiler from complaining. - final String __message = "the `shellQuote` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - shellQuote = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.loadContents = (java.util.Optional) loadContents; - this.position = (Object) position; - this.prefix = (java.util.Optional) prefix; - this.separate = (java.util.Optional) separate; - this.itemSeparator = (java.util.Optional) itemSeparator; - this.valueFrom = (Object) valueFrom; - this.shellQuote = (java.util.Optional) shellQuote; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("loadContents", "position", "prefix", "separate", "itemSeparator", "valueFrom", "shellQuote"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineTool.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineTool.java deleted file mode 100644 index d94c1ac0..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineTool.java +++ /dev/null @@ -1,250 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineTool
This interface is implemented by {@link CommandLineToolImpl}
- This defines the schema of the CWL Command Line Tool Description document. -
- */ -public interface CommandLineTool extends Process, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/id
- *
- * The unique identifier for this object. - * - * Only useful for `$graph` at `Process` level. Should not be exposed - * to users in graphical or terminal user interfaces. - * *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/class
- - */ - - CommandLineTool_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - java.util.List getInputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - java.util.List getOutputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - java.util.Optional> getRequirements(); - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - java.util.Optional> getHints(); - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - java.util.Optional getCwlVersion(); - /** - * Getter for property https://w3id.org/cwl/cwl#Process/intent
- *
- * An identifier for the type of computational operation, of this Process. - * Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for - * [`CommandLineTool`](CommandLineTool.html#CommandLineTool), - * [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). - * - * If provided, then this must be an IRI of a concept node that - * represents the type of operation, preferably defined within an ontology. - * - * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), - * like [Alignment](http://edamontology.org/operation_2928), - * or [Clustering](http://edamontology.org/operation_3432); or a more - * specific Operation concept like - * [Split read mapping](http://edamontology.org/operation_3199). - * *
- */ - - java.util.Optional> getIntent(); - /** - * Getter for property https://w3id.org/cwl/cwl#baseCommand
- *
- * Specifies the program to execute. If an array, the first element of - * the array is the command to execute, and subsequent elements are - * mandatory command line arguments. The elements in `baseCommand` must - * appear before any command line bindings from `inputBinding` or - * `arguments`. - * - * If `baseCommand` is not provided or is an empty array, the first - * element of the command line produced after processing `inputBinding` or - * `arguments` must be used as the program to execute. - * - * If the program includes a path separator character it must - * be an absolute path, otherwise it is an error. If the program does not - * include a path separator, search the `$PATH` variable in the runtime - * environment of the workflow runner find the absolute path of the - * executable. - * *
- */ - - Object getBaseCommand(); - /** - * Getter for property https://w3id.org/cwl/cwl#arguments
- *
- * Command line bindings which are not directly associated with input - * parameters. If the value is a string, it is used as a string literal - * argument. If it is an Expression, the result of the evaluation is used - * as an argument. - * *
- */ - - java.util.Optional> getArguments(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdin
- *
- * A path to a file whose contents must be piped into the command's - * standard input stream. - * *
- */ - - Object getStdin(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stderr
- *
- * Capture the command's standard error stream to a file written to - * the designated output directory. - * - * If `stderr` is a string, it specifies the file name to use. - * - * If `stderr` is an expression, the expression is evaluated and must - * return a string with the file name to use to capture stderr. If the - * return value is not a string, or the resulting path contains illegal - * characters (such as the path separator `/`) it is an error. - * *
- */ - - Object getStderr(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdout
- *
- * Capture the command's standard output stream to a file written to - * the designated output directory. - * - * If the `CommandLineTool` contains logically chained commands - * (e.g. `echo a && echo b`) `stdout` must include the output of - * every command. - * - * If `stdout` is a string, it specifies the file name to use. - * - * If `stdout` is an expression, the expression is evaluated and must - * return a string with the file name to use to capture stdout. If the - * return value is not a string, or the resulting path contains illegal - * characters (such as the path separator `/`) it is an error. - * *
- */ - - Object getStdout(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/successCodes
- *
- * Exit codes that indicate the process completed successfully. - * - * If not specified, only exit code 0 is considered success. - * *
- */ - - java.util.Optional> getSuccessCodes(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/temporaryFailCodes
- *
- * Exit codes that indicate the process failed due to a possibly - * temporary condition, where executing the process with the same - * runtime environment and inputs may produce different results. - * - * If not specified, no exit codes are considered temporary failure. - * *
- */ - - java.util.Optional> getTemporaryFailCodes(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/permanentFailCodes
- *
- * Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail. - * If not specified, all exit codes except 0 are considered permanent failure. *
- */ - - java.util.Optional> getPermanentFailCodes(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineToolImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineToolImpl.java deleted file mode 100644 index 72daf708..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineToolImpl.java +++ /dev/null @@ -1,712 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandLineTool
- This defines the schema of the CWL Command Line Tool Description document. -
- */ -public class CommandLineToolImpl extends SaveableImpl implements CommandLineTool { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/id
- *
- * The unique identifier for this object. - * - * Only useful for `$graph` at `Process` level. Should not be exposed - * to users in graphical or terminal user interfaces. - * *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private CommandLineTool_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/class
- - */ - - public CommandLineTool_class getClass_() { - return this.class_; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.List inputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - public java.util.List getInputs() { - return this.inputs; - } - - private java.util.List outputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - public java.util.List getOutputs() { - return this.outputs; - } - - private java.util.Optional> requirements; - - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - public java.util.Optional> getRequirements() { - return this.requirements; - } - - private java.util.Optional> hints; - - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - public java.util.Optional> getHints() { - return this.hints; - } - - private java.util.Optional cwlVersion; - - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - public java.util.Optional getCwlVersion() { - return this.cwlVersion; - } - - private java.util.Optional> intent; - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/intent
- *
- * An identifier for the type of computational operation, of this Process. - * Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for - * [`CommandLineTool`](CommandLineTool.html#CommandLineTool), - * [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). - * - * If provided, then this must be an IRI of a concept node that - * represents the type of operation, preferably defined within an ontology. - * - * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), - * like [Alignment](http://edamontology.org/operation_2928), - * or [Clustering](http://edamontology.org/operation_3432); or a more - * specific Operation concept like - * [Split read mapping](http://edamontology.org/operation_3199). - * *
- */ - - public java.util.Optional> getIntent() { - return this.intent; - } - - private Object baseCommand; - - /** - * Getter for property https://w3id.org/cwl/cwl#baseCommand
- *
- * Specifies the program to execute. If an array, the first element of - * the array is the command to execute, and subsequent elements are - * mandatory command line arguments. The elements in `baseCommand` must - * appear before any command line bindings from `inputBinding` or - * `arguments`. - * - * If `baseCommand` is not provided or is an empty array, the first - * element of the command line produced after processing `inputBinding` or - * `arguments` must be used as the program to execute. - * - * If the program includes a path separator character it must - * be an absolute path, otherwise it is an error. If the program does not - * include a path separator, search the `$PATH` variable in the runtime - * environment of the workflow runner find the absolute path of the - * executable. - * *
- */ - - public Object getBaseCommand() { - return this.baseCommand; - } - - private java.util.Optional> arguments; - - /** - * Getter for property https://w3id.org/cwl/cwl#arguments
- *
- * Command line bindings which are not directly associated with input - * parameters. If the value is a string, it is used as a string literal - * argument. If it is an Expression, the result of the evaluation is used - * as an argument. - * *
- */ - - public java.util.Optional> getArguments() { - return this.arguments; - } - - private Object stdin; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdin
- *
- * A path to a file whose contents must be piped into the command's - * standard input stream. - * *
- */ - - public Object getStdin() { - return this.stdin; - } - - private Object stderr; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stderr
- *
- * Capture the command's standard error stream to a file written to - * the designated output directory. - * - * If `stderr` is a string, it specifies the file name to use. - * - * If `stderr` is an expression, the expression is evaluated and must - * return a string with the file name to use to capture stderr. If the - * return value is not a string, or the resulting path contains illegal - * characters (such as the path separator `/`) it is an error. - * *
- */ - - public Object getStderr() { - return this.stderr; - } - - private Object stdout; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/stdout
- *
- * Capture the command's standard output stream to a file written to - * the designated output directory. - * - * If the `CommandLineTool` contains logically chained commands - * (e.g. `echo a && echo b`) `stdout` must include the output of - * every command. - * - * If `stdout` is a string, it specifies the file name to use. - * - * If `stdout` is an expression, the expression is evaluated and must - * return a string with the file name to use to capture stdout. If the - * return value is not a string, or the resulting path contains illegal - * characters (such as the path separator `/`) it is an error. - * *
- */ - - public Object getStdout() { - return this.stdout; - } - - private java.util.Optional> successCodes; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/successCodes
- *
- * Exit codes that indicate the process completed successfully. - * - * If not specified, only exit code 0 is considered success. - * *
- */ - - public java.util.Optional> getSuccessCodes() { - return this.successCodes; - } - - private java.util.Optional> temporaryFailCodes; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/temporaryFailCodes
- *
- * Exit codes that indicate the process failed due to a possibly - * temporary condition, where executing the process with the same - * runtime environment and inputs may produce different results. - * - * If not specified, no exit codes are considered temporary failure. - * *
- */ - - public java.util.Optional> getTemporaryFailCodes() { - return this.temporaryFailCodes; - } - - private java.util.Optional> permanentFailCodes; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandLineTool/permanentFailCodes
- *
- * Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail. - * If not specified, all exit codes except 0 are considered permanent failure. *
- */ - - public java.util.Optional> getPermanentFailCodes() { - return this.permanentFailCodes; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandLineToolImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandLineToolImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandLineToolImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - CommandLineTool_class class_; - try { - class_ = - LoaderInstances - .uri_CommandLineTool_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.List inputs; - try { - inputs = - LoaderInstances - .idmap_inputs_array_of_CommandInputParameter - .loadField(__doc.get("inputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List outputs; - try { - outputs = - LoaderInstances - .idmap_outputs_array_of_CommandOutputParameter - .loadField(__doc.get("outputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> requirements; - - if (__doc.containsKey("requirements")) { - try { - requirements = - LoaderInstances - .idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize - .loadField(__doc.get("requirements"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - requirements = null; // won't be used but prevents compiler from complaining. - final String __message = "the `requirements` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - requirements = null; - } - java.util.Optional> hints; - - if (__doc.containsKey("hints")) { - try { - hints = - LoaderInstances - .idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_AnyInstance - .loadField(__doc.get("hints"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - hints = null; // won't be used but prevents compiler from complaining. - final String __message = "the `hints` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - hints = null; - } - java.util.Optional cwlVersion; - - if (__doc.containsKey("cwlVersion")) { - try { - cwlVersion = - LoaderInstances - .uri_optional_CWLVersion_False_True_None_None - .loadField(__doc.get("cwlVersion"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - cwlVersion = null; // won't be used but prevents compiler from complaining. - final String __message = "the `cwlVersion` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - cwlVersion = null; - } - java.util.Optional> intent; - - if (__doc.containsKey("intent")) { - try { - intent = - LoaderInstances - .uri_optional_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("intent"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - intent = null; // won't be used but prevents compiler from complaining. - final String __message = "the `intent` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - intent = null; - } - Object baseCommand; - - if (__doc.containsKey("baseCommand")) { - try { - baseCommand = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("baseCommand"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - baseCommand = null; // won't be used but prevents compiler from complaining. - final String __message = "the `baseCommand` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - baseCommand = null; - } - java.util.Optional> arguments; - - if (__doc.containsKey("arguments")) { - try { - arguments = - LoaderInstances - .optional_array_of_union_of_StringInstance_or_ExpressionLoader_or_CommandLineBinding - .loadField(__doc.get("arguments"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - arguments = null; // won't be used but prevents compiler from complaining. - final String __message = "the `arguments` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - arguments = null; - } - Object stdin; - - if (__doc.containsKey("stdin")) { - try { - stdin = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("stdin"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - stdin = null; // won't be used but prevents compiler from complaining. - final String __message = "the `stdin` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - stdin = null; - } - Object stderr; - - if (__doc.containsKey("stderr")) { - try { - stderr = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("stderr"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - stderr = null; // won't be used but prevents compiler from complaining. - final String __message = "the `stderr` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - stderr = null; - } - Object stdout; - - if (__doc.containsKey("stdout")) { - try { - stdout = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("stdout"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - stdout = null; // won't be used but prevents compiler from complaining. - final String __message = "the `stdout` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - stdout = null; - } - java.util.Optional> successCodes; - - if (__doc.containsKey("successCodes")) { - try { - successCodes = - LoaderInstances - .optional_array_of_IntegerInstance - .loadField(__doc.get("successCodes"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - successCodes = null; // won't be used but prevents compiler from complaining. - final String __message = "the `successCodes` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - successCodes = null; - } - java.util.Optional> temporaryFailCodes; - - if (__doc.containsKey("temporaryFailCodes")) { - try { - temporaryFailCodes = - LoaderInstances - .optional_array_of_IntegerInstance - .loadField(__doc.get("temporaryFailCodes"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - temporaryFailCodes = null; // won't be used but prevents compiler from complaining. - final String __message = "the `temporaryFailCodes` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - temporaryFailCodes = null; - } - java.util.Optional> permanentFailCodes; - - if (__doc.containsKey("permanentFailCodes")) { - try { - permanentFailCodes = - LoaderInstances - .optional_array_of_IntegerInstance - .loadField(__doc.get("permanentFailCodes"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - permanentFailCodes = null; // won't be used but prevents compiler from complaining. - final String __message = "the `permanentFailCodes` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - permanentFailCodes = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (java.util.Optional) id; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.inputs = (java.util.List) inputs; - this.outputs = (java.util.List) outputs; - this.requirements = (java.util.Optional>) requirements; - this.hints = (java.util.Optional>) hints; - this.cwlVersion = (java.util.Optional) cwlVersion; - this.intent = (java.util.Optional>) intent; - this.class_ = (CommandLineTool_class) class_; - this.baseCommand = (Object) baseCommand; - this.arguments = (java.util.Optional>) arguments; - this.stdin = (Object) stdin; - this.stderr = (Object) stderr; - this.stdout = (Object) stdout; - this.successCodes = (java.util.Optional>) successCodes; - this.temporaryFailCodes = (java.util.Optional>) temporaryFailCodes; - this.permanentFailCodes = (java.util.Optional>) permanentFailCodes; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id", "label", "doc", "inputs", "outputs", "requirements", "hints", "cwlVersion", "intent", "class", "baseCommand", "arguments", "stdin", "stderr", "stdout", "successCodes", "temporaryFailCodes", "permanentFailCodes"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineTool_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineTool_class.java deleted file mode 100644 index ca9bb74b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandLineTool_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum CommandLineTool_class { - COMMANDLINETOOL("CommandLineTool"); - - private static String[] symbols = new String[] {"CommandLineTool"}; - private String docVal; - - private CommandLineTool_class(final String docVal) { - this.docVal = docVal; - } - - public static CommandLineTool_class fromDocumentVal(final String docVal) { - for(final CommandLineTool_class val : CommandLineTool_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", CommandLineTool_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputArraySchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputArraySchema.java deleted file mode 100644 index 5456f569..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputArraySchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputArraySchema
This interface is implemented by {@link CommandOutputArraySchemaImpl}
- */ -public interface CommandOutputArraySchema extends OutputArraySchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - Object getItems(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - Array_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputArraySchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputArraySchemaImpl.java deleted file mode 100644 index f7aded0f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputArraySchemaImpl.java +++ /dev/null @@ -1,232 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputArraySchema
- */ -public class CommandOutputArraySchemaImpl extends SaveableImpl implements CommandOutputArraySchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private Object items; - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - public Object getItems() { - return this.items; - } - - private Array_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - public Array_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandOutputArraySchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandOutputArraySchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandOutputArraySchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - Object items; - try { - items = - LoaderInstances - .uri_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("items"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - items = null; // won't be used but prevents compiler from complaining. - final String __message = "the `items` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Array_name type; - try { - type = - LoaderInstances - .typedsl_Array_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.items = (Object) items; - this.type = (Array_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("items", "type", "label", "doc", "name"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBinding.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBinding.java deleted file mode 100644 index be7e7d0f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBinding.java +++ /dev/null @@ -1,139 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputBinding
This interface is implemented by {@link CommandOutputBindingImpl}
- Describes how to generate an output parameter based on the files produced - by a CommandLineTool. - - The output parameter value is generated by applying these operations in the - following order: - - - glob - - loadContents - - outputEval - - secondaryFiles -
- */ -public interface CommandOutputBinding extends LoadContents, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputBinding/glob
- *
- * Find files or directories relative to the output directory, using POSIX - * glob(3) pathname matching. If an array is provided, find files or - * directories that match any pattern in the array. If an expression is - * provided, the expression must return a string or an array of strings, - * which will then be evaluated as one or more glob patterns. Must only - * match and return files/directories which actually exist. - * - * If the value of glob is a relative path pattern (does not - * begin with a slash '/') then it is resolved relative to the - * output directory. If the value of the glob is an absolute - * path pattern (it does begin with a slash '/') then it must - * refer to a path within the output directory. It is an error - * if any glob resolves to a path outside the output directory. - * Specifically this means globs that resolve to paths outside the output - * directory are illegal. - * - * A glob may match a path within the output directory which is - * actually a symlink to another file. In this case, the - * expected behavior is for the resulting File/Directory object to take the - * `basename` (and corresponding `nameroot` and `nameext`) of the - * symlink. The `location` of the File/Directory is implementation - * dependent, but logically the File/Directory should have the same content - * as the symlink target. Platforms may stage output files/directories to - * cloud storage that lack the concept of a symlink. In - * this case file content and directories may be duplicated, or (to avoid - * duplication) the File/Directory `location` may refer to the symlink - * target. - * - * It is an error if a symlink in the output directory (or any - * symlink in a chain of links) refers to any file or directory - * that is not under an input or output directory. - * - * Implementations may shut down a container before globbing - * output, so globs and expressions must not assume access to the - * container filesystem except for declared input and output. - * *
- */ - - Object getGlob(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputBinding/outputEval
- *
- * Evaluate an expression to generate the output value. If - * `glob` was specified, the value of `self` must be an array - * containing file objects that were matched. If no files were - * matched, `self` must be a zero length array; if a single file - * was matched, the value of `self` is an array of a single - * element. The exit code of the process is - * available in the expression as `runtime.exitCode`. - * - * Additionally, if `loadContents` is true, the file must be a - * UTF-8 text file 64 KiB or smaller, and the implementation must - * read the entire contents of the file (or file array) and place - * it in the `contents` field of the File object for use in - * `outputEval`. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * - * If a tool needs to return a large amount of structured data to - * the workflow, loading the output object from `cwl.output.json` - * bypasses `outputEval` and is not subject to the 64 KiB - * `loadContents` limit. - * *
- */ - - java.util.Optional getOutputEval(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBindingImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBindingImpl.java deleted file mode 100644 index 14eda29e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputBindingImpl.java +++ /dev/null @@ -1,283 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputBinding
- Describes how to generate an output parameter based on the files produced - by a CommandLineTool. - - The output parameter value is generated by applying these operations in the - following order: - - - glob - - loadContents - - outputEval - - secondaryFiles -
- */ -public class CommandOutputBindingImpl extends SaveableImpl implements CommandOutputBinding { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - private Object glob; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputBinding/glob
- *
- * Find files or directories relative to the output directory, using POSIX - * glob(3) pathname matching. If an array is provided, find files or - * directories that match any pattern in the array. If an expression is - * provided, the expression must return a string or an array of strings, - * which will then be evaluated as one or more glob patterns. Must only - * match and return files/directories which actually exist. - * - * If the value of glob is a relative path pattern (does not - * begin with a slash '/') then it is resolved relative to the - * output directory. If the value of the glob is an absolute - * path pattern (it does begin with a slash '/') then it must - * refer to a path within the output directory. It is an error - * if any glob resolves to a path outside the output directory. - * Specifically this means globs that resolve to paths outside the output - * directory are illegal. - * - * A glob may match a path within the output directory which is - * actually a symlink to another file. In this case, the - * expected behavior is for the resulting File/Directory object to take the - * `basename` (and corresponding `nameroot` and `nameext`) of the - * symlink. The `location` of the File/Directory is implementation - * dependent, but logically the File/Directory should have the same content - * as the symlink target. Platforms may stage output files/directories to - * cloud storage that lack the concept of a symlink. In - * this case file content and directories may be duplicated, or (to avoid - * duplication) the File/Directory `location` may refer to the symlink - * target. - * - * It is an error if a symlink in the output directory (or any - * symlink in a chain of links) refers to any file or directory - * that is not under an input or output directory. - * - * Implementations may shut down a container before globbing - * output, so globs and expressions must not assume access to the - * container filesystem except for declared input and output. - * *
- */ - - public Object getGlob() { - return this.glob; - } - - private java.util.Optional outputEval; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputBinding/outputEval
- *
- * Evaluate an expression to generate the output value. If - * `glob` was specified, the value of `self` must be an array - * containing file objects that were matched. If no files were - * matched, `self` must be a zero length array; if a single file - * was matched, the value of `self` is an array of a single - * element. The exit code of the process is - * available in the expression as `runtime.exitCode`. - * - * Additionally, if `loadContents` is true, the file must be a - * UTF-8 text file 64 KiB or smaller, and the implementation must - * read the entire contents of the file (or file array) and place - * it in the `contents` field of the File object for use in - * `outputEval`. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * - * If a tool needs to return a large amount of structured data to - * the workflow, loading the output object from `cwl.output.json` - * bypasses `outputEval` and is not subject to the 64 KiB - * `loadContents` limit. - * *
- */ - - public java.util.Optional getOutputEval() { - return this.outputEval; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandOutputBindingImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandOutputBindingImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandOutputBindingImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - Object glob; - - if (__doc.containsKey("glob")) { - try { - glob = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader_or_array_of_StringInstance - .loadField(__doc.get("glob"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - glob = null; // won't be used but prevents compiler from complaining. - final String __message = "the `glob` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - glob = null; - } - java.util.Optional outputEval; - - if (__doc.containsKey("outputEval")) { - try { - outputEval = - LoaderInstances - .optional_ExpressionLoader - .loadField(__doc.get("outputEval"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputEval = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputEval` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - outputEval = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - this.glob = (Object) glob; - this.outputEval = (java.util.Optional) outputEval; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("loadContents", "loadListing", "glob", "outputEval"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputEnumSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputEnumSchema.java deleted file mode 100644 index 34d2562e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputEnumSchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputEnumSchema
This interface is implemented by {@link CommandOutputEnumSchemaImpl}
- */ -public interface CommandOutputEnumSchema extends OutputEnumSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - java.util.List getSymbols(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - Enum_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputEnumSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputEnumSchemaImpl.java deleted file mode 100644 index 5ddcaf32..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputEnumSchemaImpl.java +++ /dev/null @@ -1,232 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputEnumSchema
- */ -public class CommandOutputEnumSchemaImpl extends SaveableImpl implements CommandOutputEnumSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.List symbols; - - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - public java.util.List getSymbols() { - return this.symbols; - } - - private Enum_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - public Enum_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandOutputEnumSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandOutputEnumSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandOutputEnumSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.List symbols; - try { - symbols = - LoaderInstances - .uri_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("symbols"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - symbols = null; // won't be used but prevents compiler from complaining. - final String __message = "the `symbols` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Enum_name type; - try { - type = - LoaderInstances - .typedsl_Enum_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.name = (java.util.Optional) name; - this.symbols = (java.util.List) symbols; - this.type = (Enum_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("name", "symbols", "type", "label", "doc"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameter.java deleted file mode 100644 index 9ebbbcc9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameter.java +++ /dev/null @@ -1,137 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputParameter
This interface is implemented by {@link CommandOutputParameterImpl}
- An output parameter for a CommandLineTool.
- */ -public interface CommandOutputParameter extends OutputParameter, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - String getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputParameter/outputBinding
- *
- * Describes how to generate this output object based on the files produced by a CommandLineTool *
- */ - - java.util.Optional getOutputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameterImpl.java deleted file mode 100644 index 66e3b3cf..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputParameterImpl.java +++ /dev/null @@ -1,376 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputParameter
- An output parameter for a CommandLineTool.
- */ -public class CommandOutputParameterImpl extends SaveableImpl implements CommandOutputParameter { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - public String getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional outputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputParameter/outputBinding
- *
- * Describes how to generate this output object based on the files produced by a CommandLineTool *
- */ - - public java.util.Optional getOutputBinding() { - return this.outputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandOutputParameterImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandOutputParameterImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandOutputParameterImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - if (id == null) { - if (__docRoot != null) { - id = __docRoot; - } else { - throw new ValidationException("Missing id"); - } - } - __baseUri = (String) id; - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_stdout_or_stderr_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional outputBinding; - - if (__doc.containsKey("outputBinding")) { - try { - outputBinding = - LoaderInstances - .optional_CommandOutputBinding - .loadField(__doc.get("outputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - outputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.doc = (Object) doc; - this.id = (String) id; - this.format = (Object) format; - this.type = (Object) type; - this.outputBinding = (java.util.Optional) outputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("label", "secondaryFiles", "streamable", "doc", "id", "format", "type", "outputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordField.java deleted file mode 100644 index 835ec36e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordField.java +++ /dev/null @@ -1,139 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputRecordField
This interface is implemented by {@link CommandOutputRecordFieldImpl}
- */ -public interface CommandOutputRecordField extends OutputRecordField, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - String getName(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputRecordField/outputBinding
- *
- * Describes how to generate this output object based on the files - * produced by a CommandLineTool - * *
- */ - - java.util.Optional getOutputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordFieldImpl.java deleted file mode 100644 index 38f5477c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordFieldImpl.java +++ /dev/null @@ -1,378 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordField
- */ -public class CommandOutputRecordFieldImpl extends SaveableImpl implements CommandOutputRecordField { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String name; - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - public String getName() { - return this.name; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private java.util.Optional outputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#CommandOutputRecordField/outputBinding
- *
- * Describes how to generate this output object based on the files - * produced by a CommandLineTool - * *
- */ - - public java.util.Optional getOutputBinding() { - return this.outputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandOutputRecordFieldImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandOutputRecordFieldImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandOutputRecordFieldImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - if (name == null) { - if (__docRoot != null) { - name = __docRoot; - } else { - throw new ValidationException("Missing name"); - } - } - __baseUri = (String) name; - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional outputBinding; - - if (__doc.containsKey("outputBinding")) { - try { - outputBinding = - LoaderInstances - .optional_CommandOutputBinding - .loadField(__doc.get("outputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - outputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.doc = (Object) doc; - this.name = (String) name; - this.type = (Object) type; - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.format = (Object) format; - this.outputBinding = (java.util.Optional) outputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("doc", "name", "type", "label", "secondaryFiles", "streamable", "format", "outputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordSchema.java deleted file mode 100644 index 97b04cb0..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordSchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputRecordSchema
This interface is implemented by {@link CommandOutputRecordSchemaImpl}
- */ -public interface CommandOutputRecordSchema extends OutputRecordSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - java.util.Optional> getFields(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - Record_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordSchemaImpl.java deleted file mode 100644 index f0b9e058..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/CommandOutputRecordSchemaImpl.java +++ /dev/null @@ -1,238 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordSchema
- */ -public class CommandOutputRecordSchemaImpl extends SaveableImpl implements CommandOutputRecordSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.Optional> fields; - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - public java.util.Optional> getFields() { - return this.fields; - } - - private Record_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - public Record_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of CommandOutputRecordSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public CommandOutputRecordSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("CommandOutputRecordSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.Optional> fields; - - if (__doc.containsKey("fields")) { - try { - fields = - LoaderInstances - .idmap_fields_optional_array_of_CommandOutputRecordField - .loadField(__doc.get("fields"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - fields = null; // won't be used but prevents compiler from complaining. - final String __message = "the `fields` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - fields = null; - } - Record_name type; - try { - type = - LoaderInstances - .typedsl_Record_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.fields = (java.util.Optional>) fields; - this.type = (Record_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("fields", "type", "label", "doc", "name"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Directory.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Directory.java deleted file mode 100644 index 45ebf075..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Directory.java +++ /dev/null @@ -1,154 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Directory
This interface is implemented by {@link DirectoryImpl}
- Represents a directory to present to a command line tool. - - Directories are represented as objects with `class` of `Directory`. Directory objects have - a number of properties that provide metadata about the directory. - - The `location` property of a Directory is a IRI that uniquely identifies - the directory. Implementations must support the file:// IRI scheme and may - support other schemes such as http://. Alternately to `location`, - implementations must also accept the `path` property on Directory, which - must be a filesystem path available on the same host as the CWL runner (for - inputs) or the runtime environment of a command line tool execution (for - command line tool outputs). - - A Directory object may have a `listing` field. This is a list of File and - Directory objects that are contained in the Directory. For each entry in - `listing`, the `basename` property defines the name of the File or - Subdirectory when staged to disk. If `listing` is not provided, the - implementation must have some way of fetching the Directory listing at - runtime based on the `location` field. - - If a Directory does not have `location`, it is a Directory literal. A - Directory literal must provide `listing`. Directory literals must be - created on disk at runtime as needed. - - The resources in a Directory literal do not need to have any implied - relationship in their `location`. For example, a Directory listing may - contain two files located on different hosts. It is the responsibility of - the runtime to ensure that those files are staged to disk appropriately. - Secondary files associated with files in `listing` must also be staged to - the same Directory. - - When executing a CommandLineTool, Directories must be recursively staged - first and have local values of `path` assigned. - - Directory objects in CommandLineTool output must provide either a - `location` IRI or a `path` property in the context of the tool execution - runtime (local to the compute node, or within the executing container). - - An ExpressionTool may forward file references from input to output by using - the same value for `location`. - - Name conflicts (the same `basename` appearing multiple times in `listing` - or in any entry in `secondaryFiles` in the listing) is a fatal error. -
- */ -public interface Directory extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Directory/class
- *
- * Must be `Directory` to indicate this object describes a Directory. *
- */ - - Directory_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#Directory/location
- *
- * An IRI that identifies the directory resource. This may be a relative - * reference, in which case it must be resolved using the base IRI of the - * document. The location may refer to a local or remote resource. If - * the `listing` field is not set, the implementation must use the - * location IRI to retrieve directory listing. If an implementation is - * unable to retrieve the directory listing stored at a remote resource (due to - * unsupported protocol, access denied, or other issue) it must signal an - * error. - * - * If the `location` field is not provided, the `listing` field must be - * provided. The implementation must assign a unique identifier for - * the `location` field. - * - * If the `path` field is provided but the `location` field is not, an - * implementation may assign the value of the `path` field to `location`, - * then follow the rules above. - * *
- */ - - java.util.Optional getLocation(); - /** - * Getter for property https://w3id.org/cwl/cwl#path
- *
- * The local path where the Directory is made available prior to executing a - * CommandLineTool. This must be set by the implementation. This field - * must not be used in any other context. The command line tool being - * executed must be able to access the directory at `path` using the POSIX - * `opendir(2)` syscall. - * - * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * `<space>`, `<tab>`, and `<newline>`) or characters - * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) - * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) - * then implementations may terminate the process with a - * `permanentFailure`. - * *
- */ - - java.util.Optional getPath(); - /** - * Getter for property https://w3id.org/cwl/cwl#Directory/basename
- *
- * The base name of the directory, that is, the name of the file without any - * leading directory path. The base name must not contain a slash `/`. - * - * If not provided, the implementation must set this field based on the - * `location` field by taking the final path component after parsing - * `location` as an IRI. If `basename` is provided, it is not required to - * match the value from `location`. - * - * When this file is made available to a CommandLineTool, it must be named - * with `basename`, i.e. the final component of the `path` field must match - * `basename`. - * *
- */ - - java.util.Optional getBasename(); - /** - * Getter for property https://w3id.org/cwl/cwl#listing
- *
- * List of files or subdirectories contained in this directory. The name - * of each file or subdirectory is determined by the `basename` field of - * each `File` or `Directory` object. It is an error if a `File` shares a - * `basename` with any other entry in `listing`. If two or more - * `Directory` object share the same `basename`, this must be treated as - * equivalent to a single subdirectory with the listings recursively - * merged. - * *
- */ - - java.util.Optional> getListing(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirectoryImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirectoryImpl.java deleted file mode 100644 index c3fe5326..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirectoryImpl.java +++ /dev/null @@ -1,315 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#Directory
- Represents a directory to present to a command line tool. - - Directories are represented as objects with `class` of `Directory`. Directory objects have - a number of properties that provide metadata about the directory. - - The `location` property of a Directory is a IRI that uniquely identifies - the directory. Implementations must support the file:// IRI scheme and may - support other schemes such as http://. Alternately to `location`, - implementations must also accept the `path` property on Directory, which - must be a filesystem path available on the same host as the CWL runner (for - inputs) or the runtime environment of a command line tool execution (for - command line tool outputs). - - A Directory object may have a `listing` field. This is a list of File and - Directory objects that are contained in the Directory. For each entry in - `listing`, the `basename` property defines the name of the File or - Subdirectory when staged to disk. If `listing` is not provided, the - implementation must have some way of fetching the Directory listing at - runtime based on the `location` field. - - If a Directory does not have `location`, it is a Directory literal. A - Directory literal must provide `listing`. Directory literals must be - created on disk at runtime as needed. - - The resources in a Directory literal do not need to have any implied - relationship in their `location`. For example, a Directory listing may - contain two files located on different hosts. It is the responsibility of - the runtime to ensure that those files are staged to disk appropriately. - Secondary files associated with files in `listing` must also be staged to - the same Directory. - - When executing a CommandLineTool, Directories must be recursively staged - first and have local values of `path` assigned. - - Directory objects in CommandLineTool output must provide either a - `location` IRI or a `path` property in the context of the tool execution - runtime (local to the compute node, or within the executing container). - - An ExpressionTool may forward file references from input to output by using - the same value for `location`. - - Name conflicts (the same `basename` appearing multiple times in `listing` - or in any entry in `secondaryFiles` in the listing) is a fatal error. -
- */ -public class DirectoryImpl extends SaveableImpl implements Directory { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Directory_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#Directory/class
- *
- * Must be `Directory` to indicate this object describes a Directory. *
- */ - - public Directory_class getClass_() { - return this.class_; - } - - private java.util.Optional location; - - /** - * Getter for property https://w3id.org/cwl/cwl#Directory/location
- *
- * An IRI that identifies the directory resource. This may be a relative - * reference, in which case it must be resolved using the base IRI of the - * document. The location may refer to a local or remote resource. If - * the `listing` field is not set, the implementation must use the - * location IRI to retrieve directory listing. If an implementation is - * unable to retrieve the directory listing stored at a remote resource (due to - * unsupported protocol, access denied, or other issue) it must signal an - * error. - * - * If the `location` field is not provided, the `listing` field must be - * provided. The implementation must assign a unique identifier for - * the `location` field. - * - * If the `path` field is provided but the `location` field is not, an - * implementation may assign the value of the `path` field to `location`, - * then follow the rules above. - * *
- */ - - public java.util.Optional getLocation() { - return this.location; - } - - private java.util.Optional path; - - /** - * Getter for property https://w3id.org/cwl/cwl#path
- *
- * The local path where the Directory is made available prior to executing a - * CommandLineTool. This must be set by the implementation. This field - * must not be used in any other context. The command line tool being - * executed must be able to access the directory at `path` using the POSIX - * `opendir(2)` syscall. - * - * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * `<space>`, `<tab>`, and `<newline>`) or characters - * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) - * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) - * then implementations may terminate the process with a - * `permanentFailure`. - * *
- */ - - public java.util.Optional getPath() { - return this.path; - } - - private java.util.Optional basename; - - /** - * Getter for property https://w3id.org/cwl/cwl#Directory/basename
- *
- * The base name of the directory, that is, the name of the file without any - * leading directory path. The base name must not contain a slash `/`. - * - * If not provided, the implementation must set this field based on the - * `location` field by taking the final path component after parsing - * `location` as an IRI. If `basename` is provided, it is not required to - * match the value from `location`. - * - * When this file is made available to a CommandLineTool, it must be named - * with `basename`, i.e. the final component of the `path` field must match - * `basename`. - * *
- */ - - public java.util.Optional getBasename() { - return this.basename; - } - - private java.util.Optional> listing; - - /** - * Getter for property https://w3id.org/cwl/cwl#listing
- *
- * List of files or subdirectories contained in this directory. The name - * of each file or subdirectory is determined by the `basename` field of - * each `File` or `Directory` object. It is an error if a `File` shares a - * `basename` with any other entry in `listing`. If two or more - * `Directory` object share the same `basename`, this must be treated as - * equivalent to a single subdirectory with the listings recursively - * merged. - * *
- */ - - public java.util.Optional> getListing() { - return this.listing; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of DirectoryImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public DirectoryImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("DirectoryImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Directory_class class_; - try { - class_ = - LoaderInstances - .uri_Directory_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional location; - - if (__doc.containsKey("location")) { - try { - location = - LoaderInstances - .uri_optional_StringInstance_False_False_None_None - .loadField(__doc.get("location"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - location = null; // won't be used but prevents compiler from complaining. - final String __message = "the `location` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - location = null; - } - java.util.Optional path; - - if (__doc.containsKey("path")) { - try { - path = - LoaderInstances - .uri_optional_StringInstance_False_False_None_None - .loadField(__doc.get("path"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - path = null; // won't be used but prevents compiler from complaining. - final String __message = "the `path` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - path = null; - } - java.util.Optional basename; - - if (__doc.containsKey("basename")) { - try { - basename = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("basename"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - basename = null; // won't be used but prevents compiler from complaining. - final String __message = "the `basename` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - basename = null; - } - java.util.Optional> listing; - - if (__doc.containsKey("listing")) { - try { - listing = - LoaderInstances - .optional_array_of_union_of_File_or_Directory - .loadField(__doc.get("listing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - listing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `listing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - listing = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (Directory_class) class_; - this.location = (java.util.Optional) location; - this.path = (java.util.Optional) path; - this.basename = (java.util.Optional) basename; - this.listing = (java.util.Optional>) listing; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "location", "path", "basename", "listing"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Directory_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Directory_class.java deleted file mode 100644 index aa95ad48..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Directory_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum Directory_class { - DIRECTORY("Directory"); - - private static String[] symbols = new String[] {"Directory"}; - private String docVal; - - private Directory_class(final String docVal) { - this.docVal = docVal; - } - - public static Directory_class fromDocumentVal(final String docVal) { - for(final Directory_class val : Directory_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Directory_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Dirent.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Dirent.java deleted file mode 100644 index 1db78fe6..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Dirent.java +++ /dev/null @@ -1,123 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Dirent
This interface is implemented by {@link DirentImpl}
- Define a file or subdirectory that must be staged to a particular - place prior to executing the command line tool. May be the result - of executing an expression, such as building a configuration file - from a template. - - Usually files are staged within the [designated output directory](#Runtime_environment). - However, under certain circumstances, files may be staged at - arbitrary locations, see discussion for `entryname`. -
- */ -public interface Dirent extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#entryname
- *
- * The "target" name of the file or subdirectory. If `entry` is - * a File or Directory, the `entryname` field overrides the value - * of `basename` of the File or Directory object. - * - * * Required when `entry` evaluates to file contents only - * * Optional when `entry` evaluates to a File or Directory object with a `basename` - * * Invalid when `entry` evaluates to an array of File or Directory objects. - * - * If `entryname` is a relative path, it specifies a name within - * the designated output directory. A relative path starting - * with `../` or that resolves to location above the designated output directory is an error. - * - * If `entryname` is an absolute path (starts with a slash `/`) - * it is an error unless the following conditions are met: - * - * * `DockerRequirement` is present in `requirements` - * * The program is will run inside a software container - * where, from the perspective of the program, the root - * filesystem is not shared with any other user or - * running program. - * - * In this case, and the above conditions are met, then - * `entryname` may specify the absolute path within the container - * where the file or directory must be placed. - * *
- */ - - Object getEntryname(); - /** - * Getter for property https://w3id.org/cwl/cwl#entry
- *
- * If the value is a string literal or an expression which evaluates to a - * string, a new text file must be created with the string as the file contents. - * - * If the value is an expression that evaluates to a `File` or - * `Directory` object, or an array of `File` or `Directory` - * objects, this indicates the referenced file or directory - * should be added to the designated output directory prior to - * executing the tool. - * - * If the value is an expression that evaluates to `null`, - * nothing is added to the designated output directory, the entry - * has no effect. - * - * If the value is an expression that evaluates to some other - * array, number, or object not consisting of `File` or - * `Directory` objects, a new file must be created with the value - * serialized to JSON text as the file contents. The JSON - * serialization behavior should match the behavior of string - * interpolation of [Parameter - * references](#Parameter_references). - * *
- */ - - Object getEntry(); - /** - * Getter for property https://w3id.org/cwl/cwl#Dirent/writable
- *
- * If true, the File or Directory (or array of Files or - * Directories) declared in `entry` must be writable by the tool. - * - * Changes to the file or directory must be isolated and not - * visible by any other CommandLineTool process. This may be - * implemented by making a copy of the original file or - * directory. - * - * Disruptive changes to the referenced file or directory must not - * be allowed unless `InplaceUpdateRequirement.inplaceUpdate` is true. - * - * Default false (files and directories read-only by default). - * - * A directory marked as `writable: true` implies that all files and - * subdirectories are recursively writable as well. - * - * If `writable` is false, the file may be made available using a - * bind mount or file system link to avoid unnecessary copying of - * the input file. Command line tools may receive an error on - * attempting to rename or delete files or directories that are - * not explicitly marked as writable. - * *
- */ - - java.util.Optional getWritable(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirentImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirentImpl.java deleted file mode 100644 index 9c547a2d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DirentImpl.java +++ /dev/null @@ -1,238 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#Dirent
- Define a file or subdirectory that must be staged to a particular - place prior to executing the command line tool. May be the result - of executing an expression, such as building a configuration file - from a template. - - Usually files are staged within the [designated output directory](#Runtime_environment). - However, under certain circumstances, files may be staged at - arbitrary locations, see discussion for `entryname`. -
- */ -public class DirentImpl extends SaveableImpl implements Dirent { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Object entryname; - - /** - * Getter for property https://w3id.org/cwl/cwl#entryname
- *
- * The "target" name of the file or subdirectory. If `entry` is - * a File or Directory, the `entryname` field overrides the value - * of `basename` of the File or Directory object. - * - * * Required when `entry` evaluates to file contents only - * * Optional when `entry` evaluates to a File or Directory object with a `basename` - * * Invalid when `entry` evaluates to an array of File or Directory objects. - * - * If `entryname` is a relative path, it specifies a name within - * the designated output directory. A relative path starting - * with `../` or that resolves to location above the designated output directory is an error. - * - * If `entryname` is an absolute path (starts with a slash `/`) - * it is an error unless the following conditions are met: - * - * * `DockerRequirement` is present in `requirements` - * * The program is will run inside a software container - * where, from the perspective of the program, the root - * filesystem is not shared with any other user or - * running program. - * - * In this case, and the above conditions are met, then - * `entryname` may specify the absolute path within the container - * where the file or directory must be placed. - * *
- */ - - public Object getEntryname() { - return this.entryname; - } - - private Object entry; - - /** - * Getter for property https://w3id.org/cwl/cwl#entry
- *
- * If the value is a string literal or an expression which evaluates to a - * string, a new text file must be created with the string as the file contents. - * - * If the value is an expression that evaluates to a `File` or - * `Directory` object, or an array of `File` or `Directory` - * objects, this indicates the referenced file or directory - * should be added to the designated output directory prior to - * executing the tool. - * - * If the value is an expression that evaluates to `null`, - * nothing is added to the designated output directory, the entry - * has no effect. - * - * If the value is an expression that evaluates to some other - * array, number, or object not consisting of `File` or - * `Directory` objects, a new file must be created with the value - * serialized to JSON text as the file contents. The JSON - * serialization behavior should match the behavior of string - * interpolation of [Parameter - * references](#Parameter_references). - * *
- */ - - public Object getEntry() { - return this.entry; - } - - private java.util.Optional writable; - - /** - * Getter for property https://w3id.org/cwl/cwl#Dirent/writable
- *
- * If true, the File or Directory (or array of Files or - * Directories) declared in `entry` must be writable by the tool. - * - * Changes to the file or directory must be isolated and not - * visible by any other CommandLineTool process. This may be - * implemented by making a copy of the original file or - * directory. - * - * Disruptive changes to the referenced file or directory must not - * be allowed unless `InplaceUpdateRequirement.inplaceUpdate` is true. - * - * Default false (files and directories read-only by default). - * - * A directory marked as `writable: true` implies that all files and - * subdirectories are recursively writable as well. - * - * If `writable` is false, the file may be made available using a - * bind mount or file system link to avoid unnecessary copying of - * the input file. Command line tools may receive an error on - * attempting to rename or delete files or directories that are - * not explicitly marked as writable. - * *
- */ - - public java.util.Optional getWritable() { - return this.writable; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of DirentImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public DirentImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("DirentImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Object entryname; - - if (__doc.containsKey("entryname")) { - try { - entryname = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("entryname"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - entryname = null; // won't be used but prevents compiler from complaining. - final String __message = "the `entryname` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - entryname = null; - } - Object entry; - try { - entry = - LoaderInstances - .union_of_StringInstance_or_ExpressionLoader - .loadField(__doc.get("entry"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - entry = null; // won't be used but prevents compiler from complaining. - final String __message = "the `entry` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional writable; - - if (__doc.containsKey("writable")) { - try { - writable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("writable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - writable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `writable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - writable = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.entryname = (Object) entryname; - this.entry = (Object) entry; - this.writable = (java.util.Optional) writable; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("entryname", "entry", "writable"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirement.java deleted file mode 100644 index 81d46d9d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirement.java +++ /dev/null @@ -1,138 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#DockerRequirement
This interface is implemented by {@link DockerRequirementImpl}
- Indicates that a workflow component should be run in a - [Docker](https://docker.com) or Docker-compatible (such as - [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and - specifies how to fetch or build the image. - - If a CommandLineTool lists `DockerRequirement` under - `hints` (or `requirements`), it may (or must) be run in the specified Docker - container. - - The platform must first acquire or install the correct Docker image as - specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`. - - The platform must execute the tool in the container using `docker run` with - the appropriate Docker image and tool command line. - - The workflow platform may provide input files and the designated output - directory through the use of volume bind mounts. The platform should rewrite - file paths in the input object to correspond to the Docker bind mounted - locations. That is, the platform should rewrite values in the parameter context - such as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths - within the container. The platform must ensure that `runtime.outdir` and - `runtime.tmpdir` are distinct directories. - - When running a tool contained in Docker, the workflow platform must not - assume anything about the contents of the Docker container, such as the - presence or absence of specific software, except to assume that the - generated command line represents a valid command within the runtime - environment of the container. - - A container image may specify an - [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint) - and/or - [CMD](https://docs.docker.com/engine/reference/builder/#cmd). - Command line arguments will be appended after all elements of - ENTRYPOINT, and will override all elements specified using CMD (in - other words, CMD is only used when the CommandLineTool definition - produces an empty command line). - - Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility - concerns of the implicit hidden execution point (For further discussion, see - [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable - CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD. - CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the - `requirements` section. - - ## Interaction with other requirements - - If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a - DockerRequirement, the environment variables must be provided to Docker - using `--env` or `--env-file` and interact with the container's preexisting - environment as defined by Docker. -
- */ -public interface DockerRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/class
- *
- * Always 'DockerRequirement' *
- */ - - DockerRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerPull
- *
- * Specify a Docker image to retrieve using `docker pull`. Can contain the - * immutable digest to ensure an exact container is used: - * `dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2` - * *
- */ - - java.util.Optional getDockerPull(); - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerLoad
- *
- * Specify an HTTP URL from which to download a Docker image using `docker load`. *
- */ - - java.util.Optional getDockerLoad(); - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerFile
- *
- * Supply the contents of a Dockerfile which will be built using `docker build`. *
- */ - - java.util.Optional getDockerFile(); - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerImport
- *
- * Provide HTTP URL to download and gunzip a Docker images using `docker import. *
- */ - - java.util.Optional getDockerImport(); - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerImageId
- *
- * The image id that will be used for `docker run`. May be a - * human-readable image name or the image identifier hash. May be skipped - * if `dockerPull` is specified, in which case the `dockerPull` image id - * must be used. - * *
- */ - - java.util.Optional getDockerImageId(); - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerOutputDirectory
- *
- * Set the designated output directory to a specific location inside the - * Docker container. - * *
- */ - - java.util.Optional getDockerOutputDirectory(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirementImpl.java deleted file mode 100644 index 4db71713..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirementImpl.java +++ /dev/null @@ -1,345 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#DockerRequirement
- Indicates that a workflow component should be run in a - [Docker](https://docker.com) or Docker-compatible (such as - [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and - specifies how to fetch or build the image. - - If a CommandLineTool lists `DockerRequirement` under - `hints` (or `requirements`), it may (or must) be run in the specified Docker - container. - - The platform must first acquire or install the correct Docker image as - specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`. - - The platform must execute the tool in the container using `docker run` with - the appropriate Docker image and tool command line. - - The workflow platform may provide input files and the designated output - directory through the use of volume bind mounts. The platform should rewrite - file paths in the input object to correspond to the Docker bind mounted - locations. That is, the platform should rewrite values in the parameter context - such as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths - within the container. The platform must ensure that `runtime.outdir` and - `runtime.tmpdir` are distinct directories. - - When running a tool contained in Docker, the workflow platform must not - assume anything about the contents of the Docker container, such as the - presence or absence of specific software, except to assume that the - generated command line represents a valid command within the runtime - environment of the container. - - A container image may specify an - [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint) - and/or - [CMD](https://docs.docker.com/engine/reference/builder/#cmd). - Command line arguments will be appended after all elements of - ENTRYPOINT, and will override all elements specified using CMD (in - other words, CMD is only used when the CommandLineTool definition - produces an empty command line). - - Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility - concerns of the implicit hidden execution point (For further discussion, see - [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable - CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD. - CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the - `requirements` section. - - ## Interaction with other requirements - - If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a - DockerRequirement, the environment variables must be provided to Docker - using `--env` or `--env-file` and interact with the container's preexisting - environment as defined by Docker. -
- */ -public class DockerRequirementImpl extends SaveableImpl implements DockerRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private DockerRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/class
- *
- * Always 'DockerRequirement' *
- */ - - public DockerRequirement_class getClass_() { - return this.class_; - } - - private java.util.Optional dockerPull; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerPull
- *
- * Specify a Docker image to retrieve using `docker pull`. Can contain the - * immutable digest to ensure an exact container is used: - * `dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2` - * *
- */ - - public java.util.Optional getDockerPull() { - return this.dockerPull; - } - - private java.util.Optional dockerLoad; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerLoad
- *
- * Specify an HTTP URL from which to download a Docker image using `docker load`. *
- */ - - public java.util.Optional getDockerLoad() { - return this.dockerLoad; - } - - private java.util.Optional dockerFile; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerFile
- *
- * Supply the contents of a Dockerfile which will be built using `docker build`. *
- */ - - public java.util.Optional getDockerFile() { - return this.dockerFile; - } - - private java.util.Optional dockerImport; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerImport
- *
- * Provide HTTP URL to download and gunzip a Docker images using `docker import. *
- */ - - public java.util.Optional getDockerImport() { - return this.dockerImport; - } - - private java.util.Optional dockerImageId; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerImageId
- *
- * The image id that will be used for `docker run`. May be a - * human-readable image name or the image identifier hash. May be skipped - * if `dockerPull` is specified, in which case the `dockerPull` image id - * must be used. - * *
- */ - - public java.util.Optional getDockerImageId() { - return this.dockerImageId; - } - - private java.util.Optional dockerOutputDirectory; - - /** - * Getter for property https://w3id.org/cwl/cwl#DockerRequirement/dockerOutputDirectory
- *
- * Set the designated output directory to a specific location inside the - * Docker container. - * *
- */ - - public java.util.Optional getDockerOutputDirectory() { - return this.dockerOutputDirectory; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of DockerRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public DockerRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("DockerRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - DockerRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_DockerRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional dockerPull; - - if (__doc.containsKey("dockerPull")) { - try { - dockerPull = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dockerPull"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dockerPull = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dockerPull` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dockerPull = null; - } - java.util.Optional dockerLoad; - - if (__doc.containsKey("dockerLoad")) { - try { - dockerLoad = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dockerLoad"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dockerLoad = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dockerLoad` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dockerLoad = null; - } - java.util.Optional dockerFile; - - if (__doc.containsKey("dockerFile")) { - try { - dockerFile = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dockerFile"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dockerFile = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dockerFile` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dockerFile = null; - } - java.util.Optional dockerImport; - - if (__doc.containsKey("dockerImport")) { - try { - dockerImport = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dockerImport"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dockerImport = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dockerImport` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dockerImport = null; - } - java.util.Optional dockerImageId; - - if (__doc.containsKey("dockerImageId")) { - try { - dockerImageId = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dockerImageId"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dockerImageId = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dockerImageId` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dockerImageId = null; - } - java.util.Optional dockerOutputDirectory; - - if (__doc.containsKey("dockerOutputDirectory")) { - try { - dockerOutputDirectory = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dockerOutputDirectory"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dockerOutputDirectory = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dockerOutputDirectory` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dockerOutputDirectory = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (DockerRequirement_class) class_; - this.dockerPull = (java.util.Optional) dockerPull; - this.dockerLoad = (java.util.Optional) dockerLoad; - this.dockerFile = (java.util.Optional) dockerFile; - this.dockerImport = (java.util.Optional) dockerImport; - this.dockerImageId = (java.util.Optional) dockerImageId; - this.dockerOutputDirectory = (java.util.Optional) dockerOutputDirectory; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "dockerPull", "dockerLoad", "dockerFile", "dockerImport", "dockerImageId", "dockerOutputDirectory"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirement_class.java deleted file mode 100644 index 37761629..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/DockerRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum DockerRequirement_class { - DOCKERREQUIREMENT("DockerRequirement"); - - private static String[] symbols = new String[] {"DockerRequirement"}; - private String docVal; - - private DockerRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static DockerRequirement_class fromDocumentVal(final String docVal) { - for(final DockerRequirement_class val : DockerRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", DockerRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Documented.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Documented.java deleted file mode 100644 index 9980e551..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Documented.java +++ /dev/null @@ -1,35 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#Documented
- */ -public interface Documented extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnumSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnumSchema.java deleted file mode 100644 index 9daf2f80..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnumSchema.java +++ /dev/null @@ -1,50 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#EnumSchema
This interface is implemented by {@link EnumSchemaImpl}
- Define an enumerated type. -
- */ -public interface EnumSchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#EnumSchema/name
- - */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - java.util.List getSymbols(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - Enum_name getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnumSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnumSchemaImpl.java deleted file mode 100644 index 1945eefd..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnumSchemaImpl.java +++ /dev/null @@ -1,173 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/salad#EnumSchema
- Define an enumerated type. -
- */ -public class EnumSchemaImpl extends SaveableImpl implements EnumSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/salad#EnumSchema/name
- - */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.List symbols; - - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - public java.util.List getSymbols() { - return this.symbols; - } - - private Enum_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - public Enum_name getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of EnumSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public EnumSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("EnumSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.List symbols; - try { - symbols = - LoaderInstances - .uri_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("symbols"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - symbols = null; // won't be used but prevents compiler from complaining. - final String __message = "the `symbols` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Enum_name type; - try { - type = - LoaderInstances - .typedsl_Enum_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.name = (java.util.Optional) name; - this.symbols = (java.util.List) symbols; - this.type = (Enum_name) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("name", "symbols", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Enum_name.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Enum_name.java deleted file mode 100644 index eb814c9f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Enum_name.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum Enum_name { - ENUM("enum"); - - private static String[] symbols = new String[] {"enum"}; - private String docVal; - - private Enum_name(final String docVal) { - this.docVal = docVal; - } - - public static Enum_name fromDocumentVal(final String docVal) { - for(final Enum_name val : Enum_name.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Enum_name.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirement.java deleted file mode 100644 index 073635a3..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirement.java +++ /dev/null @@ -1,45 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#EnvVarRequirement
This interface is implemented by {@link EnvVarRequirementImpl}
- Define a list of environment variables which will be set in the - execution environment of the tool. See `EnvironmentDef` for details. -
- */ -public interface EnvVarRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/class
- *
- * Always 'EnvVarRequirement' *
- */ - - EnvVarRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/envDef
- *
- * The list of environment variables. *
- */ - - java.util.List getEnvDef(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirementImpl.java deleted file mode 100644 index 9e34d369..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirementImpl.java +++ /dev/null @@ -1,131 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#EnvVarRequirement
- Define a list of environment variables which will be set in the - execution environment of the tool. See `EnvironmentDef` for details. -
- */ -public class EnvVarRequirementImpl extends SaveableImpl implements EnvVarRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private EnvVarRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/class
- *
- * Always 'EnvVarRequirement' *
- */ - - public EnvVarRequirement_class getClass_() { - return this.class_; - } - - private java.util.List envDef; - - /** - * Getter for property https://w3id.org/cwl/cwl#EnvVarRequirement/envDef
- *
- * The list of environment variables. *
- */ - - public java.util.List getEnvDef() { - return this.envDef; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of EnvVarRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public EnvVarRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("EnvVarRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - EnvVarRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_EnvVarRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List envDef; - try { - envDef = - LoaderInstances - .idmap_envDef_array_of_EnvironmentDef - .loadField(__doc.get("envDef"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - envDef = null; // won't be used but prevents compiler from complaining. - final String __message = "the `envDef` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (EnvVarRequirement_class) class_; - this.envDef = (java.util.List) envDef; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "envDef"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirement_class.java deleted file mode 100644 index b02c8af1..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvVarRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum EnvVarRequirement_class { - ENVVARREQUIREMENT("EnvVarRequirement"); - - private static String[] symbols = new String[] {"EnvVarRequirement"}; - private String docVal; - - private EnvVarRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static EnvVarRequirement_class fromDocumentVal(final String docVal) { - for(final EnvVarRequirement_class val : EnvVarRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", EnvVarRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvironmentDef.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvironmentDef.java deleted file mode 100644 index 309578d4..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvironmentDef.java +++ /dev/null @@ -1,46 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#EnvironmentDef
This interface is implemented by {@link EnvironmentDefImpl}
- Define an environment variable that will be set in the runtime environment - by the workflow platform when executing the command line tool. May be the - result of executing an expression, such as getting a parameter from input. -
- */ -public interface EnvironmentDef extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#EnvironmentDef/envName
- *
- * The environment variable name *
- */ - - String getEnvName(); - /** - * Getter for property https://w3id.org/cwl/cwl#EnvironmentDef/envValue
- *
- * The environment variable value *
- */ - - Object getEnvValue(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvironmentDefImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvironmentDefImpl.java deleted file mode 100644 index 1bb4af69..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/EnvironmentDefImpl.java +++ /dev/null @@ -1,132 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#EnvironmentDef
- Define an environment variable that will be set in the runtime environment - by the workflow platform when executing the command line tool. May be the - result of executing an expression, such as getting a parameter from input. -
- */ -public class EnvironmentDefImpl extends SaveableImpl implements EnvironmentDef { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String envName; - - /** - * Getter for property https://w3id.org/cwl/cwl#EnvironmentDef/envName
- *
- * The environment variable name *
- */ - - public String getEnvName() { - return this.envName; - } - - private Object envValue; - - /** - * Getter for property https://w3id.org/cwl/cwl#EnvironmentDef/envValue
- *
- * The environment variable value *
- */ - - public Object getEnvValue() { - return this.envValue; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of EnvironmentDefImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public EnvironmentDefImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("EnvironmentDefImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String envName; - try { - envName = - LoaderInstances - .StringInstance - .loadField(__doc.get("envName"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - envName = null; // won't be used but prevents compiler from complaining. - final String __message = "the `envName` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object envValue; - try { - envValue = - LoaderInstances - .union_of_StringInstance_or_ExpressionLoader - .loadField(__doc.get("envValue"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - envValue = null; // won't be used but prevents compiler from complaining. - final String __message = "the `envValue` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.envName = (String) envName; - this.envValue = (Object) envValue; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("envName", "envValue"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Expression.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Expression.java deleted file mode 100644 index d2a1f251..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Expression.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum Expression { - EXPRESSIONPLACEHOLDER("ExpressionPlaceholder"); - - private static String[] symbols = new String[] {"ExpressionPlaceholder"}; - private String docVal; - - private Expression(final String docVal) { - this.docVal = docVal; - } - - public static Expression fromDocumentVal(final String docVal) { - for(final Expression val : Expression.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Expression.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionTool.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionTool.java deleted file mode 100644 index 1b8cd65e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionTool.java +++ /dev/null @@ -1,158 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ExpressionTool
This interface is implemented by {@link ExpressionToolImpl}
- An ExpressionTool is a type of Process object that can be run by itself - or as a Workflow step. It executes a pure Javascript expression that has - access to the same input parameters as a workflow. It is meant to be used - sparingly as a way to isolate complex Javascript expressions that need to - operate on input data and produce some result; perhaps just a - rearrangement of the inputs. No Docker software container is required - or allowed. -
- */ -public interface ExpressionTool extends Process, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/id
- *
- * The unique identifier for this object. - * - * Only useful for `$graph` at `Process` level. Should not be exposed - * to users in graphical or terminal user interfaces. - * *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#ExpressionTool/class
- - */ - - ExpressionTool_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - java.util.List getInputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - java.util.List getOutputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - java.util.Optional> getRequirements(); - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - java.util.Optional> getHints(); - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - java.util.Optional getCwlVersion(); - /** - * Getter for property https://w3id.org/cwl/cwl#Process/intent
- *
- * An identifier for the type of computational operation, of this Process. - * Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for - * [`CommandLineTool`](CommandLineTool.html#CommandLineTool), - * [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). - * - * If provided, then this must be an IRI of a concept node that - * represents the type of operation, preferably defined within an ontology. - * - * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), - * like [Alignment](http://edamontology.org/operation_2928), - * or [Clustering](http://edamontology.org/operation_3432); or a more - * specific Operation concept like - * [Split read mapping](http://edamontology.org/operation_3199). - * *
- */ - - java.util.Optional> getIntent(); - /** - * Getter for property https://w3id.org/cwl/cwl#ExpressionTool/expression
- *
- * The expression to execute. The expression must return a plain - * Javascript object which matches the output parameters of the - * ExpressionTool. - * *
- */ - - String getExpression(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolImpl.java deleted file mode 100644 index ec5f613d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolImpl.java +++ /dev/null @@ -1,453 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#ExpressionTool
- An ExpressionTool is a type of Process object that can be run by itself - or as a Workflow step. It executes a pure Javascript expression that has - access to the same input parameters as a workflow. It is meant to be used - sparingly as a way to isolate complex Javascript expressions that need to - operate on input data and produce some result; perhaps just a - rearrangement of the inputs. No Docker software container is required - or allowed. -
- */ -public class ExpressionToolImpl extends SaveableImpl implements ExpressionTool { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/id
- *
- * The unique identifier for this object. - * - * Only useful for `$graph` at `Process` level. Should not be exposed - * to users in graphical or terminal user interfaces. - * *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private ExpressionTool_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#ExpressionTool/class
- - */ - - public ExpressionTool_class getClass_() { - return this.class_; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.List inputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - public java.util.List getInputs() { - return this.inputs; - } - - private java.util.List outputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - public java.util.List getOutputs() { - return this.outputs; - } - - private java.util.Optional> requirements; - - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - public java.util.Optional> getRequirements() { - return this.requirements; - } - - private java.util.Optional> hints; - - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - public java.util.Optional> getHints() { - return this.hints; - } - - private java.util.Optional cwlVersion; - - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - public java.util.Optional getCwlVersion() { - return this.cwlVersion; - } - - private java.util.Optional> intent; - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/intent
- *
- * An identifier for the type of computational operation, of this Process. - * Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for - * [`CommandLineTool`](CommandLineTool.html#CommandLineTool), - * [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). - * - * If provided, then this must be an IRI of a concept node that - * represents the type of operation, preferably defined within an ontology. - * - * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), - * like [Alignment](http://edamontology.org/operation_2928), - * or [Clustering](http://edamontology.org/operation_3432); or a more - * specific Operation concept like - * [Split read mapping](http://edamontology.org/operation_3199). - * *
- */ - - public java.util.Optional> getIntent() { - return this.intent; - } - - private String expression; - - /** - * Getter for property https://w3id.org/cwl/cwl#ExpressionTool/expression
- *
- * The expression to execute. The expression must return a plain - * Javascript object which matches the output parameters of the - * ExpressionTool. - * *
- */ - - public String getExpression() { - return this.expression; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of ExpressionToolImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ExpressionToolImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ExpressionToolImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - ExpressionTool_class class_; - try { - class_ = - LoaderInstances - .uri_ExpressionTool_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.List inputs; - try { - inputs = - LoaderInstances - .idmap_inputs_array_of_WorkflowInputParameter - .loadField(__doc.get("inputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List outputs; - try { - outputs = - LoaderInstances - .idmap_outputs_array_of_ExpressionToolOutputParameter - .loadField(__doc.get("outputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> requirements; - - if (__doc.containsKey("requirements")) { - try { - requirements = - LoaderInstances - .idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize - .loadField(__doc.get("requirements"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - requirements = null; // won't be used but prevents compiler from complaining. - final String __message = "the `requirements` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - requirements = null; - } - java.util.Optional> hints; - - if (__doc.containsKey("hints")) { - try { - hints = - LoaderInstances - .idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_AnyInstance - .loadField(__doc.get("hints"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - hints = null; // won't be used but prevents compiler from complaining. - final String __message = "the `hints` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - hints = null; - } - java.util.Optional cwlVersion; - - if (__doc.containsKey("cwlVersion")) { - try { - cwlVersion = - LoaderInstances - .uri_optional_CWLVersion_False_True_None_None - .loadField(__doc.get("cwlVersion"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - cwlVersion = null; // won't be used but prevents compiler from complaining. - final String __message = "the `cwlVersion` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - cwlVersion = null; - } - java.util.Optional> intent; - - if (__doc.containsKey("intent")) { - try { - intent = - LoaderInstances - .uri_optional_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("intent"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - intent = null; // won't be used but prevents compiler from complaining. - final String __message = "the `intent` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - intent = null; - } - String expression; - try { - expression = - LoaderInstances - .ExpressionLoader - .loadField(__doc.get("expression"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - expression = null; // won't be used but prevents compiler from complaining. - final String __message = "the `expression` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (java.util.Optional) id; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.inputs = (java.util.List) inputs; - this.outputs = (java.util.List) outputs; - this.requirements = (java.util.Optional>) requirements; - this.hints = (java.util.Optional>) hints; - this.cwlVersion = (java.util.Optional) cwlVersion; - this.intent = (java.util.Optional>) intent; - this.class_ = (ExpressionTool_class) class_; - this.expression = (String) expression; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id", "label", "doc", "inputs", "outputs", "requirements", "hints", "cwlVersion", "intent", "class", "expression"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameter.java deleted file mode 100644 index 2a0041a6..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameter.java +++ /dev/null @@ -1,131 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ExpressionToolOutputParameter
This interface is implemented by {@link ExpressionToolOutputParameterImpl}
- */ -public interface ExpressionToolOutputParameter extends OutputParameter, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - String getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * Note that this field just acts as a hint, as the outputs of an - * ExpressionTool process are always considered valid. - * *
- */ - - Object getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameterImpl.java deleted file mode 100644 index 06824072..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionToolOutputParameterImpl.java +++ /dev/null @@ -1,347 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#ExpressionToolOutputParameter
- */ -public class ExpressionToolOutputParameterImpl extends SaveableImpl implements ExpressionToolOutputParameter { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - public String getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * Note that this field just acts as a hint, as the outputs of an - * ExpressionTool process are always considered valid. - * *
- */ - - public Object getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of ExpressionToolOutputParameterImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ExpressionToolOutputParameterImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ExpressionToolOutputParameterImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - if (id == null) { - if (__docRoot != null) { - id = __docRoot; - } else { - throw new ValidationException("Missing id"); - } - } - __baseUri = (String) id; - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.doc = (Object) doc; - this.id = (String) id; - this.format = (Object) format; - this.type = (Object) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("label", "secondaryFiles", "streamable", "doc", "id", "format", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionTool_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionTool_class.java deleted file mode 100644 index 76c00adc..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ExpressionTool_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum ExpressionTool_class { - EXPRESSIONTOOL("ExpressionTool"); - - private static String[] symbols = new String[] {"ExpressionTool"}; - private String docVal; - - private ExpressionTool_class(final String docVal) { - this.docVal = docVal; - } - - public static ExpressionTool_class fromDocumentVal(final String docVal) { - for(final ExpressionTool_class val : ExpressionTool_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", ExpressionTool_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/FieldBase.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/FieldBase.java deleted file mode 100644 index 9a9bea2a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/FieldBase.java +++ /dev/null @@ -1,96 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#FieldBase
- */ -public interface FieldBase extends Labeled, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/File.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/File.java deleted file mode 100644 index e49370ac..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/File.java +++ /dev/null @@ -1,289 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#File
This interface is implemented by {@link FileImpl}
- Represents a file (or group of files when `secondaryFiles` is provided) that - will be accessible by tools using standard POSIX file system call API such as - open(2) and read(2). - - Files are represented as objects with `class` of `File`. File objects have - a number of properties that provide metadata about the file. - - The `location` property of a File is a IRI that uniquely identifies the - file. Implementations must support the `file://` IRI scheme and may support - other schemes such as `http://` and `https://`. The value of `location` may also be a - relative reference, in which case it must be resolved relative to the IRI - of the document it appears in. Alternately to `location`, implementations - must also accept the `path` property on File, which must be a filesystem - path available on the same host as the CWL runner (for inputs) or the - runtime environment of a command line tool execution (for command line tool - outputs). - - If no `location` or `path` is specified, a file object must specify - `contents` with the UTF-8 text content of the file. This is a "file - literal". File literals do not correspond to external resources, but are - created on disk with `contents` with when needed for executing a tool. - Where appropriate, expressions can return file literals to define new files - on a runtime. The maximum size of `contents` is 64 kilobytes. - - The `basename` property defines the filename on disk where the file is - staged. This may differ from the resource name. If not provided, - `basename` must be computed from the last path part of `location` and made - available to expressions. - - The `secondaryFiles` property is a list of File or Directory objects that - must be staged in the same directory as the primary file. It is an error - for file names to be duplicated in `secondaryFiles`. - - The `size` property is the size in bytes of the File. It must be computed - from the resource and made available to expressions. The `checksum` field - contains a cryptographic hash of the file content for use it verifying file - contents. Implementations may, at user option, enable or disable - computation of the `checksum` field for performance or other reasons. - However, the ability to compute output checksums is required to pass the - CWL conformance test suite. - - When executing a CommandLineTool, the files and secondary files may be - staged to an arbitrary directory, but must use the value of `basename` for - the filename. The `path` property must be file path in the context of the - tool execution runtime (local to the compute node, or within the executing - container). All computed properties should be available to expressions. - File literals also must be staged and `path` must be set. - - When collecting CommandLineTool outputs, `glob` matching returns file paths - (with the `path` property) and the derived properties. This can all be - modified by `outputEval`. Alternately, if the file `cwl.output.json` is - present in the output, `outputBinding` is ignored. - - File objects in the output must provide either a `location` IRI or a `path` - property in the context of the tool execution runtime (local to the compute - node, or within the executing container). - - When evaluating an ExpressionTool, file objects must be referenced via - `location` (the expression tool does not have access to files on disk so - `path` is meaningless) or as file literals. It is legal to return a file - object with an existing `location` but a different `basename`. The - `loadContents` field of ExpressionTool inputs behaves the same as on - CommandLineTool inputs, however it is not meaningful on the outputs. - - An ExpressionTool may forward file references from input to output by using - the same value for `location`. -
- */ -public interface File extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#File/class
- *
- * Must be `File` to indicate this object describes a file. *
- */ - - File_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/location
- *
- * An IRI that identifies the file resource. This may be a relative - * reference, in which case it must be resolved using the base IRI of the - * document. The location may refer to a local or remote resource; the - * implementation must use the IRI to retrieve file content. If an - * implementation is unable to retrieve the file content stored at a - * remote resource (due to unsupported protocol, access denied, or other - * issue) it must signal an error. - * - * If the `location` field is not provided, the `contents` field must be - * provided. The implementation must assign a unique identifier for - * the `location` field. - * - * If the `path` field is provided but the `location` field is not, an - * implementation may assign the value of the `path` field to `location`, - * then follow the rules above. - * *
- */ - - java.util.Optional getLocation(); - /** - * Getter for property https://w3id.org/cwl/cwl#path
- *
- * The local host path where the File is available when a CommandLineTool is - * executed. This field must be set by the implementation. The final - * path component must match the value of `basename`. This field - * must not be used in any other context. The command line tool being - * executed must be able to access the file at `path` using the POSIX - * `open(2)` syscall. - * - * As a special case, if the `path` field is provided but the `location` - * field is not, an implementation may assign the value of the `path` - * field to `location`, and remove the `path` field. - * - * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * `<space>`, `<tab>`, and `<newline>`) or characters - * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) - * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) - * then implementations may terminate the process with a - * `permanentFailure`. - * *
- */ - - java.util.Optional getPath(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/basename
- *
- * The base name of the file, that is, the name of the file without any - * leading directory path. The base name must not contain a slash `/`. - * - * If not provided, the implementation must set this field based on the - * `location` field by taking the final path component after parsing - * `location` as an IRI. If `basename` is provided, it is not required to - * match the value from `location`. - * - * When this file is made available to a CommandLineTool, it must be named - * with `basename`, i.e. the final component of the `path` field must match - * `basename`. - * *
- */ - - java.util.Optional getBasename(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/dirname
- *
- * The name of the directory containing file, that is, the path leading up - * to the final slash in the path such that `dirname + '/' + basename == - * path`. - * - * The implementation must set this field based on the value of `path` - * prior to evaluating parameter references or expressions in a - * CommandLineTool document. This field must not be used in any other - * context. - * *
- */ - - java.util.Optional getDirname(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/nameroot
- *
- * The basename root such that `nameroot + nameext == basename`, and - * `nameext` is empty or begins with a period and contains at most one - * period. For the purposes of path splitting leading periods on the - * basename are ignored; a basename of `.cshrc` will have a nameroot of - * `.cshrc`. - * - * The implementation must set this field automatically based on the value - * of `basename` prior to evaluating parameter references or expressions. - * *
- */ - - java.util.Optional getNameroot(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/nameext
- *
- * The basename extension such that `nameroot + nameext == basename`, and - * `nameext` is empty or begins with a period and contains at most one - * period. Leading periods on the basename are ignored; a basename of - * `.cshrc` will have an empty `nameext`. - * - * The implementation must set this field automatically based on the value - * of `basename` prior to evaluating parameter references or expressions. - * *
- */ - - java.util.Optional getNameext(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/checksum
- *
- * Optional hash code for validating file integrity. Currently, must be in the form - * "sha1$ + hexadecimal string" using the SHA-1 algorithm. - * *
- */ - - java.util.Optional getChecksum(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/size
- *
- * Optional file size (in bytes) *
- */ - - Object getSize(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * A list of additional files or directories that are associated with the - * primary file and must be transferred alongside the primary file. - * Examples include indexes of the primary file, or external references - * which must be included when loading primary document. A file object - * listed in `secondaryFiles` may itself include `secondaryFiles` for - * which the same rules apply. - * *
- */ - - java.util.Optional> getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * The format of the file: this must be an IRI of a concept node that - * represents the file format, preferably defined within an ontology. - * If no ontology is available, file formats may be tested by exact match. - * - * Reasoning about format compatibility must be done by checking that an - * input file format is the same, `owl:equivalentClass` or - * `rdfs:subClassOf` the format required by the input parameter. - * `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if - * `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer - * `<C> owl:subclassOf <A>`. - * - * File format ontologies may be provided in the "$schemas" metadata at the - * root of the document. If no ontologies are specified in `$schemas`, the - * runtime may perform exact file format matches. - * *
- */ - - java.util.Optional getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#File/contents
- *
- * File contents literal. - * - * If neither `location` nor `path` is provided, `contents` must be - * non-null. The implementation must assign a unique identifier for the - * `location` field. When the file is staged as input to CommandLineTool, - * the value of `contents` must be written to a file. - * - * If `contents` is set as a result of a Javascript expression, - * an `entry` in `InitialWorkDirRequirement`, or read in from - * `cwl.output.json`, there is no specified upper limit on the - * size of `contents`. Implementations may have practical limits - * on the size of `contents` based on memory and storage - * available to the workflow runner or other factors. - * - * If the `loadContents` field of an `InputParameter` or - * `OutputParameter` is true, and the input or output File object - * `location` is valid, the file must be a UTF-8 text file 64 KiB - * or smaller, and the implementation must read the entire - * contents of the file and place it in the `contents` field. If - * the size of the file is greater than 64 KiB, the - * implementation must raise a fatal error. - * *
- */ - - java.util.Optional getContents(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/FileImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/FileImpl.java deleted file mode 100644 index b375a23e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/FileImpl.java +++ /dev/null @@ -1,611 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#File
- Represents a file (or group of files when `secondaryFiles` is provided) that - will be accessible by tools using standard POSIX file system call API such as - open(2) and read(2). - - Files are represented as objects with `class` of `File`. File objects have - a number of properties that provide metadata about the file. - - The `location` property of a File is a IRI that uniquely identifies the - file. Implementations must support the `file://` IRI scheme and may support - other schemes such as `http://` and `https://`. The value of `location` may also be a - relative reference, in which case it must be resolved relative to the IRI - of the document it appears in. Alternately to `location`, implementations - must also accept the `path` property on File, which must be a filesystem - path available on the same host as the CWL runner (for inputs) or the - runtime environment of a command line tool execution (for command line tool - outputs). - - If no `location` or `path` is specified, a file object must specify - `contents` with the UTF-8 text content of the file. This is a "file - literal". File literals do not correspond to external resources, but are - created on disk with `contents` with when needed for executing a tool. - Where appropriate, expressions can return file literals to define new files - on a runtime. The maximum size of `contents` is 64 kilobytes. - - The `basename` property defines the filename on disk where the file is - staged. This may differ from the resource name. If not provided, - `basename` must be computed from the last path part of `location` and made - available to expressions. - - The `secondaryFiles` property is a list of File or Directory objects that - must be staged in the same directory as the primary file. It is an error - for file names to be duplicated in `secondaryFiles`. - - The `size` property is the size in bytes of the File. It must be computed - from the resource and made available to expressions. The `checksum` field - contains a cryptographic hash of the file content for use it verifying file - contents. Implementations may, at user option, enable or disable - computation of the `checksum` field for performance or other reasons. - However, the ability to compute output checksums is required to pass the - CWL conformance test suite. - - When executing a CommandLineTool, the files and secondary files may be - staged to an arbitrary directory, but must use the value of `basename` for - the filename. The `path` property must be file path in the context of the - tool execution runtime (local to the compute node, or within the executing - container). All computed properties should be available to expressions. - File literals also must be staged and `path` must be set. - - When collecting CommandLineTool outputs, `glob` matching returns file paths - (with the `path` property) and the derived properties. This can all be - modified by `outputEval`. Alternately, if the file `cwl.output.json` is - present in the output, `outputBinding` is ignored. - - File objects in the output must provide either a `location` IRI or a `path` - property in the context of the tool execution runtime (local to the compute - node, or within the executing container). - - When evaluating an ExpressionTool, file objects must be referenced via - `location` (the expression tool does not have access to files on disk so - `path` is meaningless) or as file literals. It is legal to return a file - object with an existing `location` but a different `basename`. The - `loadContents` field of ExpressionTool inputs behaves the same as on - CommandLineTool inputs, however it is not meaningful on the outputs. - - An ExpressionTool may forward file references from input to output by using - the same value for `location`. -
- */ -public class FileImpl extends SaveableImpl implements File { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private File_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/class
- *
- * Must be `File` to indicate this object describes a file. *
- */ - - public File_class getClass_() { - return this.class_; - } - - private java.util.Optional location; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/location
- *
- * An IRI that identifies the file resource. This may be a relative - * reference, in which case it must be resolved using the base IRI of the - * document. The location may refer to a local or remote resource; the - * implementation must use the IRI to retrieve file content. If an - * implementation is unable to retrieve the file content stored at a - * remote resource (due to unsupported protocol, access denied, or other - * issue) it must signal an error. - * - * If the `location` field is not provided, the `contents` field must be - * provided. The implementation must assign a unique identifier for - * the `location` field. - * - * If the `path` field is provided but the `location` field is not, an - * implementation may assign the value of the `path` field to `location`, - * then follow the rules above. - * *
- */ - - public java.util.Optional getLocation() { - return this.location; - } - - private java.util.Optional path; - - /** - * Getter for property https://w3id.org/cwl/cwl#path
- *
- * The local host path where the File is available when a CommandLineTool is - * executed. This field must be set by the implementation. The final - * path component must match the value of `basename`. This field - * must not be used in any other context. The command line tool being - * executed must be able to access the file at `path` using the POSIX - * `open(2)` syscall. - * - * As a special case, if the `path` field is provided but the `location` - * field is not, an implementation may assign the value of the `path` - * field to `location`, and remove the `path` field. - * - * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) - * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, - * `<space>`, `<tab>`, and `<newline>`) or characters - * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) - * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) - * then implementations may terminate the process with a - * `permanentFailure`. - * *
- */ - - public java.util.Optional getPath() { - return this.path; - } - - private java.util.Optional basename; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/basename
- *
- * The base name of the file, that is, the name of the file without any - * leading directory path. The base name must not contain a slash `/`. - * - * If not provided, the implementation must set this field based on the - * `location` field by taking the final path component after parsing - * `location` as an IRI. If `basename` is provided, it is not required to - * match the value from `location`. - * - * When this file is made available to a CommandLineTool, it must be named - * with `basename`, i.e. the final component of the `path` field must match - * `basename`. - * *
- */ - - public java.util.Optional getBasename() { - return this.basename; - } - - private java.util.Optional dirname; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/dirname
- *
- * The name of the directory containing file, that is, the path leading up - * to the final slash in the path such that `dirname + '/' + basename == - * path`. - * - * The implementation must set this field based on the value of `path` - * prior to evaluating parameter references or expressions in a - * CommandLineTool document. This field must not be used in any other - * context. - * *
- */ - - public java.util.Optional getDirname() { - return this.dirname; - } - - private java.util.Optional nameroot; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/nameroot
- *
- * The basename root such that `nameroot + nameext == basename`, and - * `nameext` is empty or begins with a period and contains at most one - * period. For the purposes of path splitting leading periods on the - * basename are ignored; a basename of `.cshrc` will have a nameroot of - * `.cshrc`. - * - * The implementation must set this field automatically based on the value - * of `basename` prior to evaluating parameter references or expressions. - * *
- */ - - public java.util.Optional getNameroot() { - return this.nameroot; - } - - private java.util.Optional nameext; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/nameext
- *
- * The basename extension such that `nameroot + nameext == basename`, and - * `nameext` is empty or begins with a period and contains at most one - * period. Leading periods on the basename are ignored; a basename of - * `.cshrc` will have an empty `nameext`. - * - * The implementation must set this field automatically based on the value - * of `basename` prior to evaluating parameter references or expressions. - * *
- */ - - public java.util.Optional getNameext() { - return this.nameext; - } - - private java.util.Optional checksum; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/checksum
- *
- * Optional hash code for validating file integrity. Currently, must be in the form - * "sha1$ + hexadecimal string" using the SHA-1 algorithm. - * *
- */ - - public java.util.Optional getChecksum() { - return this.checksum; - } - - private Object size; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/size
- *
- * Optional file size (in bytes) *
- */ - - public Object getSize() { - return this.size; - } - - private java.util.Optional> secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * A list of additional files or directories that are associated with the - * primary file and must be transferred alongside the primary file. - * Examples include indexes of the primary file, or external references - * which must be included when loading primary document. A file object - * listed in `secondaryFiles` may itself include `secondaryFiles` for - * which the same rules apply. - * *
- */ - - public java.util.Optional> getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * The format of the file: this must be an IRI of a concept node that - * represents the file format, preferably defined within an ontology. - * If no ontology is available, file formats may be tested by exact match. - * - * Reasoning about format compatibility must be done by checking that an - * input file format is the same, `owl:equivalentClass` or - * `rdfs:subClassOf` the format required by the input parameter. - * `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if - * `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer - * `<C> owl:subclassOf <A>`. - * - * File format ontologies may be provided in the "$schemas" metadata at the - * root of the document. If no ontologies are specified in `$schemas`, the - * runtime may perform exact file format matches. - * *
- */ - - public java.util.Optional getFormat() { - return this.format; - } - - private java.util.Optional contents; - - /** - * Getter for property https://w3id.org/cwl/cwl#File/contents
- *
- * File contents literal. - * - * If neither `location` nor `path` is provided, `contents` must be - * non-null. The implementation must assign a unique identifier for the - * `location` field. When the file is staged as input to CommandLineTool, - * the value of `contents` must be written to a file. - * - * If `contents` is set as a result of a Javascript expression, - * an `entry` in `InitialWorkDirRequirement`, or read in from - * `cwl.output.json`, there is no specified upper limit on the - * size of `contents`. Implementations may have practical limits - * on the size of `contents` based on memory and storage - * available to the workflow runner or other factors. - * - * If the `loadContents` field of an `InputParameter` or - * `OutputParameter` is true, and the input or output File object - * `location` is valid, the file must be a UTF-8 text file 64 KiB - * or smaller, and the implementation must read the entire - * contents of the file and place it in the `contents` field. If - * the size of the file is greater than 64 KiB, the - * implementation must raise a fatal error. - * *
- */ - - public java.util.Optional getContents() { - return this.contents; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of FileImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public FileImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("FileImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - File_class class_; - try { - class_ = - LoaderInstances - .uri_File_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional location; - - if (__doc.containsKey("location")) { - try { - location = - LoaderInstances - .uri_optional_StringInstance_False_False_None_None - .loadField(__doc.get("location"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - location = null; // won't be used but prevents compiler from complaining. - final String __message = "the `location` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - location = null; - } - java.util.Optional path; - - if (__doc.containsKey("path")) { - try { - path = - LoaderInstances - .uri_optional_StringInstance_False_False_None_None - .loadField(__doc.get("path"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - path = null; // won't be used but prevents compiler from complaining. - final String __message = "the `path` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - path = null; - } - java.util.Optional basename; - - if (__doc.containsKey("basename")) { - try { - basename = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("basename"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - basename = null; // won't be used but prevents compiler from complaining. - final String __message = "the `basename` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - basename = null; - } - java.util.Optional dirname; - - if (__doc.containsKey("dirname")) { - try { - dirname = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("dirname"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - dirname = null; // won't be used but prevents compiler from complaining. - final String __message = "the `dirname` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - dirname = null; - } - java.util.Optional nameroot; - - if (__doc.containsKey("nameroot")) { - try { - nameroot = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("nameroot"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - nameroot = null; // won't be used but prevents compiler from complaining. - final String __message = "the `nameroot` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - nameroot = null; - } - java.util.Optional nameext; - - if (__doc.containsKey("nameext")) { - try { - nameext = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("nameext"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - nameext = null; // won't be used but prevents compiler from complaining. - final String __message = "the `nameext` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - nameext = null; - } - java.util.Optional checksum; - - if (__doc.containsKey("checksum")) { - try { - checksum = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("checksum"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - checksum = null; // won't be used but prevents compiler from complaining. - final String __message = "the `checksum` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - checksum = null; - } - Object size; - - if (__doc.containsKey("size")) { - try { - size = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance - .loadField(__doc.get("size"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - size = null; // won't be used but prevents compiler from complaining. - final String __message = "the `size` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - size = null; - } - java.util.Optional> secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_optional_array_of_union_of_File_or_Directory - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_optional_StringInstance_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional contents; - - if (__doc.containsKey("contents")) { - try { - contents = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("contents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - contents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `contents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - contents = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (File_class) class_; - this.location = (java.util.Optional) location; - this.path = (java.util.Optional) path; - this.basename = (java.util.Optional) basename; - this.dirname = (java.util.Optional) dirname; - this.nameroot = (java.util.Optional) nameroot; - this.nameext = (java.util.Optional) nameext; - this.checksum = (java.util.Optional) checksum; - this.size = (Object) size; - this.secondaryFiles = (java.util.Optional>) secondaryFiles; - this.format = (java.util.Optional) format; - this.contents = (java.util.Optional) contents; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "location", "path", "basename", "dirname", "nameroot", "nameext", "checksum", "size", "secondaryFiles", "format", "contents"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/File_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/File_class.java deleted file mode 100644 index d8ae0b3d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/File_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum File_class { - FILE("File"); - - private static String[] symbols = new String[] {"File"}; - private String docVal; - - private File_class(final String docVal) { - this.docVal = docVal; - } - - public static File_class fromDocumentVal(final String docVal) { - for(final File_class val : File_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", File_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/IOSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/IOSchema.java deleted file mode 100644 index 4fa4facc..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/IOSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#IOSchema
- */ -public interface IOSchema extends Labeled, Documented, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Identified.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Identified.java deleted file mode 100644 index 15736c75..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Identified.java +++ /dev/null @@ -1,28 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Identified
- */ -public interface Identified extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/IdentifierRequired.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/IdentifierRequired.java deleted file mode 100644 index a4f0c7ad..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/IdentifierRequired.java +++ /dev/null @@ -1,28 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#IdentifierRequired
- */ -public interface IdentifierRequired extends Identified, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirement.java deleted file mode 100644 index 922060ff..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirement.java +++ /dev/null @@ -1,68 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InitialWorkDirRequirement
This interface is implemented by {@link InitialWorkDirRequirementImpl}
- Define a list of files and subdirectories that must be staged by the workflow platform prior to executing the command line tool. - Normally files are staged within the designated output directory. However, when running inside containers, files may be staged at arbitrary locations, see discussion for [`Dirent.entryname`](#Dirent). Together with `DockerRequirement.dockerOutputDirectory` it is possible to control the locations of both input and output files when running in containers.
- */ -public interface InitialWorkDirRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#InitialWorkDirRequirement/class
- *
- * InitialWorkDirRequirement *
- */ - - InitialWorkDirRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#listing
- *
- * The list of files or subdirectories that must be staged prior - * to executing the command line tool. - * - * Return type of each expression must validate as `["null", - * File, Directory, Dirent, {type: array, items: [File, - * Directory]}]`. - * - * Each `File` or `Directory` that is returned by an Expression - * must be added to the designated output directory prior to - * executing the tool. - * - * Each `Dirent` record that is listed or returned by an - * expression specifies a file to be created or staged in the - * designated output directory prior to executing the tool. - * - * Expressions may return null, in which case they have no effect. - * - * Files or Directories which are listed in the input parameters - * and appear in the `InitialWorkDirRequirement` listing must - * have their `path` set to their staged location. If the same - * File or Directory appears more than once in the - * `InitialWorkDirRequirement` listing, the implementation must - * choose exactly one value for `path`; how this value is chosen - * is undefined. - * *
- */ - - Object getListing(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirementImpl.java deleted file mode 100644 index 5f0dd804..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirementImpl.java +++ /dev/null @@ -1,154 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InitialWorkDirRequirement
- Define a list of files and subdirectories that must be staged by the workflow platform prior to executing the command line tool. - Normally files are staged within the designated output directory. However, when running inside containers, files may be staged at arbitrary locations, see discussion for [`Dirent.entryname`](#Dirent). Together with `DockerRequirement.dockerOutputDirectory` it is possible to control the locations of both input and output files when running in containers.
- */ -public class InitialWorkDirRequirementImpl extends SaveableImpl implements InitialWorkDirRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private InitialWorkDirRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#InitialWorkDirRequirement/class
- *
- * InitialWorkDirRequirement *
- */ - - public InitialWorkDirRequirement_class getClass_() { - return this.class_; - } - - private Object listing; - - /** - * Getter for property https://w3id.org/cwl/cwl#listing
- *
- * The list of files or subdirectories that must be staged prior - * to executing the command line tool. - * - * Return type of each expression must validate as `["null", - * File, Directory, Dirent, {type: array, items: [File, - * Directory]}]`. - * - * Each `File` or `Directory` that is returned by an Expression - * must be added to the designated output directory prior to - * executing the tool. - * - * Each `Dirent` record that is listed or returned by an - * expression specifies a file to be created or staged in the - * designated output directory prior to executing the tool. - * - * Expressions may return null, in which case they have no effect. - * - * Files or Directories which are listed in the input parameters - * and appear in the `InitialWorkDirRequirement` listing must - * have their `path` set to their staged location. If the same - * File or Directory appears more than once in the - * `InitialWorkDirRequirement` listing, the implementation must - * choose exactly one value for `path`; how this value is chosen - * is undefined. - * *
- */ - - public Object getListing() { - return this.listing; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of InitialWorkDirRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InitialWorkDirRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InitialWorkDirRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - InitialWorkDirRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_InitialWorkDirRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object listing; - try { - listing = - LoaderInstances - .union_of_ExpressionLoader_or_array_of_union_of_NullInstance_or_Dirent_or_ExpressionLoader_or_File_or_Directory_or_array_of_union_of_File_or_Directory - .loadField(__doc.get("listing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - listing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `listing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (InitialWorkDirRequirement_class) class_; - this.listing = (Object) listing; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "listing"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirement_class.java deleted file mode 100644 index 297a71fa..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InitialWorkDirRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum InitialWorkDirRequirement_class { - INITIALWORKDIRREQUIREMENT("InitialWorkDirRequirement"); - - private static String[] symbols = new String[] {"InitialWorkDirRequirement"}; - private String docVal; - - private InitialWorkDirRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static InitialWorkDirRequirement_class fromDocumentVal(final String docVal) { - for(final InitialWorkDirRequirement_class val : InitialWorkDirRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", InitialWorkDirRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirement.java deleted file mode 100644 index 45e00df9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirement.java +++ /dev/null @@ -1,49 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InlineJavascriptRequirement
This interface is implemented by {@link InlineJavascriptRequirementImpl}
- Indicates that the workflow platform must support inline Javascript expressions. - If this requirement is not present, the workflow platform must not perform expression - interpolation. -
- */ -public interface InlineJavascriptRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/class
- *
- * Always 'InlineJavascriptRequirement' *
- */ - - InlineJavascriptRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/expressionLib
- *
- * Additional code fragments that will also be inserted - * before executing the expression code. Allows for function definitions that may - * be called from CWL expressions. - * *
- */ - - java.util.Optional> getExpressionLib(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirementImpl.java deleted file mode 100644 index 3d573758..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirementImpl.java +++ /dev/null @@ -1,141 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InlineJavascriptRequirement
- Indicates that the workflow platform must support inline Javascript expressions. - If this requirement is not present, the workflow platform must not perform expression - interpolation. -
- */ -public class InlineJavascriptRequirementImpl extends SaveableImpl implements InlineJavascriptRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private InlineJavascriptRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/class
- *
- * Always 'InlineJavascriptRequirement' *
- */ - - public InlineJavascriptRequirement_class getClass_() { - return this.class_; - } - - private java.util.Optional> expressionLib; - - /** - * Getter for property https://w3id.org/cwl/cwl#InlineJavascriptRequirement/expressionLib
- *
- * Additional code fragments that will also be inserted - * before executing the expression code. Allows for function definitions that may - * be called from CWL expressions. - * *
- */ - - public java.util.Optional> getExpressionLib() { - return this.expressionLib; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of InlineJavascriptRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InlineJavascriptRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InlineJavascriptRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - InlineJavascriptRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_InlineJavascriptRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> expressionLib; - - if (__doc.containsKey("expressionLib")) { - try { - expressionLib = - LoaderInstances - .optional_array_of_StringInstance - .loadField(__doc.get("expressionLib"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - expressionLib = null; // won't be used but prevents compiler from complaining. - final String __message = "the `expressionLib` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - expressionLib = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (InlineJavascriptRequirement_class) class_; - this.expressionLib = (java.util.Optional>) expressionLib; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "expressionLib"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirement_class.java deleted file mode 100644 index d5944c02..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InlineJavascriptRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum InlineJavascriptRequirement_class { - INLINEJAVASCRIPTREQUIREMENT("InlineJavascriptRequirement"); - - private static String[] symbols = new String[] {"InlineJavascriptRequirement"}; - private String docVal; - - private InlineJavascriptRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static InlineJavascriptRequirement_class fromDocumentVal(final String docVal) { - for(final InlineJavascriptRequirement_class val : InlineJavascriptRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", InlineJavascriptRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirement.java deleted file mode 100644 index 671dc574..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirement.java +++ /dev/null @@ -1,72 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InplaceUpdateRequirement
This interface is implemented by {@link InplaceUpdateRequirementImpl}
- - If `inplaceUpdate` is true, then an implementation supporting this - feature may permit tools to directly update files with `writable: - true` in InitialWorkDirRequirement. That is, as an optimization, - files may be destructively modified in place as opposed to copied - and updated. - - An implementation must ensure that only one workflow step may - access a writable file at a time. It is an error if a file which - is writable by one workflow step file is accessed (for reading or - writing) by any other workflow step running independently. - However, a file which has been updated in a previous completed - step may be used as input to multiple steps, provided it is - read-only in every step. - - Workflow steps which modify a file must produce the modified file - as output. Downstream steps which further process the file must - use the output of previous steps, and not refer to a common input - (this is necessary for both ordering and correctness). - - Workflow authors should provide this in the `hints` section. The - intent of this feature is that workflows produce the same results - whether or not InplaceUpdateRequirement is supported by the - implementation, and this feature is primarily available as an - optimization for particular environments. - - Users and implementers should be aware that workflows that - destructively modify inputs may not be repeatable or reproducible. - In particular, enabling this feature implies that WorkReuse should - not be enabled. -
- */ -public interface InplaceUpdateRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/class
- *
- * Always 'InplaceUpdateRequirement' *
- */ - - InplaceUpdateRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/inplaceUpdate
- - */ - - Boolean getInplaceUpdate(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirementImpl.java deleted file mode 100644 index 07f5a598..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirementImpl.java +++ /dev/null @@ -1,158 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InplaceUpdateRequirement
- - If `inplaceUpdate` is true, then an implementation supporting this - feature may permit tools to directly update files with `writable: - true` in InitialWorkDirRequirement. That is, as an optimization, - files may be destructively modified in place as opposed to copied - and updated. - - An implementation must ensure that only one workflow step may - access a writable file at a time. It is an error if a file which - is writable by one workflow step file is accessed (for reading or - writing) by any other workflow step running independently. - However, a file which has been updated in a previous completed - step may be used as input to multiple steps, provided it is - read-only in every step. - - Workflow steps which modify a file must produce the modified file - as output. Downstream steps which further process the file must - use the output of previous steps, and not refer to a common input - (this is necessary for both ordering and correctness). - - Workflow authors should provide this in the `hints` section. The - intent of this feature is that workflows produce the same results - whether or not InplaceUpdateRequirement is supported by the - implementation, and this feature is primarily available as an - optimization for particular environments. - - Users and implementers should be aware that workflows that - destructively modify inputs may not be repeatable or reproducible. - In particular, enabling this feature implies that WorkReuse should - not be enabled. -
- */ -public class InplaceUpdateRequirementImpl extends SaveableImpl implements InplaceUpdateRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private InplaceUpdateRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/class
- *
- * Always 'InplaceUpdateRequirement' *
- */ - - public InplaceUpdateRequirement_class getClass_() { - return this.class_; - } - - private Boolean inplaceUpdate; - - /** - * Getter for property https://w3id.org/cwl/cwl#InplaceUpdateRequirement/inplaceUpdate
- - */ - - public Boolean getInplaceUpdate() { - return this.inplaceUpdate; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of InplaceUpdateRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InplaceUpdateRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InplaceUpdateRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - InplaceUpdateRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_InplaceUpdateRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Boolean inplaceUpdate; - try { - inplaceUpdate = - LoaderInstances - .BooleanInstance - .loadField(__doc.get("inplaceUpdate"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inplaceUpdate = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inplaceUpdate` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (InplaceUpdateRequirement_class) class_; - this.inplaceUpdate = (Boolean) inplaceUpdate; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "inplaceUpdate"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirement_class.java deleted file mode 100644 index 05c0a2b0..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InplaceUpdateRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum InplaceUpdateRequirement_class { - INPLACEUPDATEREQUIREMENT("InplaceUpdateRequirement"); - - private static String[] symbols = new String[] {"InplaceUpdateRequirement"}; - private String docVal; - - private InplaceUpdateRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static InplaceUpdateRequirement_class fromDocumentVal(final String docVal) { - for(final InplaceUpdateRequirement_class val : InplaceUpdateRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", InplaceUpdateRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputArraySchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputArraySchema.java deleted file mode 100644 index c1e3b024..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputArraySchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputArraySchema
This interface is implemented by {@link InputArraySchemaImpl}
- */ -public interface InputArraySchema extends CWLArraySchema, InputSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - Object getItems(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - Array_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputArraySchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputArraySchemaImpl.java deleted file mode 100644 index bffce6ed..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputArraySchemaImpl.java +++ /dev/null @@ -1,232 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InputArraySchema
- */ -public class InputArraySchemaImpl extends SaveableImpl implements InputArraySchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private Object items; - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - public Object getItems() { - return this.items; - } - - private Array_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - public Array_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of InputArraySchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InputArraySchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InputArraySchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - Object items; - try { - items = - LoaderInstances - .uri_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("items"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - items = null; // won't be used but prevents compiler from complaining. - final String __message = "the `items` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Array_name type; - try { - type = - LoaderInstances - .typedsl_Array_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.items = (Object) items; - this.type = (Array_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("items", "type", "label", "doc", "name"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputBinding.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputBinding.java deleted file mode 100644 index 8c101b9b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputBinding.java +++ /dev/null @@ -1,38 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputBinding
This interface is implemented by {@link InputBindingImpl}
- */ -public interface InputBinding extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#InputBinding/loadContents
- *
- * Use of `loadContents` in `InputBinding` is deprecated. - * Preserved for v1.0 backwards compatibility. Will be removed in - * CWL v2.0. Use `InputParameter.loadContents` instead. - * *
- */ - - java.util.Optional getLoadContents(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputBindingImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputBindingImpl.java deleted file mode 100644 index 7afedd9f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputBindingImpl.java +++ /dev/null @@ -1,113 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InputBinding
- */ -public class InputBindingImpl extends SaveableImpl implements InputBinding { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#InputBinding/loadContents
- *
- * Use of `loadContents` in `InputBinding` is deprecated. - * Preserved for v1.0 backwards compatibility. Will be removed in - * CWL v2.0. Use `InputParameter.loadContents` instead. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of InputBindingImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InputBindingImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InputBindingImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.loadContents = (java.util.Optional) loadContents; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("loadContents"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputEnumSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputEnumSchema.java deleted file mode 100644 index 9a252c27..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputEnumSchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputEnumSchema
This interface is implemented by {@link InputEnumSchemaImpl}
- */ -public interface InputEnumSchema extends EnumSchema, InputSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - java.util.List getSymbols(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - Enum_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputEnumSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputEnumSchemaImpl.java deleted file mode 100644 index 1f6cb8d5..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputEnumSchemaImpl.java +++ /dev/null @@ -1,232 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InputEnumSchema
- */ -public class InputEnumSchemaImpl extends SaveableImpl implements InputEnumSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.List symbols; - - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - public java.util.List getSymbols() { - return this.symbols; - } - - private Enum_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - public Enum_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of InputEnumSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InputEnumSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InputEnumSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.List symbols; - try { - symbols = - LoaderInstances - .uri_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("symbols"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - symbols = null; // won't be used but prevents compiler from complaining. - final String __message = "the `symbols` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Enum_name type; - try { - type = - LoaderInstances - .typedsl_Enum_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.name = (java.util.Optional) name; - this.symbols = (java.util.List) symbols; - this.type = (Enum_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("name", "symbols", "type", "label", "doc"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputFormat.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputFormat.java deleted file mode 100644 index 094ceb90..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputFormat.java +++ /dev/null @@ -1,41 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputFormat
- */ -public interface InputFormat extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputParameter.java deleted file mode 100644 index 01155244..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputParameter.java +++ /dev/null @@ -1,159 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputParameter
- */ -public interface InputParameter extends Parameter, InputFormat, LoadContents, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value to use for this parameter if the parameter is missing - * from the input object, or if the value of the parameter in the input - * object is `null`. Default values are applied before evaluating expressions - * (e.g. dependent `valueFrom` fields). - * *
- */ - - java.util.Optional getDefault(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordField.java deleted file mode 100644 index 644b9999..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordField.java +++ /dev/null @@ -1,164 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputRecordField
This interface is implemented by {@link InputRecordFieldImpl}
- */ -public interface InputRecordField extends CWLRecordField, FieldBase, InputFormat, LoadContents, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - String getName(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordFieldImpl.java deleted file mode 100644 index dec00e08..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordFieldImpl.java +++ /dev/null @@ -1,426 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordField
- */ -public class InputRecordFieldImpl extends SaveableImpl implements InputRecordField { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String name; - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - public String getName() { - return this.name; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of InputRecordFieldImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InputRecordFieldImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InputRecordFieldImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - if (name == null) { - if (__docRoot != null) { - name = __docRoot; - } else { - throw new ValidationException("Missing name"); - } - } - __baseUri = (String) name; - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.doc = (Object) doc; - this.name = (String) name; - this.type = (Object) type; - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.format = (Object) format; - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("doc", "name", "type", "label", "secondaryFiles", "streamable", "format", "loadContents", "loadListing"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordSchema.java deleted file mode 100644 index c9acc178..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordSchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputRecordSchema
This interface is implemented by {@link InputRecordSchemaImpl}
- */ -public interface InputRecordSchema extends CWLRecordSchema, InputSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - java.util.Optional> getFields(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - Record_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordSchemaImpl.java deleted file mode 100644 index 31cf073e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputRecordSchemaImpl.java +++ /dev/null @@ -1,238 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordSchema
- */ -public class InputRecordSchemaImpl extends SaveableImpl implements InputRecordSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.Optional> fields; - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - public java.util.Optional> getFields() { - return this.fields; - } - - private Record_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - public Record_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of InputRecordSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public InputRecordSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("InputRecordSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.Optional> fields; - - if (__doc.containsKey("fields")) { - try { - fields = - LoaderInstances - .idmap_fields_optional_array_of_InputRecordField - .loadField(__doc.get("fields"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - fields = null; // won't be used but prevents compiler from complaining. - final String __message = "the `fields` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - fields = null; - } - Record_name type; - try { - type = - LoaderInstances - .typedsl_Record_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.fields = (java.util.Optional>) fields; - this.type = (Record_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("fields", "type", "label", "doc", "name"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputSchema.java deleted file mode 100644 index 933fbb39..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/InputSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#InputSchema
- */ -public interface InputSchema extends IOSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Labeled.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Labeled.java deleted file mode 100644 index 057c76fe..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Labeled.java +++ /dev/null @@ -1,35 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Labeled
- */ -public interface Labeled extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LinkMergeMethod.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LinkMergeMethod.java deleted file mode 100644 index 4e55cf1e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LinkMergeMethod.java +++ /dev/null @@ -1,38 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum LinkMergeMethod { - MERGE_NESTED("merge_nested"), - MERGE_FLATTENED("merge_flattened"); - - private static String[] symbols = new String[] {"merge_nested", "merge_flattened"}; - private String docVal; - - private LinkMergeMethod(final String docVal) { - this.docVal = docVal; - } - - public static LinkMergeMethod fromDocumentVal(final String docVal) { - for(final LinkMergeMethod val : LinkMergeMethod.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", LinkMergeMethod.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadContents.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadContents.java deleted file mode 100644 index 2d7c7fb7..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadContents.java +++ /dev/null @@ -1,60 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#LoadContents
- */ -public interface LoadContents extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingEnum.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingEnum.java deleted file mode 100644 index 63cecdde..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingEnum.java +++ /dev/null @@ -1,39 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum LoadListingEnum { - NO_LISTING("no_listing"), - SHALLOW_LISTING("shallow_listing"), - DEEP_LISTING("deep_listing"); - - private static String[] symbols = new String[] {"no_listing", "shallow_listing", "deep_listing"}; - private String docVal; - - private LoadListingEnum(final String docVal) { - this.docVal = docVal; - } - - public static LoadListingEnum fromDocumentVal(final String docVal) { - for(final LoadListingEnum val : LoadListingEnum.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", LoadListingEnum.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirement.java deleted file mode 100644 index f0ceaaeb..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirement.java +++ /dev/null @@ -1,44 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#LoadListingRequirement
This interface is implemented by {@link LoadListingRequirementImpl}
- Specify the desired behavior for loading the `listing` field of - a Directory object for use by expressions. -
- */ -public interface LoadListingRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/class
- *
- * Always 'LoadListingRequirement' *
- */ - - LoadListingRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/loadListing
- - */ - - java.util.Optional getLoadListing(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirementImpl.java deleted file mode 100644 index 5467fadd..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirementImpl.java +++ /dev/null @@ -1,136 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#LoadListingRequirement
- Specify the desired behavior for loading the `listing` field of - a Directory object for use by expressions. -
- */ -public class LoadListingRequirementImpl extends SaveableImpl implements LoadListingRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private LoadListingRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/class
- *
- * Always 'LoadListingRequirement' *
- */ - - public LoadListingRequirement_class getClass_() { - return this.class_; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadListingRequirement/loadListing
- - */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of LoadListingRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public LoadListingRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("LoadListingRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - LoadListingRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_LoadListingRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (LoadListingRequirement_class) class_; - this.loadListing = (java.util.Optional) loadListing; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "loadListing"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirement_class.java deleted file mode 100644 index 80353e40..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoadListingRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum LoadListingRequirement_class { - LOADLISTINGREQUIREMENT("LoadListingRequirement"); - - private static String[] symbols = new String[] {"LoadListingRequirement"}; - private String docVal; - - private LoadListingRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static LoadListingRequirement_class fromDocumentVal(final String docVal) { - for(final LoadListingRequirement_class val : LoadListingRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", LoadListingRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Loop.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Loop.java deleted file mode 100644 index 5af9ce4d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Loop.java +++ /dev/null @@ -1,84 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for http://commonwl.org/cwltool#Loop
This interface is implemented by {@link LoopImpl}
- Prototype to enable workflow-level looping of a step. - - Valid only under `requirements` of a https://www.commonwl.org/v1.2/Workflow.html#WorkflowStep. - Unlike other CWL requirements, Loop requirement is not propagated to inner steps. - - `loopWhen` is an expansion of the CWL v1.2 `when` construct which controls - conditional execution. - - Using `loopWhen` and `when` for the same step will produce an error. - - `loopWhen` is not compatible with `scatter` at this time and combining the - two in the same step will produce an error. -
- */ -public interface Loop extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property http://commonwl.org/cwltool#Loop/class
- *
- * cwltool:Loop *
- */ - - String getClass_(); - /** - * Getter for property http://commonwl.org/cwltool#loop
- *
- * Defines the input parameters of the loop iterations after the first one - * (inputs of the first iteration are the step input parameters). If no - * `loop` rule is specified for a given step `in` field, the initial value - * is kept constant among all iterations. - * *
- */ - - java.util.List getLoop(); - /** - * Getter for property http://commonwl.org/cwltool#Loop/loopWhen
- *
- * Only run the step while the expression evaluates to `true`. - * If `false` and no iteration has been performed, the step is skipped. - * - * A skipped step produces a `null` on each output. - * - * The `inputs` value in the expression must be the step input object. - * - * It is an error if this expression returns a value other than `true` or `false`. - * *
- */ - - String getLoopWhen(); - /** - * Getter for property http://commonwl.org/cwltool#Loop/outputMethod
- *
- * - Specify the desired method of dealing with loop outputs - * - Default. Propagates only the last computed element to the subsequent steps when the loop terminates. - * - Propagates a single array with all output values to the subsequent steps when the loop terminates. - * *
- */ - - LoopOutputModes getOutputMethod(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoopImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoopImpl.java deleted file mode 100644 index 1f8cb545..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoopImpl.java +++ /dev/null @@ -1,204 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for http://commonwl.org/cwltool#Loop
- Prototype to enable workflow-level looping of a step. - - Valid only under `requirements` of a https://www.commonwl.org/v1.2/Workflow.html#WorkflowStep. - Unlike other CWL requirements, Loop requirement is not propagated to inner steps. - - `loopWhen` is an expansion of the CWL v1.2 `when` construct which controls - conditional execution. - - Using `loopWhen` and `when` for the same step will produce an error. - - `loopWhen` is not compatible with `scatter` at this time and combining the - two in the same step will produce an error. -
- */ -public class LoopImpl extends SaveableImpl implements Loop { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String class_; - - /** - * Getter for property http://commonwl.org/cwltool#Loop/class
- *
- * cwltool:Loop *
- */ - - public String getClass_() { - return this.class_; - } - - private java.util.List loop; - - /** - * Getter for property http://commonwl.org/cwltool#loop
- *
- * Defines the input parameters of the loop iterations after the first one - * (inputs of the first iteration are the step input parameters). If no - * `loop` rule is specified for a given step `in` field, the initial value - * is kept constant among all iterations. - * *
- */ - - public java.util.List getLoop() { - return this.loop; - } - - private String loopWhen; - - /** - * Getter for property http://commonwl.org/cwltool#Loop/loopWhen
- *
- * Only run the step while the expression evaluates to `true`. - * If `false` and no iteration has been performed, the step is skipped. - * - * A skipped step produces a `null` on each output. - * - * The `inputs` value in the expression must be the step input object. - * - * It is an error if this expression returns a value other than `true` or `false`. - * *
- */ - - public String getLoopWhen() { - return this.loopWhen; - } - - private LoopOutputModes outputMethod; - - /** - * Getter for property http://commonwl.org/cwltool#Loop/outputMethod
- *
- * - Specify the desired method of dealing with loop outputs - * - Default. Propagates only the last computed element to the subsequent steps when the loop terminates. - * - Propagates a single array with all output values to the subsequent steps when the loop terminates. - * *
- */ - - public LoopOutputModes getOutputMethod() { - return this.outputMethod; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of LoopImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public LoopImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("LoopImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String class_; - try { - class_ = - LoaderInstances - .uri_StringInstance_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List loop; - try { - loop = - LoaderInstances - .idmap_loop_array_of_LoopInput - .loadField(__doc.get("loop"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loop = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loop` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - String loopWhen; - try { - loopWhen = - LoaderInstances - .ExpressionLoader - .loadField(__doc.get("loopWhen"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loopWhen = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loopWhen` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - LoopOutputModes outputMethod; - try { - outputMethod = - LoaderInstances - .LoopOutputModes - .loadField(__doc.get("outputMethod"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputMethod = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputMethod` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (String) class_; - this.loop = (java.util.List) loop; - this.loopWhen = (String) loopWhen; - this.outputMethod = (LoopOutputModes) outputMethod; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "loop", "loopWhen", "outputMethod"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoopInput.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoopInput.java deleted file mode 100644 index 72faa68b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoopInput.java +++ /dev/null @@ -1,95 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for http://commonwl.org/cwltool#LoopInput
This interface is implemented by {@link LoopInputImpl}
- */ -public interface LoopInput extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property http://commonwl.org/cwltool#LoopInput/id
- *
- * It must reference the `id` of one of the elements in the `in` field of the step. *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value for this parameter to use if either there is no - * `source` field, or the value produced by the `source` is `null`. The - * default must be applied prior to scattering or evaluating `valueFrom`. - * *
- */ - - java.util.Optional getDefault(); - /** - * Getter for property http://commonwl.org/cwltool#LoopInput/linkMerge
- *
- * The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". - * *
- */ - - java.util.Optional getLinkMerge(); - /** - * Getter for property http://commonwl.org/cwltool#LoopInput/loopSource
- *
- * Specifies one or more of the step output parameters that will - * provide input to the loop iterations after the first one (inputs - * of the first iteration are the step input parameters). - * *
- */ - - Object getLoopSource(); - /** - * Getter for property http://commonwl.org/cwltool#LoopInput/pickValue
- *
- * The method to use to choose non-null elements among multiple sources. - * *
- */ - - java.util.Optional getPickValue(); - /** - * Getter for property http://commonwl.org/cwltool#LoopInput/valueFrom
- *
- * To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must - * be specified in the workflow or workflow step requirements. - * - * If `valueFrom` is a constant string value, use this as the value for - * this input parameter. - * - * If `valueFrom` is a parameter reference or expression, it must be - * evaluated to yield the actual value to be assigned to the input field. - * - * The `self` value in the parameter reference or expression must be - * `null` if there is no `loopSource` field, or the value of the - * parameter(s) specified in the `loopSource` field. - * - * The value of `inputs` in the parameter reference or expression must be - * the input object to the previous iteration of the workflow step (or the initial - * inputs for the first iteration). - * *
- */ - - Object getValueFrom(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoopInputImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoopInputImpl.java deleted file mode 100644 index cd531943..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoopInputImpl.java +++ /dev/null @@ -1,299 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for http://commonwl.org/cwltool#LoopInput
- */ -public class LoopInputImpl extends SaveableImpl implements LoopInput { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property http://commonwl.org/cwltool#LoopInput/id
- *
- * It must reference the `id` of one of the elements in the `in` field of the step. *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private java.util.Optional default_; - - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value for this parameter to use if either there is no - * `source` field, or the value produced by the `source` is `null`. The - * default must be applied prior to scattering or evaluating `valueFrom`. - * *
- */ - - public java.util.Optional getDefault() { - return this.default_; - } - - private java.util.Optional linkMerge; - - /** - * Getter for property http://commonwl.org/cwltool#LoopInput/linkMerge
- *
- * The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". - * *
- */ - - public java.util.Optional getLinkMerge() { - return this.linkMerge; - } - - private Object loopSource; - - /** - * Getter for property http://commonwl.org/cwltool#LoopInput/loopSource
- *
- * Specifies one or more of the step output parameters that will - * provide input to the loop iterations after the first one (inputs - * of the first iteration are the step input parameters). - * *
- */ - - public Object getLoopSource() { - return this.loopSource; - } - - private java.util.Optional pickValue; - - /** - * Getter for property http://commonwl.org/cwltool#LoopInput/pickValue
- *
- * The method to use to choose non-null elements among multiple sources. - * *
- */ - - public java.util.Optional getPickValue() { - return this.pickValue; - } - - private Object valueFrom; - - /** - * Getter for property http://commonwl.org/cwltool#LoopInput/valueFrom
- *
- * To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must - * be specified in the workflow or workflow step requirements. - * - * If `valueFrom` is a constant string value, use this as the value for - * this input parameter. - * - * If `valueFrom` is a parameter reference or expression, it must be - * evaluated to yield the actual value to be assigned to the input field. - * - * The `self` value in the parameter reference or expression must be - * `null` if there is no `loopSource` field, or the value of the - * parameter(s) specified in the `loopSource` field. - * - * The value of `inputs` in the parameter reference or expression must be - * the input object to the previous iteration of the workflow step (or the initial - * inputs for the first iteration). - * *
- */ - - public Object getValueFrom() { - return this.valueFrom; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of LoopInputImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public LoopInputImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("LoopInputImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - java.util.Optional default_; - - if (__doc.containsKey("default")) { - try { - default_ = - LoaderInstances - .optional_AnyInstance - .loadField(__doc.get("default"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - default_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `default` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - default_ = null; - } - java.util.Optional linkMerge; - - if (__doc.containsKey("linkMerge")) { - try { - linkMerge = - LoaderInstances - .optional_LinkMergeMethod - .loadField(__doc.get("linkMerge"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - linkMerge = null; // won't be used but prevents compiler from complaining. - final String __message = "the `linkMerge` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - linkMerge = null; - } - Object loopSource; - - if (__doc.containsKey("loopSource")) { - try { - loopSource = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_1_None - .loadField(__doc.get("loopSource"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loopSource = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loopSource` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loopSource = null; - } - java.util.Optional pickValue; - - if (__doc.containsKey("pickValue")) { - try { - pickValue = - LoaderInstances - .optional_PickValueMethod - .loadField(__doc.get("pickValue"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - pickValue = null; // won't be used but prevents compiler from complaining. - final String __message = "the `pickValue` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - pickValue = null; - } - Object valueFrom; - - if (__doc.containsKey("valueFrom")) { - try { - valueFrom = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("valueFrom"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - valueFrom = null; // won't be used but prevents compiler from complaining. - final String __message = "the `valueFrom` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - valueFrom = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.default_ = (java.util.Optional) default_; - this.id = (java.util.Optional) id; - this.linkMerge = (java.util.Optional) linkMerge; - this.loopSource = (Object) loopSource; - this.pickValue = (java.util.Optional) pickValue; - this.valueFrom = (Object) valueFrom; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("default", "id", "linkMerge", "loopSource", "pickValue", "valueFrom"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoopOutputModes.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoopOutputModes.java deleted file mode 100644 index 760c1915..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/LoopOutputModes.java +++ /dev/null @@ -1,38 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum LoopOutputModes { - LAST("last"), - ALL("all"); - - private static String[] symbols = new String[] {"last", "all"}; - private String docVal; - - private LoopOutputModes(final String docVal) { - this.docVal = docVal; - } - - public static LoopOutputModes fromDocumentVal(final String docVal) { - for(final LoopOutputModes val : LoopOutputModes.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", LoopOutputModes.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MPIRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/MPIRequirement.java deleted file mode 100644 index bef91f12..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MPIRequirement.java +++ /dev/null @@ -1,47 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for http://commonwl.org/cwltool#MPIRequirement
This interface is implemented by {@link MPIRequirementImpl}
- Indicates that a process requires an MPI runtime. -
- */ -public interface MPIRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property http://commonwl.org/cwltool#MPIRequirement/class
- *
- * Always 'MPIRequirement' *
- */ - - String getClass_(); - /** - * Getter for property http://commonwl.org/cwltool#MPIRequirement/processes
- *
- * The number of MPI processes to start. If you give a string, - * this will be evaluated as a CWL Expression and it must - * evaluate to an integer. - * *
- */ - - Object getProcesses(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MPIRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/MPIRequirementImpl.java deleted file mode 100644 index 91b1ec60..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MPIRequirementImpl.java +++ /dev/null @@ -1,133 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for http://commonwl.org/cwltool#MPIRequirement
- Indicates that a process requires an MPI runtime. -
- */ -public class MPIRequirementImpl extends SaveableImpl implements MPIRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String class_; - - /** - * Getter for property http://commonwl.org/cwltool#MPIRequirement/class
- *
- * Always 'MPIRequirement' *
- */ - - public String getClass_() { - return this.class_; - } - - private Object processes; - - /** - * Getter for property http://commonwl.org/cwltool#MPIRequirement/processes
- *
- * The number of MPI processes to start. If you give a string, - * this will be evaluated as a CWL Expression and it must - * evaluate to an integer. - * *
- */ - - public Object getProcesses() { - return this.processes; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of MPIRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public MPIRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("MPIRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String class_; - try { - class_ = - LoaderInstances - .uri_StringInstance_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object processes; - try { - processes = - LoaderInstances - .union_of_IntegerInstance_or_ExpressionLoader - .loadField(__doc.get("processes"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - processes = null; // won't be used but prevents compiler from complaining. - final String __message = "the `processes` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (String) class_; - this.processes = (Object) processes; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "processes"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MapSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/MapSchema.java deleted file mode 100644 index 54d8f0bb..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MapSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#MapSchema
This interface is implemented by {@link MapSchemaImpl}
- */ -public interface MapSchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `map` *
- */ - - Map_name getType(); - /** - * Getter for property https://w3id.org/cwl/salad#values
- *
- * Defines the type of the map elements. *
- */ - - Object getValues(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MapSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/MapSchemaImpl.java deleted file mode 100644 index bb3c2860..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MapSchemaImpl.java +++ /dev/null @@ -1,128 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/salad#MapSchema
- */ -public class MapSchemaImpl extends SaveableImpl implements MapSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Map_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `map` *
- */ - - public Map_name getType() { - return this.type; - } - - private Object values; - - /** - * Getter for property https://w3id.org/cwl/salad#values
- *
- * Defines the type of the map elements. *
- */ - - public Object getValues() { - return this.values; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of MapSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public MapSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("MapSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Map_name type; - try { - type = - LoaderInstances - .typedsl_Map_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object values; - try { - values = - LoaderInstances - .uri_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("values"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - values = null; // won't be used but prevents compiler from complaining. - final String __message = "the `values` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.type = (Map_name) type; - this.values = (Object) values; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("type", "values"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Map_name.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Map_name.java deleted file mode 100644 index 2d70a37c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Map_name.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum Map_name { - MAP("map"); - - private static String[] symbols = new String[] {"map"}; - private String docVal; - - private Map_name(final String docVal) { - this.docVal = docVal; - } - - public static Map_name fromDocumentVal(final String docVal) { - for(final Map_name val : Map_name.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Map_name.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirement.java deleted file mode 100644 index 674885a1..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirement.java +++ /dev/null @@ -1,38 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement
This interface is implemented by {@link MultipleInputFeatureRequirementImpl}
- Indicates that the workflow platform must support multiple inbound data links - listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput). -
- */ -public interface MultipleInputFeatureRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement/class
- *
- * Always 'MultipleInputFeatureRequirement' *
- */ - - MultipleInputFeatureRequirement_class getClass_(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirementImpl.java deleted file mode 100644 index d0cec697..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirementImpl.java +++ /dev/null @@ -1,107 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement
- Indicates that the workflow platform must support multiple inbound data links - listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput). -
- */ -public class MultipleInputFeatureRequirementImpl extends SaveableImpl implements MultipleInputFeatureRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private MultipleInputFeatureRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement/class
- *
- * Always 'MultipleInputFeatureRequirement' *
- */ - - public MultipleInputFeatureRequirement_class getClass_() { - return this.class_; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of MultipleInputFeatureRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public MultipleInputFeatureRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("MultipleInputFeatureRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - MultipleInputFeatureRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_MultipleInputFeatureRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (MultipleInputFeatureRequirement_class) class_; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirement_class.java deleted file mode 100644 index 0b3150d1..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/MultipleInputFeatureRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum MultipleInputFeatureRequirement_class { - MULTIPLEINPUTFEATUREREQUIREMENT("MultipleInputFeatureRequirement"); - - private static String[] symbols = new String[] {"MultipleInputFeatureRequirement"}; - private String docVal; - - private MultipleInputFeatureRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static MultipleInputFeatureRequirement_class fromDocumentVal(final String docVal) { - for(final MultipleInputFeatureRequirement_class val : MultipleInputFeatureRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", MultipleInputFeatureRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccess.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccess.java deleted file mode 100644 index 3255648c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccess.java +++ /dev/null @@ -1,57 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#NetworkAccess
This interface is implemented by {@link NetworkAccessImpl}
- Indicate whether a process requires outgoing IPv4/IPv6 network - access. Choice of IPv4 or IPv6 is implementation and site - specific, correct tools must support both. - - If `networkAccess` is false or not specified, tools must not - assume network access, except for localhost (the loopback device). - - If `networkAccess` is true, the tool must be able to make outgoing - connections to network resources. Resources may be on a private - subnet or the public Internet. However, implementations and sites - may apply their own security policies to restrict what is - accessible by the tool. - - Enabling network access does not imply a publicly routable IP - address or the ability to accept inbound connections. -
- */ -public interface NetworkAccess extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/class
- *
- * Always 'NetworkAccess' *
- */ - - NetworkAccess_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/networkAccess
- - */ - - Object getNetworkAccess(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccessImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccessImpl.java deleted file mode 100644 index 79c1dcf6..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccessImpl.java +++ /dev/null @@ -1,143 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#NetworkAccess
- Indicate whether a process requires outgoing IPv4/IPv6 network - access. Choice of IPv4 or IPv6 is implementation and site - specific, correct tools must support both. - - If `networkAccess` is false or not specified, tools must not - assume network access, except for localhost (the loopback device). - - If `networkAccess` is true, the tool must be able to make outgoing - connections to network resources. Resources may be on a private - subnet or the public Internet. However, implementations and sites - may apply their own security policies to restrict what is - accessible by the tool. - - Enabling network access does not imply a publicly routable IP - address or the ability to accept inbound connections. -
- */ -public class NetworkAccessImpl extends SaveableImpl implements NetworkAccess { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private NetworkAccess_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/class
- *
- * Always 'NetworkAccess' *
- */ - - public NetworkAccess_class getClass_() { - return this.class_; - } - - private Object networkAccess; - - /** - * Getter for property https://w3id.org/cwl/cwl#NetworkAccess/networkAccess
- - */ - - public Object getNetworkAccess() { - return this.networkAccess; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of NetworkAccessImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public NetworkAccessImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("NetworkAccessImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - NetworkAccess_class class_; - try { - class_ = - LoaderInstances - .uri_NetworkAccess_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object networkAccess; - try { - networkAccess = - LoaderInstances - .union_of_BooleanInstance_or_ExpressionLoader - .loadField(__doc.get("networkAccess"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - networkAccess = null; // won't be used but prevents compiler from complaining. - final String __message = "the `networkAccess` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (NetworkAccess_class) class_; - this.networkAccess = (Object) networkAccess; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "networkAccess"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccess_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccess_class.java deleted file mode 100644 index 584b1e01..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/NetworkAccess_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum NetworkAccess_class { - NETWORKACCESS("NetworkAccess"); - - private static String[] symbols = new String[] {"NetworkAccess"}; - private String docVal; - - private NetworkAccess_class(final String docVal) { - this.docVal = docVal; - } - - public static NetworkAccess_class fromDocumentVal(final String docVal) { - for(final NetworkAccess_class val : NetworkAccess_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", NetworkAccess_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Operation.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Operation.java deleted file mode 100644 index 609a08b9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Operation.java +++ /dev/null @@ -1,148 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Operation
This interface is implemented by {@link OperationImpl}
- This record describes an abstract operation. It is a potential - step of a workflow that has not yet been bound to a concrete - implementation. It specifies an input and output signature, but - does not provide enough information to be executed. An - implementation (or other tooling) may provide a means of binding - an Operation to a concrete process (such as Workflow, - CommandLineTool, or ExpressionTool) with a compatible signature. -
- */ -public interface Operation extends Process, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/id
- *
- * The unique identifier for this object. - * - * Only useful for `$graph` at `Process` level. Should not be exposed - * to users in graphical or terminal user interfaces. - * *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Operation/class
- - */ - - Operation_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - java.util.List getInputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - java.util.List getOutputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - java.util.Optional> getRequirements(); - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - java.util.Optional> getHints(); - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - java.util.Optional getCwlVersion(); - /** - * Getter for property https://w3id.org/cwl/cwl#Process/intent
- *
- * An identifier for the type of computational operation, of this Process. - * Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for - * [`CommandLineTool`](CommandLineTool.html#CommandLineTool), - * [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). - * - * If provided, then this must be an IRI of a concept node that - * represents the type of operation, preferably defined within an ontology. - * - * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), - * like [Alignment](http://edamontology.org/operation_2928), - * or [Clustering](http://edamontology.org/operation_3432); or a more - * specific Operation concept like - * [Split read mapping](http://edamontology.org/operation_3199). - * *
- */ - - java.util.Optional> getIntent(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationImpl.java deleted file mode 100644 index 9ac7ee25..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationImpl.java +++ /dev/null @@ -1,426 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#Operation
- This record describes an abstract operation. It is a potential - step of a workflow that has not yet been bound to a concrete - implementation. It specifies an input and output signature, but - does not provide enough information to be executed. An - implementation (or other tooling) may provide a means of binding - an Operation to a concrete process (such as Workflow, - CommandLineTool, or ExpressionTool) with a compatible signature. -
- */ -public class OperationImpl extends SaveableImpl implements Operation { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/id
- *
- * The unique identifier for this object. - * - * Only useful for `$graph` at `Process` level. Should not be exposed - * to users in graphical or terminal user interfaces. - * *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private Operation_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#Operation/class
- - */ - - public Operation_class getClass_() { - return this.class_; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.List inputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - public java.util.List getInputs() { - return this.inputs; - } - - private java.util.List outputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - public java.util.List getOutputs() { - return this.outputs; - } - - private java.util.Optional> requirements; - - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - public java.util.Optional> getRequirements() { - return this.requirements; - } - - private java.util.Optional> hints; - - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - public java.util.Optional> getHints() { - return this.hints; - } - - private java.util.Optional cwlVersion; - - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - public java.util.Optional getCwlVersion() { - return this.cwlVersion; - } - - private java.util.Optional> intent; - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/intent
- *
- * An identifier for the type of computational operation, of this Process. - * Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for - * [`CommandLineTool`](CommandLineTool.html#CommandLineTool), - * [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). - * - * If provided, then this must be an IRI of a concept node that - * represents the type of operation, preferably defined within an ontology. - * - * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), - * like [Alignment](http://edamontology.org/operation_2928), - * or [Clustering](http://edamontology.org/operation_3432); or a more - * specific Operation concept like - * [Split read mapping](http://edamontology.org/operation_3199). - * *
- */ - - public java.util.Optional> getIntent() { - return this.intent; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of OperationImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public OperationImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("OperationImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - Operation_class class_; - try { - class_ = - LoaderInstances - .uri_Operation_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.List inputs; - try { - inputs = - LoaderInstances - .idmap_inputs_array_of_OperationInputParameter - .loadField(__doc.get("inputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List outputs; - try { - outputs = - LoaderInstances - .idmap_outputs_array_of_OperationOutputParameter - .loadField(__doc.get("outputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> requirements; - - if (__doc.containsKey("requirements")) { - try { - requirements = - LoaderInstances - .idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize - .loadField(__doc.get("requirements"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - requirements = null; // won't be used but prevents compiler from complaining. - final String __message = "the `requirements` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - requirements = null; - } - java.util.Optional> hints; - - if (__doc.containsKey("hints")) { - try { - hints = - LoaderInstances - .idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_AnyInstance - .loadField(__doc.get("hints"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - hints = null; // won't be used but prevents compiler from complaining. - final String __message = "the `hints` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - hints = null; - } - java.util.Optional cwlVersion; - - if (__doc.containsKey("cwlVersion")) { - try { - cwlVersion = - LoaderInstances - .uri_optional_CWLVersion_False_True_None_None - .loadField(__doc.get("cwlVersion"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - cwlVersion = null; // won't be used but prevents compiler from complaining. - final String __message = "the `cwlVersion` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - cwlVersion = null; - } - java.util.Optional> intent; - - if (__doc.containsKey("intent")) { - try { - intent = - LoaderInstances - .uri_optional_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("intent"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - intent = null; // won't be used but prevents compiler from complaining. - final String __message = "the `intent` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - intent = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (java.util.Optional) id; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.inputs = (java.util.List) inputs; - this.outputs = (java.util.List) outputs; - this.requirements = (java.util.Optional>) requirements; - this.hints = (java.util.Optional>) hints; - this.cwlVersion = (java.util.Optional) cwlVersion; - this.intent = (java.util.Optional>) intent; - this.class_ = (Operation_class) class_; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id", "label", "doc", "inputs", "outputs", "requirements", "hints", "cwlVersion", "intent", "class"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameter.java deleted file mode 100644 index f0b9f1c4..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameter.java +++ /dev/null @@ -1,176 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OperationInputParameter
This interface is implemented by {@link OperationInputParameterImpl}
- Describe an input parameter of an operation. -
- */ -public interface OperationInputParameter extends InputParameter, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - String getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value to use for this parameter if the parameter is missing - * from the input object, or if the value of the parameter in the input - * object is `null`. Default values are applied before evaluating expressions - * (e.g. dependent `valueFrom` fields). - * *
- */ - - java.util.Optional getDefault(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - Object getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameterImpl.java deleted file mode 100644 index a1fec743..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationInputParameterImpl.java +++ /dev/null @@ -1,461 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#OperationInputParameter
- Describe an input parameter of an operation. -
- */ -public class OperationInputParameterImpl extends SaveableImpl implements OperationInputParameter { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - public String getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - private java.util.Optional default_; - - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value to use for this parameter if the parameter is missing - * from the input object, or if the value of the parameter in the input - * object is `null`. Default values are applied before evaluating expressions - * (e.g. dependent `valueFrom` fields). - * *
- */ - - public java.util.Optional getDefault() { - return this.default_; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - public Object getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of OperationInputParameterImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public OperationInputParameterImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("OperationInputParameterImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - if (id == null) { - if (__docRoot != null) { - id = __docRoot; - } else { - throw new ValidationException("Missing id"); - } - } - __baseUri = (String) id; - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - java.util.Optional default_; - - if (__doc.containsKey("default")) { - try { - default_ = - LoaderInstances - .optional_CWLObjectType - .loadField(__doc.get("default"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - default_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `default` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - default_ = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.doc = (Object) doc; - this.id = (String) id; - this.format = (Object) format; - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - this.default_ = (java.util.Optional) default_; - this.type = (Object) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("label", "secondaryFiles", "streamable", "doc", "id", "format", "loadContents", "loadListing", "default", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameter.java deleted file mode 100644 index 393cee4c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameter.java +++ /dev/null @@ -1,131 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OperationOutputParameter
This interface is implemented by {@link OperationOutputParameterImpl}
- Describe an output parameter of an operation. -
- */ -public interface OperationOutputParameter extends OutputParameter, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - String getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - Object getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameterImpl.java deleted file mode 100644 index c1e93b04..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OperationOutputParameterImpl.java +++ /dev/null @@ -1,347 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#OperationOutputParameter
- Describe an output parameter of an operation. -
- */ -public class OperationOutputParameterImpl extends SaveableImpl implements OperationOutputParameter { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - public String getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - public Object getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of OperationOutputParameterImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public OperationOutputParameterImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("OperationOutputParameterImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - if (id == null) { - if (__docRoot != null) { - id = __docRoot; - } else { - throw new ValidationException("Missing id"); - } - } - __baseUri = (String) id; - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.doc = (Object) doc; - this.id = (String) id; - this.format = (Object) format; - this.type = (Object) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("label", "secondaryFiles", "streamable", "doc", "id", "format", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Operation_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Operation_class.java deleted file mode 100644 index f102af8a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Operation_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum Operation_class { - OPERATION("Operation"); - - private static String[] symbols = new String[] {"Operation"}; - private String docVal; - - private Operation_class(final String docVal) { - this.docVal = docVal; - } - - public static Operation_class fromDocumentVal(final String docVal) { - for(final Operation_class val : Operation_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Operation_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputArraySchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputArraySchema.java deleted file mode 100644 index 9fd7d6e9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputArraySchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputArraySchema
This interface is implemented by {@link OutputArraySchemaImpl}
- */ -public interface OutputArraySchema extends CWLArraySchema, OutputSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - Object getItems(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - Array_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputArraySchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputArraySchemaImpl.java deleted file mode 100644 index f638eae4..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputArraySchemaImpl.java +++ /dev/null @@ -1,232 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputArraySchema
- */ -public class OutputArraySchemaImpl extends SaveableImpl implements OutputArraySchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private Object items; - - /** - * Getter for property https://w3id.org/cwl/salad#items
- *
- * Defines the type of the array elements. *
- */ - - public Object getItems() { - return this.items; - } - - private Array_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `array` *
- */ - - public Array_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of OutputArraySchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public OutputArraySchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("OutputArraySchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - Object items; - try { - items = - LoaderInstances - .uri_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("items"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - items = null; // won't be used but prevents compiler from complaining. - final String __message = "the `items` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Array_name type; - try { - type = - LoaderInstances - .typedsl_Array_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.items = (Object) items; - this.type = (Array_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("items", "type", "label", "doc", "name"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputEnumSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputEnumSchema.java deleted file mode 100644 index d6c66bfd..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputEnumSchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputEnumSchema
This interface is implemented by {@link OutputEnumSchemaImpl}
- */ -public interface OutputEnumSchema extends EnumSchema, OutputSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - java.util.List getSymbols(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - Enum_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputEnumSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputEnumSchemaImpl.java deleted file mode 100644 index 0ecfb5ae..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputEnumSchemaImpl.java +++ /dev/null @@ -1,232 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputEnumSchema
- */ -public class OutputEnumSchemaImpl extends SaveableImpl implements OutputEnumSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.List symbols; - - /** - * Getter for property https://w3id.org/cwl/salad#symbols
- *
- * Defines the set of valid symbols. *
- */ - - public java.util.List getSymbols() { - return this.symbols; - } - - private Enum_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `enum` *
- */ - - public Enum_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of OutputEnumSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public OutputEnumSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("OutputEnumSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.List symbols; - try { - symbols = - LoaderInstances - .uri_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("symbols"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - symbols = null; // won't be used but prevents compiler from complaining. - final String __message = "the `symbols` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Enum_name type; - try { - type = - LoaderInstances - .typedsl_Enum_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.name = (java.util.Optional) name; - this.symbols = (java.util.List) symbols; - this.type = (Enum_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("name", "symbols", "type", "label", "doc"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputFormat.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputFormat.java deleted file mode 100644 index c35a393a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputFormat.java +++ /dev/null @@ -1,39 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputFormat
- */ -public interface OutputFormat extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputParameter.java deleted file mode 100644 index d541ae9a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputParameter.java +++ /dev/null @@ -1,114 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputParameter
- */ -public interface OutputParameter extends Parameter, OutputFormat, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordField.java deleted file mode 100644 index d34876c7..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordField.java +++ /dev/null @@ -1,130 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputRecordField
This interface is implemented by {@link OutputRecordFieldImpl}
- */ -public interface OutputRecordField extends CWLRecordField, FieldBase, OutputFormat, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - String getName(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordFieldImpl.java deleted file mode 100644 index f5ded71f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordFieldImpl.java +++ /dev/null @@ -1,346 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordField
- */ -public class OutputRecordFieldImpl extends SaveableImpl implements OutputRecordField { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String name; - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - public String getName() { - return this.name; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - public Object getFormat() { - return this.format; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of OutputRecordFieldImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public OutputRecordFieldImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("OutputRecordFieldImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - if (name == null) { - if (__docRoot != null) { - name = __docRoot; - } else { - throw new ValidationException("Missing name"); - } - } - __baseUri = (String) name; - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.doc = (Object) doc; - this.name = (String) name; - this.type = (Object) type; - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.format = (Object) format; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("doc", "name", "type", "label", "secondaryFiles", "streamable", "format"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordSchema.java deleted file mode 100644 index a2cdc0c9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordSchema.java +++ /dev/null @@ -1,63 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputRecordSchema
This interface is implemented by {@link OutputRecordSchemaImpl}
- */ -public interface OutputRecordSchema extends CWLRecordSchema, OutputSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - java.util.Optional getName(); - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - java.util.Optional> getFields(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - Record_name getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordSchemaImpl.java deleted file mode 100644 index 3b4dcf0e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputRecordSchemaImpl.java +++ /dev/null @@ -1,238 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordSchema
- */ -public class OutputRecordSchemaImpl extends SaveableImpl implements OutputRecordSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional name; - - /** - * Getter for property https://w3id.org/cwl/cwl#IOSchema/name
- *
- * The identifier for this type *
- */ - - public java.util.Optional getName() { - return this.name; - } - - private java.util.Optional> fields; - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - public java.util.Optional> getFields() { - return this.fields; - } - - private Record_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - public Record_name getType() { - return this.type; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of OutputRecordSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public OutputRecordSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("OutputRecordSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - Boolean __original_is_null = name == null; - if (name == null) { - if (__docRoot != null) { - name = java.util.Optional.of(__docRoot); - } else { - name = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) name.orElse(null); - } - java.util.Optional> fields; - - if (__doc.containsKey("fields")) { - try { - fields = - LoaderInstances - .idmap_fields_optional_array_of_OutputRecordField - .loadField(__doc.get("fields"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - fields = null; // won't be used but prevents compiler from complaining. - final String __message = "the `fields` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - fields = null; - } - Record_name type; - try { - type = - LoaderInstances - .typedsl_Record_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.fields = (java.util.Optional>) fields; - this.type = (Record_name) type; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.name = (java.util.Optional) name; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("fields", "type", "label", "doc", "name"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputSchema.java deleted file mode 100644 index 3115db03..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/OutputSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#OutputSchema
- */ -public interface OutputSchema extends IOSchema, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Parameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Parameter.java deleted file mode 100644 index 5eaf40c6..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Parameter.java +++ /dev/null @@ -1,105 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Parameter
- Define an input or output parameter to a process. -
- */ -public interface Parameter extends FieldBase, Documented, IdentifierRequired, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/PickValueMethod.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/PickValueMethod.java deleted file mode 100644 index 9cd0bee6..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/PickValueMethod.java +++ /dev/null @@ -1,39 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum PickValueMethod { - FIRST_NON_NULL("first_non_null"), - THE_ONLY_NON_NULL("the_only_non_null"), - ALL_NON_NULL("all_non_null"); - - private static String[] symbols = new String[] {"first_non_null", "the_only_non_null", "all_non_null"}; - private String docVal; - - private PickValueMethod(final String docVal) { - this.docVal = docVal; - } - - public static PickValueMethod fromDocumentVal(final String docVal) { - for(final PickValueMethod val : PickValueMethod.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", PickValueMethod.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/PrimitiveType.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/PrimitiveType.java deleted file mode 100644 index 47f10785..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/PrimitiveType.java +++ /dev/null @@ -1,43 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum PrimitiveType { - NULL("null"), - BOOLEAN("boolean"), - INT("int"), - LONG("long"), - FLOAT("float"), - DOUBLE("double"), - STRING("string"); - - private static String[] symbols = new String[] {"null", "boolean", "int", "long", "float", "double", "string"}; - private String docVal; - - private PrimitiveType(final String docVal) { - this.docVal = docVal; - } - - public static PrimitiveType fromDocumentVal(final String docVal) { - for(final PrimitiveType val : PrimitiveType.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", PrimitiveType.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Process.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Process.java deleted file mode 100644 index 52590e40..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Process.java +++ /dev/null @@ -1,128 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Process
- - The base executable type in CWL is the `Process` object defined by the - document. Note that the `Process` object is abstract and cannot be - directly executed. -
- */ -public interface Process extends Identified, Labeled, Documented, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - java.util.List getInputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - java.util.List getOutputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - java.util.Optional> getRequirements(); - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - java.util.Optional> getHints(); - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - java.util.Optional getCwlVersion(); - /** - * Getter for property https://w3id.org/cwl/cwl#Process/intent
- *
- * An identifier for the type of computational operation, of this Process. - * Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for - * [`CommandLineTool`](CommandLineTool.html#CommandLineTool), - * [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). - * - * If provided, then this must be an IRI of a concept node that - * represents the type of operation, preferably defined within an ontology. - * - * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), - * like [Alignment](http://edamontology.org/operation_2928), - * or [Clustering](http://edamontology.org/operation_3432); or a more - * specific Operation concept like - * [Split read mapping](http://edamontology.org/operation_3199). - * *
- */ - - java.util.Optional> getIntent(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ProcessGenerator.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ProcessGenerator.java deleted file mode 100644 index c5c38e9b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ProcessGenerator.java +++ /dev/null @@ -1,148 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for http://commonwl.org/cwltool#ProcessGenerator
This interface is implemented by {@link ProcessGeneratorImpl}
- */ -public interface ProcessGenerator extends Process, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/id
- *
- * The unique identifier for this object. - * - * Only useful for `$graph` at `Process` level. Should not be exposed - * to users in graphical or terminal user interfaces. - * *
- */ - - java.util.Optional getId(); - /** - * Getter for property http://commonwl.org/cwltool#ProcessGenerator/class
- - */ - - String getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - java.util.List getInputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - java.util.List getOutputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - java.util.Optional> getRequirements(); - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - java.util.Optional> getHints(); - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - java.util.Optional getCwlVersion(); - /** - * Getter for property https://w3id.org/cwl/cwl#Process/intent
- *
- * An identifier for the type of computational operation, of this Process. - * Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for - * [`CommandLineTool`](CommandLineTool.html#CommandLineTool), - * [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). - * - * If provided, then this must be an IRI of a concept node that - * represents the type of operation, preferably defined within an ontology. - * - * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), - * like [Alignment](http://edamontology.org/operation_2928), - * or [Clustering](http://edamontology.org/operation_3432); or a more - * specific Operation concept like - * [Split read mapping](http://edamontology.org/operation_3199). - * *
- */ - - java.util.Optional> getIntent(); - /** - * Getter for property https://w3id.org/cwl/cwl#run
- *
- * Specifies the process to run. - * *
- */ - - Object getRun(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ProcessGeneratorImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ProcessGeneratorImpl.java deleted file mode 100644 index 80cceb86..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ProcessGeneratorImpl.java +++ /dev/null @@ -1,443 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for http://commonwl.org/cwltool#ProcessGenerator
- */ -public class ProcessGeneratorImpl extends SaveableImpl implements ProcessGenerator { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/id
- *
- * The unique identifier for this object. - * - * Only useful for `$graph` at `Process` level. Should not be exposed - * to users in graphical or terminal user interfaces. - * *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private String class_; - - /** - * Getter for property http://commonwl.org/cwltool#ProcessGenerator/class
- - */ - - public String getClass_() { - return this.class_; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.List inputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - public java.util.List getInputs() { - return this.inputs; - } - - private java.util.List outputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - public java.util.List getOutputs() { - return this.outputs; - } - - private java.util.Optional> requirements; - - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - public java.util.Optional> getRequirements() { - return this.requirements; - } - - private java.util.Optional> hints; - - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - public java.util.Optional> getHints() { - return this.hints; - } - - private java.util.Optional cwlVersion; - - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - public java.util.Optional getCwlVersion() { - return this.cwlVersion; - } - - private java.util.Optional> intent; - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/intent
- *
- * An identifier for the type of computational operation, of this Process. - * Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for - * [`CommandLineTool`](CommandLineTool.html#CommandLineTool), - * [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). - * - * If provided, then this must be an IRI of a concept node that - * represents the type of operation, preferably defined within an ontology. - * - * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), - * like [Alignment](http://edamontology.org/operation_2928), - * or [Clustering](http://edamontology.org/operation_3432); or a more - * specific Operation concept like - * [Split read mapping](http://edamontology.org/operation_3199). - * *
- */ - - public java.util.Optional> getIntent() { - return this.intent; - } - - private Object run; - - /** - * Getter for property https://w3id.org/cwl/cwl#run
- *
- * Specifies the process to run. - * *
- */ - - public Object getRun() { - return this.run; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of ProcessGeneratorImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ProcessGeneratorImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ProcessGeneratorImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - String class_; - try { - class_ = - LoaderInstances - .uri_StringInstance_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.List inputs; - try { - inputs = - LoaderInstances - .idmap_inputs_array_of_union_of_CommandInputParameter_or_WorkflowInputParameter_or_OperationInputParameter - .loadField(__doc.get("inputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List outputs; - try { - outputs = - LoaderInstances - .idmap_outputs_array_of_union_of_CommandOutputParameter_or_ExpressionToolOutputParameter_or_WorkflowOutputParameter_or_OperationOutputParameter - .loadField(__doc.get("outputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> requirements; - - if (__doc.containsKey("requirements")) { - try { - requirements = - LoaderInstances - .idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize - .loadField(__doc.get("requirements"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - requirements = null; // won't be used but prevents compiler from complaining. - final String __message = "the `requirements` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - requirements = null; - } - java.util.Optional> hints; - - if (__doc.containsKey("hints")) { - try { - hints = - LoaderInstances - .idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_AnyInstance - .loadField(__doc.get("hints"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - hints = null; // won't be used but prevents compiler from complaining. - final String __message = "the `hints` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - hints = null; - } - java.util.Optional cwlVersion; - - if (__doc.containsKey("cwlVersion")) { - try { - cwlVersion = - LoaderInstances - .uri_optional_CWLVersion_False_True_None_None - .loadField(__doc.get("cwlVersion"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - cwlVersion = null; // won't be used but prevents compiler from complaining. - final String __message = "the `cwlVersion` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - cwlVersion = null; - } - java.util.Optional> intent; - - if (__doc.containsKey("intent")) { - try { - intent = - LoaderInstances - .uri_optional_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("intent"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - intent = null; // won't be used but prevents compiler from complaining. - final String __message = "the `intent` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - intent = null; - } - Object run; - try { - run = - LoaderInstances - .uri_union_of_StringInstance_or_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator_False_False_None_None - .loadField(__doc.get("run"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - run = null; // won't be used but prevents compiler from complaining. - final String __message = "the `run` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (java.util.Optional) id; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.inputs = (java.util.List) inputs; - this.outputs = (java.util.List) outputs; - this.requirements = (java.util.Optional>) requirements; - this.hints = (java.util.Optional>) hints; - this.cwlVersion = (java.util.Optional) cwlVersion; - this.intent = (java.util.Optional>) intent; - this.class_ = (String) class_; - this.run = (Object) run; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id", "label", "doc", "inputs", "outputs", "requirements", "hints", "cwlVersion", "intent", "class", "run"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ProcessRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ProcessRequirement.java deleted file mode 100644 index 5ade099b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ProcessRequirement.java +++ /dev/null @@ -1,35 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ProcessRequirement
- A process requirement declares a prerequisite that may or must be fulfilled - before executing a process. See [`Process.hints`](#process) and - [`Process.requirements`](#process). - - Process requirements are the primary mechanism for specifying extensions to - the CWL core specification. -
- */ -public interface ProcessRequirement extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/RecordField.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/RecordField.java deleted file mode 100644 index c476e818..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/RecordField.java +++ /dev/null @@ -1,54 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#RecordField
This interface is implemented by {@link RecordFieldImpl}
- A field of a record.
- */ -public interface RecordField extends Documented, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - String getName(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type. If it is an array, it indicates - * that the field type is a union type of its elements. - * Its elements may be duplicated. - * *
- */ - - Object getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/RecordFieldImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/RecordFieldImpl.java deleted file mode 100644 index 3493cd90..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/RecordFieldImpl.java +++ /dev/null @@ -1,178 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/salad#RecordField
- A field of a record.
- */ -public class RecordFieldImpl extends SaveableImpl implements RecordField { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String name; - - /** - * Getter for property https://w3id.org/cwl/salad#RecordField/name
- *
- * The name of the field - * *
- */ - - public String getName() { - return this.name; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * The field type. If it is an array, it indicates - * that the field type is a union type of its elements. - * Its elements may be duplicated. - * *
- */ - - public Object getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of RecordFieldImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public RecordFieldImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("RecordFieldImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String name; - - if (__doc.containsKey("name")) { - try { - name = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("name"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - name = null; // won't be used but prevents compiler from complaining. - final String __message = "the `name` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - name = null; - } - - if (name == null) { - if (__docRoot != null) { - name = __docRoot; - } else { - throw new ValidationException("Missing name"); - } - } - __baseUri = (String) name; - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.doc = (Object) doc; - this.name = (String) name; - this.type = (Object) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("doc", "name", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/RecordSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/RecordSchema.java deleted file mode 100644 index 527a094a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/RecordSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#RecordSchema
This interface is implemented by {@link RecordSchemaImpl}
- */ -public interface RecordSchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - java.util.Optional> getFields(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - Record_name getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/RecordSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/RecordSchemaImpl.java deleted file mode 100644 index 70728cf2..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/RecordSchemaImpl.java +++ /dev/null @@ -1,134 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/salad#RecordSchema
- */ -public class RecordSchemaImpl extends SaveableImpl implements RecordSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional> fields; - - /** - * Getter for property https://w3id.org/cwl/salad#fields
- *
- * Defines the fields of the record. *
- */ - - public java.util.Optional> getFields() { - return this.fields; - } - - private Record_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `record` *
- */ - - public Record_name getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of RecordSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public RecordSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("RecordSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional> fields; - - if (__doc.containsKey("fields")) { - try { - fields = - LoaderInstances - .idmap_fields_optional_array_of_RecordField - .loadField(__doc.get("fields"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - fields = null; // won't be used but prevents compiler from complaining. - final String __message = "the `fields` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - fields = null; - } - Record_name type; - try { - type = - LoaderInstances - .typedsl_Record_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.fields = (java.util.Optional>) fields; - this.type = (Record_name) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("fields", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Record_name.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Record_name.java deleted file mode 100644 index a1c07e90..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Record_name.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum Record_name { - RECORD("record"); - - private static String[] symbols = new String[] {"record"}; - private String docVal; - - private Record_name(final String docVal) { - this.docVal = docVal; - } - - public static Record_name fromDocumentVal(final String docVal) { - for(final Record_name val : Record_name.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Record_name.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirement.java deleted file mode 100644 index cd82cafe..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirement.java +++ /dev/null @@ -1,175 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ResourceRequirement
This interface is implemented by {@link ResourceRequirementImpl}
- Specify basic hardware resource requirements. - - "min" is the minimum amount of a resource that must be reserved to - schedule a job. If "min" cannot be satisfied, the job should not - be run. - - "max" is the maximum amount of a resource that the job shall be - allocated. If a node has sufficient resources, multiple jobs may - be scheduled on a single node provided each job's "max" resource - requirements are met. If a job attempts to exceed its resource - allocation, an implementation may deny additional resources, which - may result in job failure. - - If both "min" and "max" are specified, an implementation may - choose to allocate any amount between "min" and "max", with the - actual allocation provided in the `runtime` object. - - If "min" is specified but "max" is not, then "max" == "min" - If "max" is specified by "min" is not, then "min" == "max". - - It is an error if max < min. - - It is an error if the value of any of these fields is negative. - - If neither "min" nor "max" is specified for a resource, use the default values below. -
- */ -public interface ResourceRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/class
- *
- * Always 'ResourceRequirement' *
- */ - - ResourceRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/coresMin
- *
- * Minimum reserved number of CPU cores (default is 1). - * - * May be a fractional value to indicate to a scheduling - * algorithm that one core can be allocated to multiple - * jobs. For example, a value of 0.25 indicates that up to 4 - * jobs may run in parallel on 1 core. A value of 1.25 means - * that up to 3 jobs can run on a 4 core system (4/1.25 ≈ 3). - * - * Processes can only share a core allocation if the sum of each - * of their `ramMax`, `tmpdirMax`, and `outdirMax` requests also - * do not exceed the capacity of the node. - * - * Processes sharing a core must have the same level of isolation - * (typically a container or VM) that they would normally have. - * - * The reported number of CPU cores reserved for the process, - * which is available to expressions on the CommandLineTool as - * `runtime.cores`, must be a non-zero integer, and may be - * calculated by rounding up the cores request to the next whole - * number. - * - * Scheduling systems may allocate fractional CPU resources by - * setting quotas or scheduling weights. Scheduling systems that - * do not support fractional CPUs may round up the request to the - * next whole number. - * *
- */ - - Object getCoresMin(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/coresMax
- *
- * Maximum reserved number of CPU cores. - * - * See `coresMin` for discussion about fractional CPU requests. - * *
- */ - - Object getCoresMax(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/ramMin
- *
- * Minimum reserved RAM in mebibytes (2**20) (default is 256) - * - * May be a fractional value. If so, the actual RAM request must - * be rounded up to the next whole number. The reported amount of - * RAM reserved for the process, which is available to - * expressions on the CommandLineTool as `runtime.ram`, must be a - * non-zero integer. - * *
- */ - - Object getRamMin(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/ramMax
- *
- * Maximum reserved RAM in mebibytes (2**20) - * - * See `ramMin` for discussion about fractional RAM requests. - * *
- */ - - Object getRamMax(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/tmpdirMin
- *
- * Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024) - * - * May be a fractional value. If so, the actual storage request - * must be rounded up to the next whole number. The reported - * amount of storage reserved for the process, which is available - * to expressions on the CommandLineTool as `runtime.tmpdirSize`, - * must be a non-zero integer. - * *
- */ - - Object getTmpdirMin(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/tmpdirMax
- *
- * Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) - * - * See `tmpdirMin` for discussion about fractional storage requests. - * *
- */ - - Object getTmpdirMax(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/outdirMin
- *
- * Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024) - * - * May be a fractional value. If so, the actual storage request - * must be rounded up to the next whole number. The reported - * amount of storage reserved for the process, which is available - * to expressions on the CommandLineTool as `runtime.outdirSize`, - * must be a non-zero integer. - * *
- */ - - Object getOutdirMin(); - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/outdirMax
- *
- * Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) - * - * See `outdirMin` for discussion about fractional storage requests. - * *
- */ - - Object getOutdirMax(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirementImpl.java deleted file mode 100644 index f1dda845..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirementImpl.java +++ /dev/null @@ -1,428 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#ResourceRequirement
- Specify basic hardware resource requirements. - - "min" is the minimum amount of a resource that must be reserved to - schedule a job. If "min" cannot be satisfied, the job should not - be run. - - "max" is the maximum amount of a resource that the job shall be - allocated. If a node has sufficient resources, multiple jobs may - be scheduled on a single node provided each job's "max" resource - requirements are met. If a job attempts to exceed its resource - allocation, an implementation may deny additional resources, which - may result in job failure. - - If both "min" and "max" are specified, an implementation may - choose to allocate any amount between "min" and "max", with the - actual allocation provided in the `runtime` object. - - If "min" is specified but "max" is not, then "max" == "min" - If "max" is specified by "min" is not, then "min" == "max". - - It is an error if max < min. - - It is an error if the value of any of these fields is negative. - - If neither "min" nor "max" is specified for a resource, use the default values below. -
- */ -public class ResourceRequirementImpl extends SaveableImpl implements ResourceRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private ResourceRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/class
- *
- * Always 'ResourceRequirement' *
- */ - - public ResourceRequirement_class getClass_() { - return this.class_; - } - - private Object coresMin; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/coresMin
- *
- * Minimum reserved number of CPU cores (default is 1). - * - * May be a fractional value to indicate to a scheduling - * algorithm that one core can be allocated to multiple - * jobs. For example, a value of 0.25 indicates that up to 4 - * jobs may run in parallel on 1 core. A value of 1.25 means - * that up to 3 jobs can run on a 4 core system (4/1.25 ≈ 3). - * - * Processes can only share a core allocation if the sum of each - * of their `ramMax`, `tmpdirMax`, and `outdirMax` requests also - * do not exceed the capacity of the node. - * - * Processes sharing a core must have the same level of isolation - * (typically a container or VM) that they would normally have. - * - * The reported number of CPU cores reserved for the process, - * which is available to expressions on the CommandLineTool as - * `runtime.cores`, must be a non-zero integer, and may be - * calculated by rounding up the cores request to the next whole - * number. - * - * Scheduling systems may allocate fractional CPU resources by - * setting quotas or scheduling weights. Scheduling systems that - * do not support fractional CPUs may round up the request to the - * next whole number. - * *
- */ - - public Object getCoresMin() { - return this.coresMin; - } - - private Object coresMax; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/coresMax
- *
- * Maximum reserved number of CPU cores. - * - * See `coresMin` for discussion about fractional CPU requests. - * *
- */ - - public Object getCoresMax() { - return this.coresMax; - } - - private Object ramMin; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/ramMin
- *
- * Minimum reserved RAM in mebibytes (2**20) (default is 256) - * - * May be a fractional value. If so, the actual RAM request must - * be rounded up to the next whole number. The reported amount of - * RAM reserved for the process, which is available to - * expressions on the CommandLineTool as `runtime.ram`, must be a - * non-zero integer. - * *
- */ - - public Object getRamMin() { - return this.ramMin; - } - - private Object ramMax; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/ramMax
- *
- * Maximum reserved RAM in mebibytes (2**20) - * - * See `ramMin` for discussion about fractional RAM requests. - * *
- */ - - public Object getRamMax() { - return this.ramMax; - } - - private Object tmpdirMin; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/tmpdirMin
- *
- * Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024) - * - * May be a fractional value. If so, the actual storage request - * must be rounded up to the next whole number. The reported - * amount of storage reserved for the process, which is available - * to expressions on the CommandLineTool as `runtime.tmpdirSize`, - * must be a non-zero integer. - * *
- */ - - public Object getTmpdirMin() { - return this.tmpdirMin; - } - - private Object tmpdirMax; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/tmpdirMax
- *
- * Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) - * - * See `tmpdirMin` for discussion about fractional storage requests. - * *
- */ - - public Object getTmpdirMax() { - return this.tmpdirMax; - } - - private Object outdirMin; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/outdirMin
- *
- * Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024) - * - * May be a fractional value. If so, the actual storage request - * must be rounded up to the next whole number. The reported - * amount of storage reserved for the process, which is available - * to expressions on the CommandLineTool as `runtime.outdirSize`, - * must be a non-zero integer. - * *
- */ - - public Object getOutdirMin() { - return this.outdirMin; - } - - private Object outdirMax; - - /** - * Getter for property https://w3id.org/cwl/cwl#ResourceRequirement/outdirMax
- *
- * Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) - * - * See `outdirMin` for discussion about fractional storage requests. - * *
- */ - - public Object getOutdirMax() { - return this.outdirMax; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of ResourceRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ResourceRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ResourceRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - ResourceRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_ResourceRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object coresMin; - - if (__doc.containsKey("coresMin")) { - try { - coresMin = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_DoubleInstance_or_ExpressionLoader - .loadField(__doc.get("coresMin"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - coresMin = null; // won't be used but prevents compiler from complaining. - final String __message = "the `coresMin` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - coresMin = null; - } - Object coresMax; - - if (__doc.containsKey("coresMax")) { - try { - coresMax = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_DoubleInstance_or_ExpressionLoader - .loadField(__doc.get("coresMax"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - coresMax = null; // won't be used but prevents compiler from complaining. - final String __message = "the `coresMax` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - coresMax = null; - } - Object ramMin; - - if (__doc.containsKey("ramMin")) { - try { - ramMin = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_DoubleInstance_or_ExpressionLoader - .loadField(__doc.get("ramMin"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - ramMin = null; // won't be used but prevents compiler from complaining. - final String __message = "the `ramMin` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - ramMin = null; - } - Object ramMax; - - if (__doc.containsKey("ramMax")) { - try { - ramMax = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_DoubleInstance_or_ExpressionLoader - .loadField(__doc.get("ramMax"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - ramMax = null; // won't be used but prevents compiler from complaining. - final String __message = "the `ramMax` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - ramMax = null; - } - Object tmpdirMin; - - if (__doc.containsKey("tmpdirMin")) { - try { - tmpdirMin = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_DoubleInstance_or_ExpressionLoader - .loadField(__doc.get("tmpdirMin"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - tmpdirMin = null; // won't be used but prevents compiler from complaining. - final String __message = "the `tmpdirMin` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - tmpdirMin = null; - } - Object tmpdirMax; - - if (__doc.containsKey("tmpdirMax")) { - try { - tmpdirMax = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_DoubleInstance_or_ExpressionLoader - .loadField(__doc.get("tmpdirMax"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - tmpdirMax = null; // won't be used but prevents compiler from complaining. - final String __message = "the `tmpdirMax` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - tmpdirMax = null; - } - Object outdirMin; - - if (__doc.containsKey("outdirMin")) { - try { - outdirMin = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_DoubleInstance_or_ExpressionLoader - .loadField(__doc.get("outdirMin"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outdirMin = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outdirMin` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - outdirMin = null; - } - Object outdirMax; - - if (__doc.containsKey("outdirMax")) { - try { - outdirMax = - LoaderInstances - .union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_DoubleInstance_or_ExpressionLoader - .loadField(__doc.get("outdirMax"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outdirMax = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outdirMax` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - outdirMax = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (ResourceRequirement_class) class_; - this.coresMin = (Object) coresMin; - this.coresMax = (Object) coresMax; - this.ramMin = (Object) ramMin; - this.ramMax = (Object) ramMax; - this.tmpdirMin = (Object) tmpdirMin; - this.tmpdirMax = (Object) tmpdirMax; - this.outdirMin = (Object) outdirMin; - this.outdirMax = (Object) outdirMax; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirement_class.java deleted file mode 100644 index 7aeb43b7..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ResourceRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum ResourceRequirement_class { - RESOURCEREQUIREMENT("ResourceRequirement"); - - private static String[] symbols = new String[] {"ResourceRequirement"}; - private String docVal; - - private ResourceRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static ResourceRequirement_class fromDocumentVal(final String docVal) { - for(final ResourceRequirement_class val : ResourceRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", ResourceRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirement.java deleted file mode 100644 index 284fee1b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirement.java +++ /dev/null @@ -1,38 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ScatterFeatureRequirement
This interface is implemented by {@link ScatterFeatureRequirementImpl}
- Indicates that the workflow platform must support the `scatter` and - `scatterMethod` fields of [WorkflowStep](#WorkflowStep). -
- */ -public interface ScatterFeatureRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#ScatterFeatureRequirement/class
- *
- * Always 'ScatterFeatureRequirement' *
- */ - - ScatterFeatureRequirement_class getClass_(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirementImpl.java deleted file mode 100644 index e6ab50eb..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirementImpl.java +++ /dev/null @@ -1,107 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#ScatterFeatureRequirement
- Indicates that the workflow platform must support the `scatter` and - `scatterMethod` fields of [WorkflowStep](#WorkflowStep). -
- */ -public class ScatterFeatureRequirementImpl extends SaveableImpl implements ScatterFeatureRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private ScatterFeatureRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#ScatterFeatureRequirement/class
- *
- * Always 'ScatterFeatureRequirement' *
- */ - - public ScatterFeatureRequirement_class getClass_() { - return this.class_; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of ScatterFeatureRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ScatterFeatureRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ScatterFeatureRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - ScatterFeatureRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_ScatterFeatureRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (ScatterFeatureRequirement_class) class_; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirement_class.java deleted file mode 100644 index 713f1fcd..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterFeatureRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum ScatterFeatureRequirement_class { - SCATTERFEATUREREQUIREMENT("ScatterFeatureRequirement"); - - private static String[] symbols = new String[] {"ScatterFeatureRequirement"}; - private String docVal; - - private ScatterFeatureRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static ScatterFeatureRequirement_class fromDocumentVal(final String docVal) { - for(final ScatterFeatureRequirement_class val : ScatterFeatureRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", ScatterFeatureRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterMethod.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterMethod.java deleted file mode 100644 index 24c76529..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ScatterMethod.java +++ /dev/null @@ -1,39 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum ScatterMethod { - DOTPRODUCT("dotproduct"), - NESTED_CROSSPRODUCT("nested_crossproduct"), - FLAT_CROSSPRODUCT("flat_crossproduct"); - - private static String[] symbols = new String[] {"dotproduct", "nested_crossproduct", "flat_crossproduct"}; - private String docVal; - - private ScatterMethod(final String docVal) { - this.docVal = docVal; - } - - public static ScatterMethod fromDocumentVal(final String docVal) { - for(final ScatterMethod val : ScatterMethod.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", ScatterMethod.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirement.java deleted file mode 100644 index 4ffa1ad0..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirement.java +++ /dev/null @@ -1,55 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#SchemaDefRequirement
This interface is implemented by {@link SchemaDefRequirementImpl}
- This field consists of an array of type definitions which must be used when - interpreting the `inputs` and `outputs` fields. When a `type` field - contains a IRI, the implementation must check if the type is defined in - `schemaDefs` and use that definition. If the type is not found in - `schemaDefs`, it is an error. The entries in `schemaDefs` must be - processed in the order listed such that later schema definitions may refer - to earlier schema definitions. - - - **Type definitions are allowed for `enum` and `record` types only.** - - Type definitions may be shared by defining them in a file and then - `$include`-ing them in the `types` field. - - A file can contain a list of type definitions -
- */ -public interface SchemaDefRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/class
- *
- * Always 'SchemaDefRequirement' *
- */ - - SchemaDefRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/types
- *
- * The list of type definitions. *
- */ - - java.util.List getTypes(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirementImpl.java deleted file mode 100644 index 253ed7d4..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirementImpl.java +++ /dev/null @@ -1,141 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#SchemaDefRequirement
- This field consists of an array of type definitions which must be used when - interpreting the `inputs` and `outputs` fields. When a `type` field - contains a IRI, the implementation must check if the type is defined in - `schemaDefs` and use that definition. If the type is not found in - `schemaDefs`, it is an error. The entries in `schemaDefs` must be - processed in the order listed such that later schema definitions may refer - to earlier schema definitions. - - - **Type definitions are allowed for `enum` and `record` types only.** - - Type definitions may be shared by defining them in a file and then - `$include`-ing them in the `types` field. - - A file can contain a list of type definitions -
- */ -public class SchemaDefRequirementImpl extends SaveableImpl implements SchemaDefRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private SchemaDefRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/class
- *
- * Always 'SchemaDefRequirement' *
- */ - - public SchemaDefRequirement_class getClass_() { - return this.class_; - } - - private java.util.List types; - - /** - * Getter for property https://w3id.org/cwl/cwl#SchemaDefRequirement/types
- *
- * The list of type definitions. *
- */ - - public java.util.List getTypes() { - return this.types; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of SchemaDefRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public SchemaDefRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("SchemaDefRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - SchemaDefRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_SchemaDefRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List types; - try { - types = - LoaderInstances - .array_of_union_of_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema - .loadField(__doc.get("types"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - types = null; // won't be used but prevents compiler from complaining. - final String __message = "the `types` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (SchemaDefRequirement_class) class_; - this.types = (java.util.List) types; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "types"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirement_class.java deleted file mode 100644 index 8c657758..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SchemaDefRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum SchemaDefRequirement_class { - SCHEMADEFREQUIREMENT("SchemaDefRequirement"); - - private static String[] symbols = new String[] {"SchemaDefRequirement"}; - private String docVal; - - private SchemaDefRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static SchemaDefRequirement_class fromDocumentVal(final String docVal) { - for(final SchemaDefRequirement_class val : SchemaDefRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", SchemaDefRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchema.java deleted file mode 100644 index cbdec02e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchema.java +++ /dev/null @@ -1,110 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#SecondaryFileSchema
This interface is implemented by {@link SecondaryFileSchemaImpl}
- Secondary files are specified using the following micro-DSL for secondary files: - - * If the value is a string, it is transformed to an object with two fields - `pattern` and `required` - * By default, the value of `required` is `null` - (this indicates default behavior, which may be based on the context) - * If the value ends with a question mark `?` the question mark is - stripped off and the value of the field `required` is set to `False` - * The remaining value is assigned to the field `pattern` - - For implementation details and examples, please see - [this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files) - in the Schema Salad specification. -
- */ -public interface SecondaryFileSchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#SecondaryFileSchema/pattern
- *
- * Provides a pattern or expression specifying files or directories that - * should be included alongside the primary file. - * - * If the value is an expression, the value of `self` in the - * expression must be the primary input or output File object to - * which this binding applies. The `basename`, `nameroot` and - * `nameext` fields must be present in `self`. For - * `CommandLineTool` inputs the `location` field must also be - * present. For `CommandLineTool` outputs the `path` field must - * also be present. If secondary files were included on an input - * File object as part of the Process invocation, they must also - * be present in `secondaryFiles` on `self`. - * - * The expression must return either: a filename string relative - * to the path to the primary File, a File or Directory object - * (`class: File` or `class: Directory`) with either `location` - * (for inputs) or `path` (for outputs) and `basename` fields - * set, or an array consisting of strings or File or Directory - * objects as previously described. - * - * It is legal to use `location` from a File or Directory object - * passed in as input, including `location` from secondary files - * on `self`. If an expression returns a File object with the - * same `location` but a different `basename` as a secondary file - * that was passed in, the expression result takes precedence. - * Setting the basename with an expression this way affects the - * `path` where the secondary file will be staged to in the - * CommandLineTool. - * - * The expression may return "null" in which case there is no - * secondary file from that expression. - * - * To work on non-filename-preserving storage systems, portable - * tool descriptions should treat `location` as an - * [opaque identifier](#opaque-strings) and avoid constructing new - * values from `location`, but should construct relative references - * using `basename` or `nameroot` instead, or propagate `location` - * from defined inputs. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getPattern(); - /** - * Getter for property https://w3id.org/cwl/cwl#SecondaryFileSchema/required
- *
- * An implementation must not fail workflow execution if `required` is - * set to `false` and the expected secondary file does not exist. - * Default value for `required` field is `true` for secondary files on - * input and `false` for secondary files on output. - * *
- */ - - Object getRequired(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchemaImpl.java deleted file mode 100644 index 97b1de5c..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecondaryFileSchemaImpl.java +++ /dev/null @@ -1,202 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#SecondaryFileSchema
- Secondary files are specified using the following micro-DSL for secondary files: - - * If the value is a string, it is transformed to an object with two fields - `pattern` and `required` - * By default, the value of `required` is `null` - (this indicates default behavior, which may be based on the context) - * If the value ends with a question mark `?` the question mark is - stripped off and the value of the field `required` is set to `False` - * The remaining value is assigned to the field `pattern` - - For implementation details and examples, please see - [this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files) - in the Schema Salad specification. -
- */ -public class SecondaryFileSchemaImpl extends SaveableImpl implements SecondaryFileSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Object pattern; - - /** - * Getter for property https://w3id.org/cwl/cwl#SecondaryFileSchema/pattern
- *
- * Provides a pattern or expression specifying files or directories that - * should be included alongside the primary file. - * - * If the value is an expression, the value of `self` in the - * expression must be the primary input or output File object to - * which this binding applies. The `basename`, `nameroot` and - * `nameext` fields must be present in `self`. For - * `CommandLineTool` inputs the `location` field must also be - * present. For `CommandLineTool` outputs the `path` field must - * also be present. If secondary files were included on an input - * File object as part of the Process invocation, they must also - * be present in `secondaryFiles` on `self`. - * - * The expression must return either: a filename string relative - * to the path to the primary File, a File or Directory object - * (`class: File` or `class: Directory`) with either `location` - * (for inputs) or `path` (for outputs) and `basename` fields - * set, or an array consisting of strings or File or Directory - * objects as previously described. - * - * It is legal to use `location` from a File or Directory object - * passed in as input, including `location` from secondary files - * on `self`. If an expression returns a File object with the - * same `location` but a different `basename` as a secondary file - * that was passed in, the expression result takes precedence. - * Setting the basename with an expression this way affects the - * `path` where the secondary file will be staged to in the - * CommandLineTool. - * - * The expression may return "null" in which case there is no - * secondary file from that expression. - * - * To work on non-filename-preserving storage systems, portable - * tool descriptions should treat `location` as an - * [opaque identifier](#opaque-strings) and avoid constructing new - * values from `location`, but should construct relative references - * using `basename` or `nameroot` instead, or propagate `location` - * from defined inputs. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getPattern() { - return this.pattern; - } - - private Object required; - - /** - * Getter for property https://w3id.org/cwl/cwl#SecondaryFileSchema/required
- *
- * An implementation must not fail workflow execution if `required` is - * set to `false` and the expected secondary file does not exist. - * Default value for `required` field is `true` for secondary files on - * input and `false` for secondary files on output. - * *
- */ - - public Object getRequired() { - return this.required; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of SecondaryFileSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public SecondaryFileSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("SecondaryFileSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Object pattern; - try { - pattern = - LoaderInstances - .union_of_StringInstance_or_ExpressionLoader - .loadField(__doc.get("pattern"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - pattern = null; // won't be used but prevents compiler from complaining. - final String __message = "the `pattern` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object required; - - if (__doc.containsKey("required")) { - try { - required = - LoaderInstances - .union_of_NullInstance_or_BooleanInstance_or_ExpressionLoader - .loadField(__doc.get("required"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - required = null; // won't be used but prevents compiler from complaining. - final String __message = "the `required` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - required = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.pattern = (Object) pattern; - this.required = (Object) required; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("pattern", "required"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Secrets.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Secrets.java deleted file mode 100644 index f192aea1..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Secrets.java +++ /dev/null @@ -1,44 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for http://commonwl.org/cwltool#Secrets
This interface is implemented by {@link SecretsImpl}
- */ -public interface Secrets extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property http://commonwl.org/cwltool#Secrets/class
- *
- * Always 'Secrets' *
- */ - - String getClass_(); - /** - * Getter for property http://commonwl.org/cwltool#Secrets/secrets
- *
- * List one or more input parameters that are sensitive (such as passwords) - * which will be deliberately obscured from logging. - * *
- */ - - java.util.List getSecrets(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecretsImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecretsImpl.java deleted file mode 100644 index 21519915..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SecretsImpl.java +++ /dev/null @@ -1,130 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for http://commonwl.org/cwltool#Secrets
- */ -public class SecretsImpl extends SaveableImpl implements Secrets { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String class_; - - /** - * Getter for property http://commonwl.org/cwltool#Secrets/class
- *
- * Always 'Secrets' *
- */ - - public String getClass_() { - return this.class_; - } - - private java.util.List secrets; - - /** - * Getter for property http://commonwl.org/cwltool#Secrets/secrets
- *
- * List one or more input parameters that are sensitive (such as passwords) - * which will be deliberately obscured from logging. - * *
- */ - - public java.util.List getSecrets() { - return this.secrets; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of SecretsImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public SecretsImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("SecretsImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String class_; - try { - class_ = - LoaderInstances - .uri_StringInstance_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List secrets; - try { - secrets = - LoaderInstances - .uri_array_of_StringInstance_False_False_0_None - .loadField(__doc.get("secrets"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secrets = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secrets` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (String) class_; - this.secrets = (java.util.List) secrets; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "secrets"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirement.java deleted file mode 100644 index 900ff621..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirement.java +++ /dev/null @@ -1,43 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ShellCommandRequirement
This interface is implemented by {@link ShellCommandRequirementImpl}
- Modify the behavior of CommandLineTool to generate a single string - containing a shell command line. Each item in the `arguments` list must - be joined into a string separated by single spaces and quoted to prevent - interpretation by the shell, unless `CommandLineBinding` for that argument - contains `shellQuote: false`. If `shellQuote: false` is specified, the - argument is joined into the command string without quoting, which allows - the use of shell metacharacters such as `|` for pipes. -
- */ -public interface ShellCommandRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#ShellCommandRequirement/class
- *
- * Always 'ShellCommandRequirement' *
- */ - - ShellCommandRequirement_class getClass_(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirementImpl.java deleted file mode 100644 index 90f80081..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirementImpl.java +++ /dev/null @@ -1,112 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#ShellCommandRequirement
- Modify the behavior of CommandLineTool to generate a single string - containing a shell command line. Each item in the `arguments` list must - be joined into a string separated by single spaces and quoted to prevent - interpretation by the shell, unless `CommandLineBinding` for that argument - contains `shellQuote: false`. If `shellQuote: false` is specified, the - argument is joined into the command string without quoting, which allows - the use of shell metacharacters such as `|` for pipes. -
- */ -public class ShellCommandRequirementImpl extends SaveableImpl implements ShellCommandRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private ShellCommandRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#ShellCommandRequirement/class
- *
- * Always 'ShellCommandRequirement' *
- */ - - public ShellCommandRequirement_class getClass_() { - return this.class_; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of ShellCommandRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ShellCommandRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ShellCommandRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - ShellCommandRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_ShellCommandRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (ShellCommandRequirement_class) class_; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirement_class.java deleted file mode 100644 index aa16182b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShellCommandRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum ShellCommandRequirement_class { - SHELLCOMMANDREQUIREMENT("ShellCommandRequirement"); - - private static String[] symbols = new String[] {"ShellCommandRequirement"}; - private String docVal; - - private ShellCommandRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static ShellCommandRequirement_class fromDocumentVal(final String docVal) { - for(final ShellCommandRequirement_class val : ShellCommandRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", ShellCommandRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShmSize.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShmSize.java deleted file mode 100644 index 814be2f7..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShmSize.java +++ /dev/null @@ -1,46 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for http://commonwl.org/cwltool#ShmSize
This interface is implemented by {@link ShmSizeImpl}
- */ -public interface ShmSize extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property http://commonwl.org/cwltool#ShmSize/class
- *
- * cwltool:ShmSize *
- */ - - String getClass_(); - /** - * Getter for property http://commonwl.org/cwltool#ShmSize/shmSize
- *
- * Size of /dev/shm. The format is `<number><unit>`. <number> must be greater - * than 0. Unit is optional and can be `b` (bytes), `k` (kilobytes), `m` - * (megabytes), or `g` (gigabytes). If you omit the unit, the default is - * bytes. If you omit the size entirely, the value is `64m`." - * *
- */ - - String getShmSize(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShmSizeImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShmSizeImpl.java deleted file mode 100644 index 282a1ca6..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ShmSizeImpl.java +++ /dev/null @@ -1,132 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for http://commonwl.org/cwltool#ShmSize
- */ -public class ShmSizeImpl extends SaveableImpl implements ShmSize { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String class_; - - /** - * Getter for property http://commonwl.org/cwltool#ShmSize/class
- *
- * cwltool:ShmSize *
- */ - - public String getClass_() { - return this.class_; - } - - private String shmSize; - - /** - * Getter for property http://commonwl.org/cwltool#ShmSize/shmSize
- *
- * Size of /dev/shm. The format is `<number><unit>`. <number> must be greater - * than 0. Unit is optional and can be `b` (bytes), `k` (kilobytes), `m` - * (megabytes), or `g` (gigabytes). If you omit the unit, the default is - * bytes. If you omit the size entirely, the value is `64m`." - * *
- */ - - public String getShmSize() { - return this.shmSize; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of ShmSizeImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ShmSizeImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ShmSizeImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String class_; - try { - class_ = - LoaderInstances - .uri_StringInstance_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - String shmSize; - try { - shmSize = - LoaderInstances - .StringInstance - .loadField(__doc.get("shmSize"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - shmSize = null; // won't be used but prevents compiler from complaining. - final String __message = "the `shmSize` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (String) class_; - this.shmSize = (String) shmSize; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "shmSize"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Sink.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Sink.java deleted file mode 100644 index 67882f37..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Sink.java +++ /dev/null @@ -1,54 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Sink
- */ -public interface Sink extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#source
- *
- * Specifies one or more workflow parameters that will provide input to - * the underlying step parameter. - * *
- */ - - Object getSource(); - /** - * Getter for property https://w3id.org/cwl/cwl#Sink/linkMerge
- *
- * The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". - * *
- */ - - java.util.Optional getLinkMerge(); - /** - * Getter for property https://w3id.org/cwl/cwl#Sink/pickValue
- *
- * The method to use to choose non-null elements among multiple sources. - * *
- */ - - java.util.Optional getPickValue(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwarePackage.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwarePackage.java deleted file mode 100644 index c64db064..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwarePackage.java +++ /dev/null @@ -1,95 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#SoftwarePackage
This interface is implemented by {@link SoftwarePackageImpl}
- */ -public interface SoftwarePackage extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/package
- *
- * The name of the software to be made available. If the name is - * common, inconsistent, or otherwise ambiguous it should be combined with - * one or more identifiers in the `specs` field. - * *
- */ - - String getPackage(); - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/version
- *
- * The (optional) versions of the software that are known to be - * compatible. - * *
- */ - - java.util.Optional> getVersion(); - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/specs
- *
- * One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s - * identifying resources for installing or enabling the software named in - * the `package` field. Implementations may provide resolvers which map - * these software identifier IRIs to some configuration action; or they can - * use only the name from the `package` field on a best effort basis. - * - * For example, the IRI https://packages.debian.org/bowtie could - * be resolved with `apt-get install bowtie`. The IRI - * https://anaconda.org/bioconda/bowtie could be resolved with `conda - * install -c bioconda bowtie`. - * - * IRIs can also be system independent and used to map to a specific - * software installation or selection mechanism. - * Using [RRID](https://www.identifiers.org/rrid/) as an example: - * https://identifiers.org/rrid/RRID:SCR_005476 - * could be fulfilled using the above-mentioned Debian or bioconda - * package, a local installation managed by [Environment Modules](https://modules.sourceforge.net/), - * or any other mechanism the platform chooses. IRIs can also be from - * identifier sources that are discipline specific yet still system - * independent. As an example, the equivalent [ELIXIR Tools and Data - * Service Registry](https://bio.tools) IRI to the previous RRID example is - * https://bio.tools/tool/bowtie2/version/2.2.8. - * If supported by a given registry, implementations are encouraged to - * query these system independent software identifier IRIs directly for - * links to packaging systems. - * - * A site specific IRI can be listed as well. For example, an academic - * computing cluster using Environment Modules could list the IRI - * `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that - * `module load bowtie-tbb/1.1.2` should be executed to make available - * `bowtie` version 1.1.2 compiled with the TBB library prior to running - * the accompanying Workflow or CommandLineTool. Note that the example IRI - * is specific to a particular institution and computing environment as - * the Environment Modules system does not have a common namespace or - * standardized naming convention. - * - * This last example is the least portable and should only be used if - * mechanisms based off of the `package` field or more generic IRIs are - * unavailable or unsuitable. While harmless to other sites, site specific - * software IRIs should be left out of shared CWL descriptions to avoid - * clutter. - * *
- */ - - java.util.Optional> getSpecs(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwarePackageImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwarePackageImpl.java deleted file mode 100644 index 9f352107..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwarePackageImpl.java +++ /dev/null @@ -1,210 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#SoftwarePackage
- */ -public class SoftwarePackageImpl extends SaveableImpl implements SoftwarePackage { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String package_; - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/package
- *
- * The name of the software to be made available. If the name is - * common, inconsistent, or otherwise ambiguous it should be combined with - * one or more identifiers in the `specs` field. - * *
- */ - - public String getPackage() { - return this.package_; - } - - private java.util.Optional> version; - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/version
- *
- * The (optional) versions of the software that are known to be - * compatible. - * *
- */ - - public java.util.Optional> getVersion() { - return this.version; - } - - private java.util.Optional> specs; - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwarePackage/specs
- *
- * One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s - * identifying resources for installing or enabling the software named in - * the `package` field. Implementations may provide resolvers which map - * these software identifier IRIs to some configuration action; or they can - * use only the name from the `package` field on a best effort basis. - * - * For example, the IRI https://packages.debian.org/bowtie could - * be resolved with `apt-get install bowtie`. The IRI - * https://anaconda.org/bioconda/bowtie could be resolved with `conda - * install -c bioconda bowtie`. - * - * IRIs can also be system independent and used to map to a specific - * software installation or selection mechanism. - * Using [RRID](https://www.identifiers.org/rrid/) as an example: - * https://identifiers.org/rrid/RRID:SCR_005476 - * could be fulfilled using the above-mentioned Debian or bioconda - * package, a local installation managed by [Environment Modules](https://modules.sourceforge.net/), - * or any other mechanism the platform chooses. IRIs can also be from - * identifier sources that are discipline specific yet still system - * independent. As an example, the equivalent [ELIXIR Tools and Data - * Service Registry](https://bio.tools) IRI to the previous RRID example is - * https://bio.tools/tool/bowtie2/version/2.2.8. - * If supported by a given registry, implementations are encouraged to - * query these system independent software identifier IRIs directly for - * links to packaging systems. - * - * A site specific IRI can be listed as well. For example, an academic - * computing cluster using Environment Modules could list the IRI - * `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that - * `module load bowtie-tbb/1.1.2` should be executed to make available - * `bowtie` version 1.1.2 compiled with the TBB library prior to running - * the accompanying Workflow or CommandLineTool. Note that the example IRI - * is specific to a particular institution and computing environment as - * the Environment Modules system does not have a common namespace or - * standardized naming convention. - * - * This last example is the least portable and should only be used if - * mechanisms based off of the `package` field or more generic IRIs are - * unavailable or unsuitable. While harmless to other sites, site specific - * software IRIs should be left out of shared CWL descriptions to avoid - * clutter. - * *
- */ - - public java.util.Optional> getSpecs() { - return this.specs; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of SoftwarePackageImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public SoftwarePackageImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("SoftwarePackageImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String package_; - try { - package_ = - LoaderInstances - .StringInstance - .loadField(__doc.get("package"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - package_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `package` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> version; - - if (__doc.containsKey("version")) { - try { - version = - LoaderInstances - .optional_array_of_StringInstance - .loadField(__doc.get("version"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - version = null; // won't be used but prevents compiler from complaining. - final String __message = "the `version` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - version = null; - } - java.util.Optional> specs; - - if (__doc.containsKey("specs")) { - try { - specs = - LoaderInstances - .uri_optional_array_of_StringInstance_False_False_None_True - .loadField(__doc.get("specs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - specs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `specs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - specs = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.package_ = (String) package_; - this.version = (java.util.Optional>) version; - this.specs = (java.util.Optional>) specs; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("package", "version", "specs"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirement.java deleted file mode 100644 index 96d4ef94..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirement.java +++ /dev/null @@ -1,45 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#SoftwareRequirement
This interface is implemented by {@link SoftwareRequirementImpl}
- A list of software packages that should be configured in the environment of - the defined process. -
- */ -public interface SoftwareRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/class
- *
- * Always 'SoftwareRequirement' *
- */ - - SoftwareRequirement_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/packages
- *
- * The list of software to be configured. *
- */ - - java.util.List getPackages(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirementImpl.java deleted file mode 100644 index 91ac0ff0..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirementImpl.java +++ /dev/null @@ -1,131 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#SoftwareRequirement
- A list of software packages that should be configured in the environment of - the defined process. -
- */ -public class SoftwareRequirementImpl extends SaveableImpl implements SoftwareRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private SoftwareRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/class
- *
- * Always 'SoftwareRequirement' *
- */ - - public SoftwareRequirement_class getClass_() { - return this.class_; - } - - private java.util.List packages; - - /** - * Getter for property https://w3id.org/cwl/cwl#SoftwareRequirement/packages
- *
- * The list of software to be configured. *
- */ - - public java.util.List getPackages() { - return this.packages; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of SoftwareRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public SoftwareRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("SoftwareRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - SoftwareRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_SoftwareRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List packages; - try { - packages = - LoaderInstances - .idmap_packages_array_of_SoftwarePackage - .loadField(__doc.get("packages"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - packages = null; // won't be used but prevents compiler from complaining. - final String __message = "the `packages` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (SoftwareRequirement_class) class_; - this.packages = (java.util.List) packages; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "packages"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirement_class.java deleted file mode 100644 index 729bad26..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SoftwareRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum SoftwareRequirement_class { - SOFTWAREREQUIREMENT("SoftwareRequirement"); - - private static String[] symbols = new String[] {"SoftwareRequirement"}; - private String docVal; - - private SoftwareRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static SoftwareRequirement_class fromDocumentVal(final String docVal) { - for(final SoftwareRequirement_class val : SoftwareRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", SoftwareRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirement.java deleted file mode 100644 index 4a69d1f3..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirement.java +++ /dev/null @@ -1,38 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#StepInputExpressionRequirement
This interface is implemented by {@link StepInputExpressionRequirementImpl}
- Indicate that the workflow platform must support the `valueFrom` field - of [WorkflowStepInput](#WorkflowStepInput). -
- */ -public interface StepInputExpressionRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#StepInputExpressionRequirement/class
- *
- * Always 'StepInputExpressionRequirement' *
- */ - - StepInputExpressionRequirement_class getClass_(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirementImpl.java deleted file mode 100644 index 358c5472..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirementImpl.java +++ /dev/null @@ -1,107 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#StepInputExpressionRequirement
- Indicate that the workflow platform must support the `valueFrom` field - of [WorkflowStepInput](#WorkflowStepInput). -
- */ -public class StepInputExpressionRequirementImpl extends SaveableImpl implements StepInputExpressionRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private StepInputExpressionRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#StepInputExpressionRequirement/class
- *
- * Always 'StepInputExpressionRequirement' *
- */ - - public StepInputExpressionRequirement_class getClass_() { - return this.class_; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of StepInputExpressionRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public StepInputExpressionRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("StepInputExpressionRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - StepInputExpressionRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_StepInputExpressionRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (StepInputExpressionRequirement_class) class_; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirement_class.java deleted file mode 100644 index 6a806b21..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/StepInputExpressionRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum StepInputExpressionRequirement_class { - STEPINPUTEXPRESSIONREQUIREMENT("StepInputExpressionRequirement"); - - private static String[] symbols = new String[] {"StepInputExpressionRequirement"}; - private String docVal; - - private StepInputExpressionRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static StepInputExpressionRequirement_class fromDocumentVal(final String docVal) { - for(final StepInputExpressionRequirement_class val : StepInputExpressionRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", StepInputExpressionRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirement.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirement.java deleted file mode 100644 index cc63a242..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirement.java +++ /dev/null @@ -1,38 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement
This interface is implemented by {@link SubworkflowFeatureRequirementImpl}
- Indicates that the workflow platform must support nested workflows in - the `run` field of [WorkflowStep](#WorkflowStep). -
- */ -public interface SubworkflowFeatureRequirement extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement/class
- *
- * Always 'SubworkflowFeatureRequirement' *
- */ - - SubworkflowFeatureRequirement_class getClass_(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirementImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirementImpl.java deleted file mode 100644 index 281e8a07..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirementImpl.java +++ /dev/null @@ -1,107 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement
- Indicates that the workflow platform must support nested workflows in - the `run` field of [WorkflowStep](#WorkflowStep). -
- */ -public class SubworkflowFeatureRequirementImpl extends SaveableImpl implements SubworkflowFeatureRequirement { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private SubworkflowFeatureRequirement_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement/class
- *
- * Always 'SubworkflowFeatureRequirement' *
- */ - - public SubworkflowFeatureRequirement_class getClass_() { - return this.class_; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of SubworkflowFeatureRequirementImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public SubworkflowFeatureRequirementImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("SubworkflowFeatureRequirementImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - SubworkflowFeatureRequirement_class class_; - try { - class_ = - LoaderInstances - .uri_SubworkflowFeatureRequirement_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (SubworkflowFeatureRequirement_class) class_; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirement_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirement_class.java deleted file mode 100644 index b035ef81..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/SubworkflowFeatureRequirement_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum SubworkflowFeatureRequirement_class { - SUBWORKFLOWFEATUREREQUIREMENT("SubworkflowFeatureRequirement"); - - private static String[] symbols = new String[] {"SubworkflowFeatureRequirement"}; - private String docVal; - - private SubworkflowFeatureRequirement_class(final String docVal) { - this.docVal = docVal; - } - - public static SubworkflowFeatureRequirement_class fromDocumentVal(final String docVal) { - for(final SubworkflowFeatureRequirement_class val : SubworkflowFeatureRequirement_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", SubworkflowFeatureRequirement_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimit.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimit.java deleted file mode 100644 index 70baa0ff..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimit.java +++ /dev/null @@ -1,52 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#ToolTimeLimit
This interface is implemented by {@link ToolTimeLimitImpl}
- Set an upper limit on the execution time of a CommandLineTool. - A CommandLineTool whose execution duration exceeds the time - limit may be preemptively terminated and considered failed. - May also be used by batch systems to make scheduling decisions. - The execution duration excludes external operations, such as - staging of files, pulling a docker image etc, and only counts - wall-time for the execution of the command line itself. -
- */ -public interface ToolTimeLimit extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/class
- *
- * Always 'ToolTimeLimit' *
- */ - - ToolTimeLimit_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/timelimit
- *
- * The time limit, in seconds. A time limit of zero means no - * time limit. Negative time limits are an error. - * *
- */ - - Object getTimelimit(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimitImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimitImpl.java deleted file mode 100644 index e6666877..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimitImpl.java +++ /dev/null @@ -1,138 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#ToolTimeLimit
- Set an upper limit on the execution time of a CommandLineTool. - A CommandLineTool whose execution duration exceeds the time - limit may be preemptively terminated and considered failed. - May also be used by batch systems to make scheduling decisions. - The execution duration excludes external operations, such as - staging of files, pulling a docker image etc, and only counts - wall-time for the execution of the command line itself. -
- */ -public class ToolTimeLimitImpl extends SaveableImpl implements ToolTimeLimit { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private ToolTimeLimit_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/class
- *
- * Always 'ToolTimeLimit' *
- */ - - public ToolTimeLimit_class getClass_() { - return this.class_; - } - - private Object timelimit; - - /** - * Getter for property https://w3id.org/cwl/cwl#ToolTimeLimit/timelimit
- *
- * The time limit, in seconds. A time limit of zero means no - * time limit. Negative time limits are an error. - * *
- */ - - public Object getTimelimit() { - return this.timelimit; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of ToolTimeLimitImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public ToolTimeLimitImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("ToolTimeLimitImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - ToolTimeLimit_class class_; - try { - class_ = - LoaderInstances - .uri_ToolTimeLimit_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object timelimit; - try { - timelimit = - LoaderInstances - .union_of_IntegerInstance_or_LongInstance_or_ExpressionLoader - .loadField(__doc.get("timelimit"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - timelimit = null; // won't be used but prevents compiler from complaining. - final String __message = "the `timelimit` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (ToolTimeLimit_class) class_; - this.timelimit = (Object) timelimit; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "timelimit"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimit_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimit_class.java deleted file mode 100644 index d607b272..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/ToolTimeLimit_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum ToolTimeLimit_class { - TOOLTIMELIMIT("ToolTimeLimit"); - - private static String[] symbols = new String[] {"ToolTimeLimit"}; - private String docVal; - - private ToolTimeLimit_class(final String docVal) { - this.docVal = docVal; - } - - public static ToolTimeLimit_class fromDocumentVal(final String docVal) { - for(final ToolTimeLimit_class val : ToolTimeLimit_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", ToolTimeLimit_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/UnionSchema.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/UnionSchema.java deleted file mode 100644 index 29d613e9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/UnionSchema.java +++ /dev/null @@ -1,42 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/salad#UnionSchema
This interface is implemented by {@link UnionSchemaImpl}
- */ -public interface UnionSchema extends Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/salad#names
- *
- * Defines the type of the union elements. *
- */ - - Object getNames(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `union` *
- */ - - Union_name getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/UnionSchemaImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/UnionSchemaImpl.java deleted file mode 100644 index 6d312d65..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/UnionSchemaImpl.java +++ /dev/null @@ -1,128 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/salad#UnionSchema
- */ -public class UnionSchemaImpl extends SaveableImpl implements UnionSchema { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private Object names; - - /** - * Getter for property https://w3id.org/cwl/salad#names
- *
- * Defines the type of the union elements. *
- */ - - public Object getNames() { - return this.names; - } - - private Union_name type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Must be `union` *
- */ - - public Union_name getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of UnionSchemaImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public UnionSchemaImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("UnionSchemaImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - Object names; - try { - names = - LoaderInstances - .uri_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_False_True_2_None - .loadField(__doc.get("names"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - names = null; // won't be used but prevents compiler from complaining. - final String __message = "the `names` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Union_name type; - try { - type = - LoaderInstances - .typedsl_Union_name_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.names = (Object) names; - this.type = (Union_name) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("names", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Union_name.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Union_name.java deleted file mode 100644 index ae0e6348..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Union_name.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum Union_name { - UNION("union"); - - private static String[] symbols = new String[] {"union"}; - private String docVal; - - private Union_name(final String docVal) { - this.docVal = docVal; - } - - public static Union_name fromDocumentVal(final String docVal) { - for(final Union_name val : Union_name.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Union_name.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuse.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuse.java deleted file mode 100644 index da56a4d9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuse.java +++ /dev/null @@ -1,51 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#WorkReuse
This interface is implemented by {@link WorkReuseImpl}
- For implementations that support reusing output from past work (on - the assumption that same code and same input produce same - results), control whether to enable or disable the reuse behavior - for a particular tool or step (to accommodate situations where that - assumption is incorrect). A reused step is not executed but - instead returns the same output as the original execution. - - If `WorkReuse` is not specified, correct tools should assume it - is enabled by default. -
- */ -public interface WorkReuse extends ProcessRequirement, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkReuse/class
- *
- * Always 'WorkReuse' *
- */ - - WorkReuse_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#WorkReuse/enableReuse
- - */ - - Object getEnableReuse(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuseImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuseImpl.java deleted file mode 100644 index 1013ffac..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuseImpl.java +++ /dev/null @@ -1,137 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkReuse
- For implementations that support reusing output from past work (on - the assumption that same code and same input produce same - results), control whether to enable or disable the reuse behavior - for a particular tool or step (to accommodate situations where that - assumption is incorrect). A reused step is not executed but - instead returns the same output as the original execution. - - If `WorkReuse` is not specified, correct tools should assume it - is enabled by default. -
- */ -public class WorkReuseImpl extends SaveableImpl implements WorkReuse { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private WorkReuse_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkReuse/class
- *
- * Always 'WorkReuse' *
- */ - - public WorkReuse_class getClass_() { - return this.class_; - } - - private Object enableReuse; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkReuse/enableReuse
- - */ - - public Object getEnableReuse() { - return this.enableReuse; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of WorkReuseImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkReuseImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkReuseImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - WorkReuse_class class_; - try { - class_ = - LoaderInstances - .uri_WorkReuse_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - Object enableReuse; - try { - enableReuse = - LoaderInstances - .union_of_BooleanInstance_or_ExpressionLoader - .loadField(__doc.get("enableReuse"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - enableReuse = null; // won't be used but prevents compiler from complaining. - final String __message = "the `enableReuse` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.class_ = (WorkReuse_class) class_; - this.enableReuse = (Object) enableReuse; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("class", "enableReuse"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuse_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuse_class.java deleted file mode 100644 index 806a8cdf..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkReuse_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum WorkReuse_class { - WORKREUSE("WorkReuse"); - - private static String[] symbols = new String[] {"WorkReuse"}; - private String docVal; - - private WorkReuse_class(final String docVal) { - this.docVal = docVal; - } - - public static WorkReuse_class fromDocumentVal(final String docVal) { - for(final WorkReuse_class val : WorkReuse_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", WorkReuse_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Workflow.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Workflow.java deleted file mode 100644 index 89cc57ba..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Workflow.java +++ /dev/null @@ -1,203 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#Workflow
This interface is implemented by {@link WorkflowImpl}
- A workflow describes a set of **steps** and the **dependencies** between - those steps. When a step produces output that will be consumed by a - second step, the first step is a dependency of the second step. - - When there is a dependency, the workflow engine must execute the preceding - step and wait for it to successfully produce output before executing the - dependent step. If two steps are defined in the workflow graph that - are not directly or indirectly dependent, these steps are **independent**, - and may execute in any order or execute concurrently. A workflow is - complete when all steps have been executed. - - Dependencies between parameters are expressed using the `source` - field on [workflow step input parameters](#WorkflowStepInput) and - `outputSource` field on [workflow output - parameters](#WorkflowOutputParameter). - - The `source` field on each workflow step input parameter expresses - the data links that contribute to the value of the step input - parameter (the "sink"). A workflow step can only begin execution - when every data link connected to a step has been fulfilled. - - The `outputSource` field on each workflow step input parameter - expresses the data links that contribute to the value of the - workflow output parameter (the "sink"). Workflow execution cannot - complete successfully until every data link connected to an output - parameter has been fulfilled. - - ## Workflow success and failure - - A completed step must result in one of `success`, `temporaryFailure` or - `permanentFailure` states. An implementation may choose to retry a step - execution which resulted in `temporaryFailure`. An implementation may - choose to either continue running other steps of a workflow, or terminate - immediately upon `permanentFailure`. - - * If any step of a workflow execution results in `permanentFailure`, then - the workflow status is `permanentFailure`. - - * If one or more steps result in `temporaryFailure` and all other steps - complete `success` or are not executed, then the workflow status is - `temporaryFailure`. - - * If all workflow steps are executed and complete with `success`, then the - workflow status is `success`. - - # Extensions - - [ScatterFeatureRequirement](#ScatterFeatureRequirement) and - [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are - available as standard [extensions](#Extensions_and_Metadata) to core - workflow semantics. -
- */ -public interface Workflow extends Process, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/id
- *
- * The unique identifier for this object. - * - * Only useful for `$graph` at `Process` level. Should not be exposed - * to users in graphical or terminal user interfaces. - * *
- */ - - java.util.Optional getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Workflow/class
- - */ - - Workflow_class getClass_(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - java.util.List getInputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - java.util.List getOutputs(); - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - java.util.Optional> getRequirements(); - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - java.util.Optional> getHints(); - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - java.util.Optional getCwlVersion(); - /** - * Getter for property https://w3id.org/cwl/cwl#Process/intent
- *
- * An identifier for the type of computational operation, of this Process. - * Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for - * [`CommandLineTool`](CommandLineTool.html#CommandLineTool), - * [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). - * - * If provided, then this must be an IRI of a concept node that - * represents the type of operation, preferably defined within an ontology. - * - * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), - * like [Alignment](http://edamontology.org/operation_2928), - * or [Clustering](http://edamontology.org/operation_3432); or a more - * specific Operation concept like - * [Split read mapping](http://edamontology.org/operation_3199). - * *
- */ - - java.util.Optional> getIntent(); - /** - * Getter for property https://w3id.org/cwl/cwl#Workflow/steps
- *
- * The individual steps that make up the workflow. Each step is executed when all of its - * input data links are fulfilled. An implementation may choose to execute - * the steps in a different order than listed and/or execute steps - * concurrently, provided that dependencies between steps are met. - * *
- */ - - java.util.List getSteps(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowImpl.java deleted file mode 100644 index 4cf53aab..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowImpl.java +++ /dev/null @@ -1,498 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#Workflow
- A workflow describes a set of **steps** and the **dependencies** between - those steps. When a step produces output that will be consumed by a - second step, the first step is a dependency of the second step. - - When there is a dependency, the workflow engine must execute the preceding - step and wait for it to successfully produce output before executing the - dependent step. If two steps are defined in the workflow graph that - are not directly or indirectly dependent, these steps are **independent**, - and may execute in any order or execute concurrently. A workflow is - complete when all steps have been executed. - - Dependencies between parameters are expressed using the `source` - field on [workflow step input parameters](#WorkflowStepInput) and - `outputSource` field on [workflow output - parameters](#WorkflowOutputParameter). - - The `source` field on each workflow step input parameter expresses - the data links that contribute to the value of the step input - parameter (the "sink"). A workflow step can only begin execution - when every data link connected to a step has been fulfilled. - - The `outputSource` field on each workflow step input parameter - expresses the data links that contribute to the value of the - workflow output parameter (the "sink"). Workflow execution cannot - complete successfully until every data link connected to an output - parameter has been fulfilled. - - ## Workflow success and failure - - A completed step must result in one of `success`, `temporaryFailure` or - `permanentFailure` states. An implementation may choose to retry a step - execution which resulted in `temporaryFailure`. An implementation may - choose to either continue running other steps of a workflow, or terminate - immediately upon `permanentFailure`. - - * If any step of a workflow execution results in `permanentFailure`, then - the workflow status is `permanentFailure`. - - * If one or more steps result in `temporaryFailure` and all other steps - complete `success` or are not executed, then the workflow status is - `temporaryFailure`. - - * If all workflow steps are executed and complete with `success`, then the - workflow status is `success`. - - # Extensions - - [ScatterFeatureRequirement](#ScatterFeatureRequirement) and - [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are - available as standard [extensions](#Extensions_and_Metadata) to core - workflow semantics. -
- */ -public class WorkflowImpl extends SaveableImpl implements Workflow { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private java.util.Optional id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/id
- *
- * The unique identifier for this object. - * - * Only useful for `$graph` at `Process` level. Should not be exposed - * to users in graphical or terminal user interfaces. - * *
- */ - - public java.util.Optional getId() { - return this.id; - } - - private Workflow_class class_; - - /** - * Getter for property https://w3id.org/cwl/cwl#Workflow/class
- - */ - - public Workflow_class getClass_() { - return this.class_; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.List inputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#inputs
- *
- * Defines the input parameters of the process. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used to build a user - * interface for constructing the input object. - * - * When accepting an input object, all input parameters must have a value. - * If an input parameter is missing from the input object, it must be - * assigned a value of `null` (or the value of `default` for that - * parameter, if provided) for the purposes of validation and evaluation - * of expressions. - * *
- */ - - public java.util.List getInputs() { - return this.inputs; - } - - private java.util.List outputs; - - /** - * Getter for property https://w3id.org/cwl/cwl#outputs
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - public java.util.List getOutputs() { - return this.outputs; - } - - private java.util.Optional> requirements; - - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this process. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - public java.util.Optional> getRequirements() { - return this.requirements; - } - - private java.util.Optional> hints; - - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this process. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - public java.util.Optional> getHints() { - return this.hints; - } - - private java.util.Optional cwlVersion; - - /** - * Getter for property https://w3id.org/cwl/cwl#cwlVersion
- *
- * CWL document version. Always required at the document root. Not - * required for a Process embedded inside another Process. - * *
- */ - - public java.util.Optional getCwlVersion() { - return this.cwlVersion; - } - - private java.util.Optional> intent; - - /** - * Getter for property https://w3id.org/cwl/cwl#Process/intent
- *
- * An identifier for the type of computational operation, of this Process. - * Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for - * [`CommandLineTool`](CommandLineTool.html#CommandLineTool), - * [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). - * - * If provided, then this must be an IRI of a concept node that - * represents the type of operation, preferably defined within an ontology. - * - * For example, in the domain of bioinformatics, one can use an IRI from - * the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), - * like [Alignment](http://edamontology.org/operation_2928), - * or [Clustering](http://edamontology.org/operation_3432); or a more - * specific Operation concept like - * [Split read mapping](http://edamontology.org/operation_3199). - * *
- */ - - public java.util.Optional> getIntent() { - return this.intent; - } - - private java.util.List steps; - - /** - * Getter for property https://w3id.org/cwl/cwl#Workflow/steps
- *
- * The individual steps that make up the workflow. Each step is executed when all of its - * input data links are fulfilled. An implementation may choose to execute - * the steps in a different order than listed and/or execute steps - * concurrently, provided that dependencies between steps are met. - * *
- */ - - public java.util.List getSteps() { - return this.steps; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of WorkflowImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkflowImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkflowImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - java.util.Optional id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_optional_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - Boolean __original_is_null = id == null; - if (id == null) { - if (__docRoot != null) { - id = java.util.Optional.of(__docRoot); - } else { - id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString()); - } - } - if (__original_is_null) { - __baseUri = __baseUri_; - } else { - __baseUri = (String) id.orElse(null); - } - Workflow_class class_; - try { - class_ = - LoaderInstances - .uri_Workflow_class_False_True_None_None - .loadField(__doc.get("class"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - class_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `class` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.List inputs; - try { - inputs = - LoaderInstances - .idmap_inputs_array_of_WorkflowInputParameter - .loadField(__doc.get("inputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List outputs; - try { - outputs = - LoaderInstances - .idmap_outputs_array_of_WorkflowOutputParameter - .loadField(__doc.get("outputs"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputs = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputs` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> requirements; - - if (__doc.containsKey("requirements")) { - try { - requirements = - LoaderInstances - .idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize - .loadField(__doc.get("requirements"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - requirements = null; // won't be used but prevents compiler from complaining. - final String __message = "the `requirements` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - requirements = null; - } - java.util.Optional> hints; - - if (__doc.containsKey("hints")) { - try { - hints = - LoaderInstances - .idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_AnyInstance - .loadField(__doc.get("hints"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - hints = null; // won't be used but prevents compiler from complaining. - final String __message = "the `hints` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - hints = null; - } - java.util.Optional cwlVersion; - - if (__doc.containsKey("cwlVersion")) { - try { - cwlVersion = - LoaderInstances - .uri_optional_CWLVersion_False_True_None_None - .loadField(__doc.get("cwlVersion"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - cwlVersion = null; // won't be used but prevents compiler from complaining. - final String __message = "the `cwlVersion` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - cwlVersion = null; - } - java.util.Optional> intent; - - if (__doc.containsKey("intent")) { - try { - intent = - LoaderInstances - .uri_optional_array_of_StringInstance_True_False_None_None - .loadField(__doc.get("intent"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - intent = null; // won't be used but prevents compiler from complaining. - final String __message = "the `intent` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - intent = null; - } - java.util.List steps; - try { - steps = - LoaderInstances - .idmap_steps_array_of_WorkflowStep - .loadField(__doc.get("steps"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - steps = null; // won't be used but prevents compiler from complaining. - final String __message = "the `steps` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (java.util.Optional) id; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.inputs = (java.util.List) inputs; - this.outputs = (java.util.List) outputs; - this.requirements = (java.util.Optional>) requirements; - this.hints = (java.util.Optional>) hints; - this.cwlVersion = (java.util.Optional) cwlVersion; - this.intent = (java.util.Optional>) intent; - this.class_ = (Workflow_class) class_; - this.steps = (java.util.List) steps; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id", "label", "doc", "inputs", "outputs", "requirements", "hints", "cwlVersion", "intent", "class", "steps"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameter.java deleted file mode 100644 index 0ee8b872..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameter.java +++ /dev/null @@ -1,183 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowInputParameter
This interface is implemented by {@link WorkflowInputParameterImpl}
- */ -public interface WorkflowInputParameter extends InputParameter, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - String getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value to use for this parameter if the parameter is missing - * from the input object, or if the value of the parameter in the input - * object is `null`. Default values are applied before evaluating expressions - * (e.g. dependent `valueFrom` fields). - * *
- */ - - java.util.Optional getDefault(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - Object getType(); - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowInputParameter/inputBinding
- *
- * Deprecated. Preserved for v1.0 backwards compatibility. Will be removed in - * CWL v2.0. Use `WorkflowInputParameter.loadContents` instead. - * *
- */ - - java.util.Optional getInputBinding(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameterImpl.java deleted file mode 100644 index 777d9252..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowInputParameterImpl.java +++ /dev/null @@ -1,491 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowInputParameter
- */ -public class WorkflowInputParameterImpl extends SaveableImpl implements WorkflowInputParameter { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - public String getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This must be one or more IRIs of concept nodes - * that represents file formats which are allowed as input to this - * parameter, preferably defined within an ontology. If no ontology is - * available, file formats may be tested by exact match. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - private java.util.Optional default_; - - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value to use for this parameter if the parameter is missing - * from the input object, or if the value of the parameter in the input - * object is `null`. Default values are applied before evaluating expressions - * (e.g. dependent `valueFrom` fields). - * *
- */ - - public java.util.Optional getDefault() { - return this.default_; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - public Object getType() { - return this.type; - } - - private java.util.Optional inputBinding; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowInputParameter/inputBinding
- *
- * Deprecated. Preserved for v1.0 backwards compatibility. Will be removed in - * CWL v2.0. Use `WorkflowInputParameter.loadContents` instead. - * *
- */ - - public java.util.Optional getInputBinding() { - return this.inputBinding; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of WorkflowInputParameterImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkflowInputParameterImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkflowInputParameterImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - if (id == null) { - if (__docRoot != null) { - id = __docRoot; - } else { - throw new ValidationException("Missing id"); - } - } - __baseUri = (String) id; - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - java.util.Optional default_; - - if (__doc.containsKey("default")) { - try { - default_ = - LoaderInstances - .optional_CWLObjectType - .loadField(__doc.get("default"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - default_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `default` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - default_ = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional inputBinding; - - if (__doc.containsKey("inputBinding")) { - try { - inputBinding = - LoaderInstances - .optional_InputBinding - .loadField(__doc.get("inputBinding"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - inputBinding = null; // won't be used but prevents compiler from complaining. - final String __message = "the `inputBinding` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - inputBinding = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.doc = (Object) doc; - this.id = (String) id; - this.format = (Object) format; - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - this.default_ = (java.util.Optional) default_; - this.type = (Object) type; - this.inputBinding = (java.util.Optional) inputBinding; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("label", "secondaryFiles", "streamable", "doc", "id", "format", "loadContents", "loadListing", "default", "type", "inputBinding"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameter.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameter.java deleted file mode 100644 index 29946e46..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameter.java +++ /dev/null @@ -1,166 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowOutputParameter
This interface is implemented by {@link WorkflowOutputParameterImpl}
- Describe an output parameter of a workflow. The parameter must be - connected to one or more parameters defined in the workflow that - will provide the value of the output parameter. It is legal to - connect a WorkflowInputParameter to a WorkflowOutputParameter. - - See [WorkflowStepInput](#WorkflowStepInput) for discussion of - `linkMerge` and `pickValue`. -
- */ -public interface WorkflowOutputParameter extends OutputParameter, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - String getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - Object getSecondaryFiles(); - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - java.util.Optional getStreamable(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - Object getFormat(); - /** - * Getter for property https://w3id.org/cwl/cwl#outputSource
- *
- * Specifies one or more names of an output from a workflow step (in the form - * `step_name/output_name` with a `/` separator`), or a workflow input name, - * that supply their value(s) to the output parameter. - * the output parameter. It is valid to reference workflow level inputs - * here. - * *
- */ - - Object getOutputSource(); - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowOutputParameter/linkMerge
- *
- * The method to use to merge multiple sources into a single array. - * If not specified, the default method is "merge_nested". - * *
- */ - - java.util.Optional getLinkMerge(); - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowOutputParameter/pickValue
- *
- * The method to use to choose non-null elements among multiple sources. - * *
- */ - - java.util.Optional getPickValue(); - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - Object getType(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameterImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameterImpl.java deleted file mode 100644 index f82c6ae7..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowOutputParameterImpl.java +++ /dev/null @@ -1,451 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowOutputParameter
- Describe an output parameter of a workflow. The parameter must be - connected to one or more parameters defined in the workflow that - will provide the value of the output parameter. It is legal to - connect a WorkflowInputParameter to a WorkflowOutputParameter. - - See [WorkflowStepInput](#WorkflowStepInput) for discussion of - `linkMerge` and `pickValue`. -
- */ -public class WorkflowOutputParameterImpl extends SaveableImpl implements WorkflowOutputParameter { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String id; - - /** - * Getter for property https://w3id.org/cwl/cwl#Parameter/id
- *
- * The unique identifier for this Parameter. *
- */ - - public String getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object secondaryFiles; - - /** - * Getter for property https://w3id.org/cwl/cwl#secondaryFiles
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * Provides a pattern or expression specifying files or - * directories that should be included alongside the primary - * file. Secondary files may be required or optional. When not - * explicitly specified, secondary files specified for `inputs` - * are required and `outputs` are optional. An implementation - * must include matching Files and Directories in the - * `secondaryFiles` property of the primary file. These Files - * and Directories must be transferred and staged alongside the - * primary file. An implementation may fail workflow execution - * if a required secondary file does not exist. - * - * If the value is an expression, the value of `self` in the expression - * must be the primary input or output File object to which this binding - * applies. The `basename`, `nameroot` and `nameext` fields must be - * present in `self`. For `CommandLineTool` outputs the `path` field must - * also be present. The expression must return a filename string relative - * to the path to the primary File, a File or Directory object with either - * `path` or `location` and `basename` fields set, or an array consisting - * of strings or File or Directory objects. It is legal to reference an - * unchanged File or Directory object taken from input as a secondaryFile. - * The expression may return "null" in which case there is no secondaryFile - * from that expression. - * - * To work on non-filename-preserving storage systems, portable tool - * descriptions should avoid constructing new values from `location`, but - * should construct relative references using `basename` or `nameroot` - * instead. - * - * If a value in `secondaryFiles` is a string that is not an expression, - * it specifies that the following pattern should be applied to the path - * of the primary file to yield a filename relative to the primary File: - * - * 1. If string ends with `?` character, remove the last `?` and mark - * the resulting secondary file as optional. - * 2. If string begins with one or more caret `^` characters, for each - * caret, remove the last file extension from the path (the last - * period `.` and all following characters). If there are no file - * extensions, the path is unchanged. - * 3. Append the remainder of the string to the end of the file path. - * *
- */ - - public Object getSecondaryFiles() { - return this.secondaryFiles; - } - - private java.util.Optional streamable; - - /** - * Getter for property https://w3id.org/cwl/cwl#FieldBase/streamable
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * A value of `true` indicates that the file is read or written - * sequentially without seeking. An implementation may use this flag to - * indicate whether it is valid to stream file contents using a named - * pipe. Default: `false`. - * *
- */ - - public java.util.Optional getStreamable() { - return this.streamable; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private Object format; - - /** - * Getter for property https://w3id.org/cwl/cwl#format
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * This is the file format that will be assigned to the output - * File object. - * *
- */ - - public Object getFormat() { - return this.format; - } - - private Object outputSource; - - /** - * Getter for property https://w3id.org/cwl/cwl#outputSource
- *
- * Specifies one or more names of an output from a workflow step (in the form - * `step_name/output_name` with a `/` separator`), or a workflow input name, - * that supply their value(s) to the output parameter. - * the output parameter. It is valid to reference workflow level inputs - * here. - * *
- */ - - public Object getOutputSource() { - return this.outputSource; - } - - private java.util.Optional linkMerge; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowOutputParameter/linkMerge
- *
- * The method to use to merge multiple sources into a single array. - * If not specified, the default method is "merge_nested". - * *
- */ - - public java.util.Optional getLinkMerge() { - return this.linkMerge; - } - - private java.util.Optional pickValue; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowOutputParameter/pickValue
- *
- * The method to use to choose non-null elements among multiple sources. - * *
- */ - - public java.util.Optional getPickValue() { - return this.pickValue; - } - - private Object type; - - /** - * Getter for property https://w3id.org/cwl/salad#type
- *
- * Specify valid types of data that may be assigned to this parameter. - * *
- */ - - public Object getType() { - return this.type; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of WorkflowOutputParameterImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkflowOutputParameterImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkflowOutputParameterImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - if (id == null) { - if (__docRoot != null) { - id = __docRoot; - } else { - throw new ValidationException("Missing id"); - } - } - __baseUri = (String) id; - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object secondaryFiles; - - if (__doc.containsKey("secondaryFiles")) { - try { - secondaryFiles = - LoaderInstances - .secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema - .loadField(__doc.get("secondaryFiles"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - secondaryFiles = null; // won't be used but prevents compiler from complaining. - final String __message = "the `secondaryFiles` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - secondaryFiles = null; - } - java.util.Optional streamable; - - if (__doc.containsKey("streamable")) { - try { - streamable = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("streamable"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - streamable = null; // won't be used but prevents compiler from complaining. - final String __message = "the `streamable` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - streamable = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - Object format; - - if (__doc.containsKey("format")) { - try { - format = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True - .loadField(__doc.get("format"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - format = null; // won't be used but prevents compiler from complaining. - final String __message = "the `format` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - format = null; - } - Object outputSource; - - if (__doc.containsKey("outputSource")) { - try { - outputSource = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_1_None - .loadField(__doc.get("outputSource"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - outputSource = null; // won't be used but prevents compiler from complaining. - final String __message = "the `outputSource` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - outputSource = null; - } - java.util.Optional linkMerge; - - if (__doc.containsKey("linkMerge")) { - try { - linkMerge = - LoaderInstances - .optional_LinkMergeMethod - .loadField(__doc.get("linkMerge"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - linkMerge = null; // won't be used but prevents compiler from complaining. - final String __message = "the `linkMerge` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - linkMerge = null; - } - java.util.Optional pickValue; - - if (__doc.containsKey("pickValue")) { - try { - pickValue = - LoaderInstances - .optional_PickValueMethod - .loadField(__doc.get("pickValue"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - pickValue = null; // won't be used but prevents compiler from complaining. - final String __message = "the `pickValue` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - pickValue = null; - } - Object type; - try { - type = - LoaderInstances - .typedsl_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_2 - .loadField(__doc.get("type"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - type = null; // won't be used but prevents compiler from complaining. - final String __message = "the `type` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.label = (java.util.Optional) label; - this.secondaryFiles = (Object) secondaryFiles; - this.streamable = (java.util.Optional) streamable; - this.doc = (Object) doc; - this.id = (String) id; - this.format = (Object) format; - this.outputSource = (Object) outputSource; - this.linkMerge = (java.util.Optional) linkMerge; - this.pickValue = (java.util.Optional) pickValue; - this.type = (Object) type; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("label", "secondaryFiles", "streamable", "doc", "id", "format", "outputSource", "linkMerge", "pickValue", "type"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStep.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStep.java deleted file mode 100644 index d926748e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStep.java +++ /dev/null @@ -1,207 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowStep
This interface is implemented by {@link WorkflowStepImpl}
- A workflow step is an executable element of a workflow. It specifies the - underlying process implementation (such as `CommandLineTool` or another - `Workflow`) in the `run` field and connects the input and output parameters - of the underlying process to workflow parameters. - - # Scatter/gather - - To use scatter/gather, - [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified - in the workflow or workflow step requirements. - - A "scatter" operation specifies that the associated workflow step or - subworkflow should execute separately over a list of input elements. Each - job making up a scatter operation is independent and may be executed - concurrently. - - The `scatter` field specifies one or more input parameters which will be - scattered. An input parameter may be listed more than once. The declared - type of each input parameter implicitly becomes an array of items of the - input parameter type. If a parameter is listed more than once, it becomes - a nested array. As a result, upstream parameters which are connected to - scattered parameters must be arrays. - - All output parameter types are also implicitly wrapped in arrays. Each job - in the scatter results in an entry in the output array. - - If any scattered parameter runtime value is an empty array, all outputs are - set to empty arrays and no work is done for the step, according to - applicable scattering rules. - - If `scatter` declares more than one input parameter, `scatterMethod` - describes how to decompose the input into a discrete set of jobs. - - * **dotproduct** specifies that each of the input arrays are aligned and one - element taken from each array to construct each job. It is an error - if all input arrays are not the same length. - - * **nested_crossproduct** specifies the Cartesian product of the inputs, - producing a job for every combination of the scattered inputs. The - output must be nested arrays for each level of scattering, in the - order that the input arrays are listed in the `scatter` field. - - * **flat_crossproduct** specifies the Cartesian product of the inputs, - producing a job for every combination of the scattered inputs. The - output arrays must be flattened to a single level, but otherwise listed in the - order that the input arrays are listed in the `scatter` field. - - # Conditional execution (Optional) - - Conditional execution makes execution of a step conditional on an - expression. A step that is not executed is "skipped". A skipped - step produces `null` for all output parameters. - - The condition is evaluated after `scatter`, using the input object - of each individual scatter job. This means over a set of scatter - jobs, some may be executed and some may be skipped. When the - results are gathered, skipped steps must be `null` in the output - arrays. - - The `when` field controls conditional execution. This is an - expression that must be evaluated with `inputs` bound to the step - input object (or individual scatter job), and returns a boolean - value. It is an error if this expression returns a value other - than `true` or `false`. - - Conditionals in CWL are an optional feature and are not required - to be implemented by all consumers of CWL documents. An - implementation that does not support conditionals must return a - fatal error when attempting to execute a workflow that uses - conditional constructs the implementation does not support. - - # Subworkflows - - To specify a nested workflow as part of a workflow step, - [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be - specified in the workflow or workflow step requirements. - - It is a fatal error if a workflow directly or indirectly invokes itself as - a subworkflow (recursive workflows are not allowed). -
- */ -public interface WorkflowStep extends IdentifierRequired, Labeled, Documented, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowStep/id
- *
- * The unique identifier for this WorkflowStep. *
- */ - - String getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - Object getDoc(); - /** - * Getter for property https://w3id.org/cwl/cwl#in
- *
- * Defines the input parameters of the workflow step. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used build a user - * interface for constructing the input object. - * *
- */ - - java.util.List getIn(); - /** - * Getter for property https://w3id.org/cwl/cwl#out
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - java.util.List getOut(); - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this workflow step. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - java.util.Optional> getRequirements(); - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this workflow step. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - java.util.Optional> getHints(); - /** - * Getter for property https://w3id.org/cwl/cwl#run
- *
- * Specifies the process to run. If `run` is a string, it must be an absolute IRI - * or a relative path from the primary document. - * *
- */ - - Object getRun(); - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowStep/when
- *
- * If defined, only run the step when the expression evaluates to - * `true`. If `false` the step is skipped. A skipped step - * produces a `null` on each output. - * *
- */ - - java.util.Optional getWhen(); - /** - * Getter for property https://w3id.org/cwl/cwl#scatter
- - */ - - Object getScatter(); - /** - * Getter for property https://w3id.org/cwl/cwl#scatterMethod
- *
- * Required if `scatter` is an array of more than one element. - * *
- */ - - java.util.Optional getScatterMethod(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepImpl.java deleted file mode 100644 index 09e21399..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepImpl.java +++ /dev/null @@ -1,503 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowStep
- A workflow step is an executable element of a workflow. It specifies the - underlying process implementation (such as `CommandLineTool` or another - `Workflow`) in the `run` field and connects the input and output parameters - of the underlying process to workflow parameters. - - # Scatter/gather - - To use scatter/gather, - [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified - in the workflow or workflow step requirements. - - A "scatter" operation specifies that the associated workflow step or - subworkflow should execute separately over a list of input elements. Each - job making up a scatter operation is independent and may be executed - concurrently. - - The `scatter` field specifies one or more input parameters which will be - scattered. An input parameter may be listed more than once. The declared - type of each input parameter implicitly becomes an array of items of the - input parameter type. If a parameter is listed more than once, it becomes - a nested array. As a result, upstream parameters which are connected to - scattered parameters must be arrays. - - All output parameter types are also implicitly wrapped in arrays. Each job - in the scatter results in an entry in the output array. - - If any scattered parameter runtime value is an empty array, all outputs are - set to empty arrays and no work is done for the step, according to - applicable scattering rules. - - If `scatter` declares more than one input parameter, `scatterMethod` - describes how to decompose the input into a discrete set of jobs. - - * **dotproduct** specifies that each of the input arrays are aligned and one - element taken from each array to construct each job. It is an error - if all input arrays are not the same length. - - * **nested_crossproduct** specifies the Cartesian product of the inputs, - producing a job for every combination of the scattered inputs. The - output must be nested arrays for each level of scattering, in the - order that the input arrays are listed in the `scatter` field. - - * **flat_crossproduct** specifies the Cartesian product of the inputs, - producing a job for every combination of the scattered inputs. The - output arrays must be flattened to a single level, but otherwise listed in the - order that the input arrays are listed in the `scatter` field. - - # Conditional execution (Optional) - - Conditional execution makes execution of a step conditional on an - expression. A step that is not executed is "skipped". A skipped - step produces `null` for all output parameters. - - The condition is evaluated after `scatter`, using the input object - of each individual scatter job. This means over a set of scatter - jobs, some may be executed and some may be skipped. When the - results are gathered, skipped steps must be `null` in the output - arrays. - - The `when` field controls conditional execution. This is an - expression that must be evaluated with `inputs` bound to the step - input object (or individual scatter job), and returns a boolean - value. It is an error if this expression returns a value other - than `true` or `false`. - - Conditionals in CWL are an optional feature and are not required - to be implemented by all consumers of CWL documents. An - implementation that does not support conditionals must return a - fatal error when attempting to execute a workflow that uses - conditional constructs the implementation does not support. - - # Subworkflows - - To specify a nested workflow as part of a workflow step, - [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be - specified in the workflow or workflow step requirements. - - It is a fatal error if a workflow directly or indirectly invokes itself as - a subworkflow (recursive workflows are not allowed). -
- */ -public class WorkflowStepImpl extends SaveableImpl implements WorkflowStep { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String id; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowStep/id
- *
- * The unique identifier for this WorkflowStep. *
- */ - - public String getId() { - return this.id; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private Object doc; - - /** - * Getter for property https://w3id.org/cwl/salad#Documented/doc
- *
- * A documentation string for this object, or an array of strings which should be concatenated. *
- */ - - public Object getDoc() { - return this.doc; - } - - private java.util.List in; - - /** - * Getter for property https://w3id.org/cwl/cwl#in
- *
- * Defines the input parameters of the workflow step. The process is ready to - * run when all required input parameters are associated with concrete - * values. Input parameters include a schema for each parameter which is - * used to validate the input object. It may also be used build a user - * interface for constructing the input object. - * *
- */ - - public java.util.List getIn() { - return this.in; - } - - private java.util.List out; - - /** - * Getter for property https://w3id.org/cwl/cwl#out
- *
- * Defines the parameters representing the output of the process. May be - * used to generate and/or validate the output object. - * *
- */ - - public java.util.List getOut() { - return this.out; - } - - private java.util.Optional> requirements; - - /** - * Getter for property https://w3id.org/cwl/cwl#requirements
- *
- * Declares requirements that apply to either the runtime environment or the - * workflow engine that must be met in order to execute this workflow step. If - * an implementation cannot satisfy all requirements, or a requirement is - * listed which is not recognized by the implementation, it is a fatal - * error and the implementation must not attempt to run the process, - * unless overridden at user option. - * *
- */ - - public java.util.Optional> getRequirements() { - return this.requirements; - } - - private java.util.Optional> hints; - - /** - * Getter for property https://w3id.org/cwl/cwl#hints
- *
- * Declares hints applying to either the runtime environment or the - * workflow engine that may be helpful in executing this workflow step. It is - * not an error if an implementation cannot satisfy all hints, however - * the implementation may report a warning. - * *
- */ - - public java.util.Optional> getHints() { - return this.hints; - } - - private Object run; - - /** - * Getter for property https://w3id.org/cwl/cwl#run
- *
- * Specifies the process to run. If `run` is a string, it must be an absolute IRI - * or a relative path from the primary document. - * *
- */ - - public Object getRun() { - return this.run; - } - - private java.util.Optional when; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowStep/when
- *
- * If defined, only run the step when the expression evaluates to - * `true`. If `false` the step is skipped. A skipped step - * produces a `null` on each output. - * *
- */ - - public java.util.Optional getWhen() { - return this.when; - } - - private Object scatter; - - /** - * Getter for property https://w3id.org/cwl/cwl#scatter
- - */ - - public Object getScatter() { - return this.scatter; - } - - private java.util.Optional scatterMethod; - - /** - * Getter for property https://w3id.org/cwl/cwl#scatterMethod
- *
- * Required if `scatter` is an array of more than one element. - * *
- */ - - public java.util.Optional getScatterMethod() { - return this.scatterMethod; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of WorkflowStepImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkflowStepImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkflowStepImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - if (id == null) { - if (__docRoot != null) { - id = __docRoot; - } else { - throw new ValidationException("Missing id"); - } - } - __baseUri = (String) id; - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - Object doc; - - if (__doc.containsKey("doc")) { - try { - doc = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_array_of_StringInstance - .loadField(__doc.get("doc"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - doc = null; // won't be used but prevents compiler from complaining. - final String __message = "the `doc` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - doc = null; - } - java.util.List in; - try { - in = - LoaderInstances - .idmap_in_array_of_WorkflowStepInput - .loadField(__doc.get("in"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - in = null; // won't be used but prevents compiler from complaining. - final String __message = "the `in` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.List out; - try { - out = - LoaderInstances - .uri_array_of_union_of_StringInstance_or_WorkflowStepOutput_True_False_None_None - .loadField(__doc.get("out"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - out = null; // won't be used but prevents compiler from complaining. - final String __message = "the `out` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional> requirements; - - if (__doc.containsKey("requirements")) { - try { - requirements = - LoaderInstances - .idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize - .loadField(__doc.get("requirements"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - requirements = null; // won't be used but prevents compiler from complaining. - final String __message = "the `requirements` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - requirements = null; - } - java.util.Optional> hints; - - if (__doc.containsKey("hints")) { - try { - hints = - LoaderInstances - .idmap_hints_optional_array_of_AnyInstance - .loadField(__doc.get("hints"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - hints = null; // won't be used but prevents compiler from complaining. - final String __message = "the `hints` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - hints = null; - } - Object run; - try { - run = - LoaderInstances - .uri_union_of_StringInstance_or_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator_False_False_None_None - .loadField(__doc.get("run"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - run = null; // won't be used but prevents compiler from complaining. - final String __message = "the `run` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - java.util.Optional when; - - if (__doc.containsKey("when")) { - try { - when = - LoaderInstances - .optional_ExpressionLoader - .loadField(__doc.get("when"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - when = null; // won't be used but prevents compiler from complaining. - final String __message = "the `when` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - when = null; - } - Object scatter; - - if (__doc.containsKey("scatter")) { - try { - scatter = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_0_None - .loadField(__doc.get("scatter"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - scatter = null; // won't be used but prevents compiler from complaining. - final String __message = "the `scatter` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - scatter = null; - } - java.util.Optional scatterMethod; - - if (__doc.containsKey("scatterMethod")) { - try { - scatterMethod = - LoaderInstances - .uri_optional_ScatterMethod_False_True_None_None - .loadField(__doc.get("scatterMethod"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - scatterMethod = null; // won't be used but prevents compiler from complaining. - final String __message = "the `scatterMethod` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - scatterMethod = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (String) id; - this.label = (java.util.Optional) label; - this.doc = (Object) doc; - this.in = (java.util.List) in; - this.out = (java.util.List) out; - this.requirements = (java.util.Optional>) requirements; - this.hints = (java.util.Optional>) hints; - this.run = (Object) run; - this.when = (java.util.Optional) when; - this.scatter = (Object) scatter; - this.scatterMethod = (java.util.Optional) scatterMethod; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id", "label", "doc", "in", "out", "requirements", "hints", "run", "when", "scatter", "scatterMethod"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInput.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInput.java deleted file mode 100644 index aca1570d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInput.java +++ /dev/null @@ -1,248 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowStepInput
This interface is implemented by {@link WorkflowStepInputImpl}
- The input of a workflow step connects an upstream parameter (from the - workflow inputs, or the outputs of other workflows steps) with the input - parameters of the process specified by the `run` field. Only input parameters - declared by the target process will be passed through at runtime to the process - though additional parameters may be specified (for use within `valueFrom` - expressions for instance) - unconnected or unused parameters do not represent an - error condition. - - # Input object - - A WorkflowStepInput object must contain an `id` field in the form - `#fieldname` or `#prefix/fieldname`. When the `id` field contains a slash - `/` the field name consists of the characters following the final slash - (the prefix portion may contain one or more slashes to indicate scope). - This defines a field of the workflow step input object with the value of - the `source` parameter(s). - - # Merging multiple inbound data links - - To merge multiple inbound data links, - [MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified - in the workflow or workflow step requirements. - - If the sink parameter is an array, or named in a [workflow - scatter](#WorkflowStep) operation, there may be multiple inbound - data links listed in the `source` field. The values from the - input links are merged depending on the method specified in the - `linkMerge` field. If both `linkMerge` and `pickValue` are null - or not specified, and there is more than one element in the - `source` array, the default method is "merge_nested". - - If both `linkMerge` and `pickValue` are null or not specified, and - there is only a single element in the `source`, then the input - parameter takes the scalar value from the single input link (it is - *not* wrapped in a single-list). - - * **merge_nested** - - The input must be an array consisting of exactly one entry for each - input link. If "merge_nested" is specified with a single link, the value - from the link must be wrapped in a single-item list. - - * **merge_flattened** - - 1. The source and sink parameters must be compatible types, or the source - type must be compatible with single element from the "items" type of - the destination array parameter. - 2. Source parameters which are arrays are concatenated. - Source parameters which are single element types are appended as - single elements. - - # Picking non-null values among inbound data links - - If present, `pickValue` specifies how to pick non-null values among inbound data links. - - `pickValue` is evaluated - 1. Once all source values from upstream step or parameters are available. - 2. After `linkMerge`. - 3. Before `scatter` or `valueFrom`. - - This is specifically intended to be useful in combination with - [conditional execution](#WorkflowStep), where several upstream - steps may be connected to a single input (`source` is a list), and - skipped steps produce null values. - - Static type checkers should check for type consistency after inferring what the type - will be after `pickValue` is applied, just as they do currently for `linkMerge`. - - * **first_non_null** - - For the first level of a list input, pick the first non-null element. The result is a scalar. - It is an error if there is no non-null element. Examples: - * `[null, x, null, y] -> x` - * `[null, [null], null, y] -> [null]` - * `[null, null, null] -> Runtime Error` - - *Intended use case*: If-else pattern where the - value comes either from a conditional step or from a default or - fallback value. The conditional step(s) should be placed first in - the list. - - * **the_only_non_null** - - For the first level of a list input, pick the single non-null element. The result is a scalar. - It is an error if there is more than one non-null element. Examples: - - * `[null, x, null] -> x` - * `[null, x, null, y] -> Runtime Error` - * `[null, [null], null] -> [null]` - * `[null, null, null] -> Runtime Error` - - *Intended use case*: Switch type patterns where developer considers - more than one active code path as a workflow error - (possibly indicating an error in writing `when` condition expressions). - - * **all_non_null** - - For the first level of a list input, pick all non-null values. - The result is a list, which may be empty. Examples: - - * `[null, x, null] -> [x]` - * `[x, null, y] -> [x, y]` - * `[null, [x], [null]] -> [[x], [null]]` - * `[null, null, null] -> []` - - *Intended use case*: It is valid to have more than one source, but - sources are conditional, so null sources (from skipped steps) - should be filtered out. -
- */ -public interface WorkflowStepInput extends IdentifierRequired, Sink, LoadContents, Labeled, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowStepInput/id
- *
- * The unique identifier of the source input field name. *
- */ - - String getId(); - /** - * Getter for property https://w3id.org/cwl/cwl#source
- *
- * Specifies one or more workflow parameters that will provide input to - * the underlying step parameter. - * *
- */ - - Object getSource(); - /** - * Getter for property https://w3id.org/cwl/cwl#Sink/linkMerge
- *
- * The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". - * *
- */ - - java.util.Optional getLinkMerge(); - /** - * Getter for property https://w3id.org/cwl/cwl#Sink/pickValue
- *
- * The method to use to choose non-null elements among multiple sources. - * *
- */ - - java.util.Optional getPickValue(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - java.util.Optional getLoadContents(); - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - java.util.Optional getLoadListing(); - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - java.util.Optional getLabel(); - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value for this parameter to use if either there is no - * `source` field, or the value produced by the `source` is `null`. The - * default must be applied prior to scattering or evaluating `valueFrom`. - * *
- */ - - java.util.Optional getDefault(); - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowStepInput/valueFrom
- *
- * To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must - * be specified in the workflow or workflow step requirements. - * - * If `valueFrom` is a constant string value, use this as the value for - * this input parameter. - * - * If `valueFrom` is a parameter reference or expression, it must be - * evaluated to yield the actual value to be assigned to the input field. - * - * The `self` value in the parameter reference or expression must be - * 1. `null` if there is no `source` field - * 2. the value of the parameter(s) specified in the `source` field when this - * workflow input parameter **is not** specified in this workflow step's `scatter` field. - * 3. an element of the parameter specified in the `source` field when this workflow input - * parameter **is** specified in this workflow step's `scatter` field. - * - * The value of `inputs` in the parameter reference or expression must be - * the input object to the workflow step after assigning the `source` - * values, applying `default`, and then scattering. The order of - * evaluating `valueFrom` among step input parameters is undefined and the - * result of evaluating `valueFrom` on a parameter must not be visible to - * evaluation of `valueFrom` on other parameters. - * *
- */ - - Object getValueFrom(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInputImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInputImpl.java deleted file mode 100644 index 37743fd9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepInputImpl.java +++ /dev/null @@ -1,516 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowStepInput
- The input of a workflow step connects an upstream parameter (from the - workflow inputs, or the outputs of other workflows steps) with the input - parameters of the process specified by the `run` field. Only input parameters - declared by the target process will be passed through at runtime to the process - though additional parameters may be specified (for use within `valueFrom` - expressions for instance) - unconnected or unused parameters do not represent an - error condition. - - # Input object - - A WorkflowStepInput object must contain an `id` field in the form - `#fieldname` or `#prefix/fieldname`. When the `id` field contains a slash - `/` the field name consists of the characters following the final slash - (the prefix portion may contain one or more slashes to indicate scope). - This defines a field of the workflow step input object with the value of - the `source` parameter(s). - - # Merging multiple inbound data links - - To merge multiple inbound data links, - [MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified - in the workflow or workflow step requirements. - - If the sink parameter is an array, or named in a [workflow - scatter](#WorkflowStep) operation, there may be multiple inbound - data links listed in the `source` field. The values from the - input links are merged depending on the method specified in the - `linkMerge` field. If both `linkMerge` and `pickValue` are null - or not specified, and there is more than one element in the - `source` array, the default method is "merge_nested". - - If both `linkMerge` and `pickValue` are null or not specified, and - there is only a single element in the `source`, then the input - parameter takes the scalar value from the single input link (it is - *not* wrapped in a single-list). - - * **merge_nested** - - The input must be an array consisting of exactly one entry for each - input link. If "merge_nested" is specified with a single link, the value - from the link must be wrapped in a single-item list. - - * **merge_flattened** - - 1. The source and sink parameters must be compatible types, or the source - type must be compatible with single element from the "items" type of - the destination array parameter. - 2. Source parameters which are arrays are concatenated. - Source parameters which are single element types are appended as - single elements. - - # Picking non-null values among inbound data links - - If present, `pickValue` specifies how to pick non-null values among inbound data links. - - `pickValue` is evaluated - 1. Once all source values from upstream step or parameters are available. - 2. After `linkMerge`. - 3. Before `scatter` or `valueFrom`. - - This is specifically intended to be useful in combination with - [conditional execution](#WorkflowStep), where several upstream - steps may be connected to a single input (`source` is a list), and - skipped steps produce null values. - - Static type checkers should check for type consistency after inferring what the type - will be after `pickValue` is applied, just as they do currently for `linkMerge`. - - * **first_non_null** - - For the first level of a list input, pick the first non-null element. The result is a scalar. - It is an error if there is no non-null element. Examples: - * `[null, x, null, y] -> x` - * `[null, [null], null, y] -> [null]` - * `[null, null, null] -> Runtime Error` - - *Intended use case*: If-else pattern where the - value comes either from a conditional step or from a default or - fallback value. The conditional step(s) should be placed first in - the list. - - * **the_only_non_null** - - For the first level of a list input, pick the single non-null element. The result is a scalar. - It is an error if there is more than one non-null element. Examples: - - * `[null, x, null] -> x` - * `[null, x, null, y] -> Runtime Error` - * `[null, [null], null] -> [null]` - * `[null, null, null] -> Runtime Error` - - *Intended use case*: Switch type patterns where developer considers - more than one active code path as a workflow error - (possibly indicating an error in writing `when` condition expressions). - - * **all_non_null** - - For the first level of a list input, pick all non-null values. - The result is a list, which may be empty. Examples: - - * `[null, x, null] -> [x]` - * `[x, null, y] -> [x, y]` - * `[null, [x], [null]] -> [[x], [null]]` - * `[null, null, null] -> []` - - *Intended use case*: It is valid to have more than one source, but - sources are conditional, so null sources (from skipped steps) - should be filtered out. -
- */ -public class WorkflowStepInputImpl extends SaveableImpl implements WorkflowStepInput { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String id; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowStepInput/id
- *
- * The unique identifier of the source input field name. *
- */ - - public String getId() { - return this.id; - } - - private Object source; - - /** - * Getter for property https://w3id.org/cwl/cwl#source
- *
- * Specifies one or more workflow parameters that will provide input to - * the underlying step parameter. - * *
- */ - - public Object getSource() { - return this.source; - } - - private java.util.Optional linkMerge; - - /** - * Getter for property https://w3id.org/cwl/cwl#Sink/linkMerge
- *
- * The method to use to merge multiple inbound links into a single array. - * If not specified, the default method is "merge_nested". - * *
- */ - - public java.util.Optional getLinkMerge() { - return this.linkMerge; - } - - private java.util.Optional pickValue; - - /** - * Getter for property https://w3id.org/cwl/cwl#Sink/pickValue
- *
- * The method to use to choose non-null elements among multiple sources. - * *
- */ - - public java.util.Optional getPickValue() { - return this.pickValue; - } - - private java.util.Optional loadContents; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadContents
- *
- * Only valid when `type: File` or is an array of `items: File`. - * - * If true, the file (or each file in the array) must be a UTF-8 - * text file 64 KiB or smaller, and the implementation must read - * the entire contents of the file (or file array) and place it - * in the `contents` field of the File object for use by - * expressions. If the size of the file is greater than 64 KiB, - * the implementation must raise a fatal error. - * *
- */ - - public java.util.Optional getLoadContents() { - return this.loadContents; - } - - private java.util.Optional loadListing; - - /** - * Getter for property https://w3id.org/cwl/cwl#LoadContents/loadListing
- *
- * Only valid when `type: Directory` or is an array of `items: Directory`. - * - * Specify the desired behavior for loading the `listing` field of - * a Directory object for use by expressions. - * - * The order of precedence for loadListing is: - * - * 1. `loadListing` on an individual parameter - * 2. Inherited from `LoadListingRequirement` - * 3. By default: `no_listing` - * *
- */ - - public java.util.Optional getLoadListing() { - return this.loadListing; - } - - private java.util.Optional label; - - /** - * Getter for property https://w3id.org/cwl/cwl#Labeled/label
- *
- * A short, human-readable label of this object. *
- */ - - public java.util.Optional getLabel() { - return this.label; - } - - private java.util.Optional default_; - - /** - * Getter for property https://w3id.org/cwl/salad#default
- *
- * The default value for this parameter to use if either there is no - * `source` field, or the value produced by the `source` is `null`. The - * default must be applied prior to scattering or evaluating `valueFrom`. - * *
- */ - - public java.util.Optional getDefault() { - return this.default_; - } - - private Object valueFrom; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowStepInput/valueFrom
- *
- * To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must - * be specified in the workflow or workflow step requirements. - * - * If `valueFrom` is a constant string value, use this as the value for - * this input parameter. - * - * If `valueFrom` is a parameter reference or expression, it must be - * evaluated to yield the actual value to be assigned to the input field. - * - * The `self` value in the parameter reference or expression must be - * 1. `null` if there is no `source` field - * 2. the value of the parameter(s) specified in the `source` field when this - * workflow input parameter **is not** specified in this workflow step's `scatter` field. - * 3. an element of the parameter specified in the `source` field when this workflow input - * parameter **is** specified in this workflow step's `scatter` field. - * - * The value of `inputs` in the parameter reference or expression must be - * the input object to the workflow step after assigning the `source` - * values, applying `default`, and then scattering. The order of - * evaluating `valueFrom` among step input parameters is undefined and the - * result of evaluating `valueFrom` on a parameter must not be visible to - * evaluation of `valueFrom` on other parameters. - * *
- */ - - public Object getValueFrom() { - return this.valueFrom; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of WorkflowStepInputImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkflowStepInputImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkflowStepInputImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - if (id == null) { - if (__docRoot != null) { - id = __docRoot; - } else { - throw new ValidationException("Missing id"); - } - } - __baseUri = (String) id; - Object source; - - if (__doc.containsKey("source")) { - try { - source = - LoaderInstances - .uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_2_None - .loadField(__doc.get("source"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - source = null; // won't be used but prevents compiler from complaining. - final String __message = "the `source` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - source = null; - } - java.util.Optional linkMerge; - - if (__doc.containsKey("linkMerge")) { - try { - linkMerge = - LoaderInstances - .optional_LinkMergeMethod - .loadField(__doc.get("linkMerge"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - linkMerge = null; // won't be used but prevents compiler from complaining. - final String __message = "the `linkMerge` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - linkMerge = null; - } - java.util.Optional pickValue; - - if (__doc.containsKey("pickValue")) { - try { - pickValue = - LoaderInstances - .optional_PickValueMethod - .loadField(__doc.get("pickValue"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - pickValue = null; // won't be used but prevents compiler from complaining. - final String __message = "the `pickValue` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - pickValue = null; - } - java.util.Optional loadContents; - - if (__doc.containsKey("loadContents")) { - try { - loadContents = - LoaderInstances - .optional_BooleanInstance - .loadField(__doc.get("loadContents"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadContents = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadContents` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadContents = null; - } - java.util.Optional loadListing; - - if (__doc.containsKey("loadListing")) { - try { - loadListing = - LoaderInstances - .optional_LoadListingEnum - .loadField(__doc.get("loadListing"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - loadListing = null; // won't be used but prevents compiler from complaining. - final String __message = "the `loadListing` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - loadListing = null; - } - java.util.Optional label; - - if (__doc.containsKey("label")) { - try { - label = - LoaderInstances - .optional_StringInstance - .loadField(__doc.get("label"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - label = null; // won't be used but prevents compiler from complaining. - final String __message = "the `label` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - label = null; - } - java.util.Optional default_; - - if (__doc.containsKey("default")) { - try { - default_ = - LoaderInstances - .optional_CWLObjectType - .loadField(__doc.get("default"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - default_ = null; // won't be used but prevents compiler from complaining. - final String __message = "the `default` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - default_ = null; - } - Object valueFrom; - - if (__doc.containsKey("valueFrom")) { - try { - valueFrom = - LoaderInstances - .union_of_NullInstance_or_StringInstance_or_ExpressionLoader - .loadField(__doc.get("valueFrom"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - valueFrom = null; // won't be used but prevents compiler from complaining. - final String __message = "the `valueFrom` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - valueFrom = null; - } - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (String) id; - this.source = (Object) source; - this.linkMerge = (java.util.Optional) linkMerge; - this.pickValue = (java.util.Optional) pickValue; - this.loadContents = (java.util.Optional) loadContents; - this.loadListing = (java.util.Optional) loadListing; - this.label = (java.util.Optional) label; - this.default_ = (java.util.Optional) default_; - this.valueFrom = (Object) valueFrom; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id", "source", "linkMerge", "pickValue", "loadContents", "loadListing", "label", "default", "valueFrom"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepOutput.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepOutput.java deleted file mode 100644 index ef1df393..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepOutput.java +++ /dev/null @@ -1,44 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.Saveable; - -/** -* Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowStepOutput
This interface is implemented by {@link WorkflowStepOutputImpl}
- Associate an output parameter of the underlying process with a workflow - parameter. The workflow parameter (given in the `id` field) be may be used - as a `source` to connect with input parameters of other workflow steps, or - with an output parameter of the process. - - A unique identifier for this workflow output parameter. This is - the identifier to use in the `source` field of `WorkflowStepInput` - to connect the output value to downstream parameters. -
- */ -public interface WorkflowStepOutput extends IdentifierRequired, Saveable { - - java.util.Map getExtensionFields(); - LoadingOptions getLoadingOptions(); - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowStepOutput/id
- *
- * The unique identifier of the workflow parameter to export. *
- */ - - String getId(); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepOutputImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepOutputImpl.java deleted file mode 100644 index 76ba950b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/WorkflowStepOutputImpl.java +++ /dev/null @@ -1,128 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions; -import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder; -import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl; -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -/** -* Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowStepOutput
- Associate an output parameter of the underlying process with a workflow - parameter. The workflow parameter (given in the `id` field) be may be used - as a `source` to connect with input parameters of other workflow steps, or - with an output parameter of the process. - - A unique identifier for this workflow output parameter. This is - the identifier to use in the `source` field of `WorkflowStepInput` - to connect the output value to downstream parameters. -
- */ -public class WorkflowStepOutputImpl extends SaveableImpl implements WorkflowStepOutput { - private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build(); - private java.util.Map extensionFields_ = - new java.util.HashMap(); - public LoadingOptions getLoadingOptions() { - return this.loadingOptions_; - } - public java.util.Map getExtensionFields() { - return this.extensionFields_; - } - - private String id; - - /** - * Getter for property https://w3id.org/cwl/cwl#WorkflowStepOutput/id
- *
- * The unique identifier of the workflow parameter to export. *
- */ - - public String getId() { - return this.id; - } - - /** - * Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of WorkflowStepOutputImpl. - * - * @param __doc_ Document fragment to load this record object from (presumably a - {@link java.util.Map}). - * @param __baseUri_ Base URI to generate child document IDs against. - * @param __loadingOptions Context for loading URIs and populating objects. - * @param __docRoot_ ID at this position in the document (if available) (maybe?) - * @throws ValidationException If the document fragment is not a {@link java.util.Map} - * or validation of fields fails. - */ - public WorkflowStepOutputImpl( - final Object __doc_, - final String __baseUri_, - LoadingOptions __loadingOptions, - final String __docRoot_) { - super(__doc_, __baseUri_, __loadingOptions, __docRoot_); - // Prefix plumbing variables with '__' to reduce likelihood of collision with - // generated names. - String __baseUri = __baseUri_; - String __docRoot = __docRoot_; - if (!(__doc_ instanceof java.util.Map)) { - throw new ValidationException("WorkflowStepOutputImpl called on non-map"); - } - final java.util.Map __doc = (java.util.Map) __doc_; - final java.util.List __errors = - new java.util.ArrayList(); - if (__loadingOptions != null) { - this.loadingOptions_ = __loadingOptions; - } - String id; - - if (__doc.containsKey("id")) { - try { - id = - LoaderInstances - .uri_StringInstance_True_False_None_None - .loadField(__doc.get("id"), __baseUri, __loadingOptions); - } catch (ValidationException e) { - id = null; // won't be used but prevents compiler from complaining. - final String __message = "the `id` field is not valid because:"; - __errors.add(new ValidationException(__message, e)); - } - - } else { - id = null; - } - - if (id == null) { - if (__docRoot != null) { - id = __docRoot; - } else { - throw new ValidationException("Missing id"); - } - } - __baseUri = (String) id; - if (!__errors.isEmpty()) { - throw new ValidationException("Trying 'RecordField'", __errors); - } - this.id = (String) id; - for (String field:__doc.keySet()) { - if (!attrs.contains(field)) { - if (field.contains(":")) { - String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null); - extensionFields_.put(expanded_field, __doc.get(field)); - } - } - } - } - private java.util.List attrs = java.util.Arrays.asList("id"); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Workflow_class.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/Workflow_class.java deleted file mode 100644 index 41c06b69..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/Workflow_class.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum Workflow_class { - WORKFLOW("Workflow"); - - private static String[] symbols = new String[] {"Workflow"}; - private String docVal; - - private Workflow_class(final String docVal) { - this.docVal = docVal; - } - - public static Workflow_class fromDocumentVal(final String docVal) { - for(final Workflow_class val : Workflow_class.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", Workflow_class.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/package.html b/src/main/java/org/commonwl/cwlsdk/cwl1_2/package.html deleted file mode 100644 index 1478017f..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/package.html +++ /dev/null @@ -1,4 +0,0 @@ - -Package for the auto-generated Java objects corresponding generated by Schema Salad -for https://w3id.org/cwl/cwl#. - diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/stderr.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/stderr.java deleted file mode 100644 index c46c73ab..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/stderr.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum stderr { - STDERR("stderr"); - - private static String[] symbols = new String[] {"stderr"}; - private String docVal; - - private stderr(final String docVal) { - this.docVal = docVal; - } - - public static stderr fromDocumentVal(final String docVal) { - for(final stderr val : stderr.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", stderr.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/stdin.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/stdin.java deleted file mode 100644 index 7d3bf755..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/stdin.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum stdin { - STDIN("stdin"); - - private static String[] symbols = new String[] {"stdin"}; - private String docVal; - - private stdin(final String docVal) { - this.docVal = docVal; - } - - public static stdin fromDocumentVal(final String docVal) { - for(final stdin val : stdin.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", stdin.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/stdout.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/stdout.java deleted file mode 100644 index a5126184..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/stdout.java +++ /dev/null @@ -1,37 +0,0 @@ -// Copyright Common Workflow Language project contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package org.commonwl.cwlsdk.cwl1_2; - -import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException; - -public enum stdout { - STDOUT("stdout"); - - private static String[] symbols = new String[] {"stdout"}; - private String docVal; - - private stdout(final String docVal) { - this.docVal = docVal; - } - - public static stdout fromDocumentVal(final String docVal) { - for(final stdout val : stdout.values()) { - if(val.docVal.equals(docVal)) { - return val; - } - } - throw new ValidationException(String.format("Expected one of %s", stdout.symbols, docVal)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/AnyLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/AnyLoader.java deleted file mode 100644 index 60b61a4e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/AnyLoader.java +++ /dev/null @@ -1,15 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -public class AnyLoader implements Loader { - - public Object load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - if (doc == null) { - throw new ValidationException("Expected non-null"); - } - return doc; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/ArrayLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/ArrayLoader.java deleted file mode 100644 index 9b06396a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/ArrayLoader.java +++ /dev/null @@ -1,43 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.ArrayList; -import java.util.List; - -public class ArrayLoader implements Loader> { - private final Loader itemLoader; - - public ArrayLoader(Loader itemLoader) { - this.itemLoader = itemLoader; - } - - public List load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - final List docList = (List) Loader.validateOfJavaType(List.class, doc); - final List r = new ArrayList(); - final List loaders = new ArrayList(); - loaders.add(this); - loaders.add(this.itemLoader); - final UnionLoader unionLoader = new UnionLoader(loaders); - final List errors = new ArrayList(); - for (final Object el : docList) { - try { - final Object loadedField = unionLoader.loadField(el, baseUri, loadingOptions); - final boolean flatten = !"@list".equals(loadingOptions.container); - if (flatten && loadedField instanceof List) { - r.addAll((List) loadedField); - } else { - r.add((T) loadedField); - } - } catch (final ValidationException e) { - errors.add(e); - } - } - if (!errors.isEmpty()) { - throw new ValidationException("", errors); - } - return r; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/ConstantMaps.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/ConstantMaps.java deleted file mode 100644 index 1fa48348..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/ConstantMaps.java +++ /dev/null @@ -1,317 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.HashMap; - -public class ConstantMaps { - // declare as HashMap for clone(). - public static final HashMap vocab = new HashMap(); - public static final HashMap rvocab = new HashMap(); - - static { - vocab.put("Any", "https://w3id.org/cwl/salad#Any"); - vocab.put("ArraySchema", "https://w3id.org/cwl/salad#ArraySchema"); - vocab.put("CUDARequirement", "http://commonwl.org/cwltool#CUDARequirement"); - vocab.put("CWLArraySchema", "https://w3id.org/cwl/cwl#CWLArraySchema"); - vocab.put("CWLInputFile", "https://w3id.org/cwl/cwl#CWLInputFile"); - vocab.put("CWLObjectType", "https://w3id.org/cwl/cwl#CWLObjectType"); - vocab.put("CWLRecordField", "https://w3id.org/cwl/cwl#CWLRecordField"); - vocab.put("CWLRecordSchema", "https://w3id.org/cwl/cwl#CWLRecordSchema"); - vocab.put("CWLType", "https://w3id.org/cwl/cwl#CWLType"); - vocab.put("CWLVersion", "https://w3id.org/cwl/cwl#CWLVersion"); - vocab.put("CommandInputArraySchema", "https://w3id.org/cwl/cwl#CommandInputArraySchema"); - vocab.put("CommandInputEnumSchema", "https://w3id.org/cwl/cwl#CommandInputEnumSchema"); - vocab.put("CommandInputParameter", "https://w3id.org/cwl/cwl#CommandInputParameter"); - vocab.put("CommandInputRecordField", "https://w3id.org/cwl/cwl#CommandInputRecordField"); - vocab.put("CommandInputRecordSchema", "https://w3id.org/cwl/cwl#CommandInputRecordSchema"); - vocab.put("CommandInputSchema", "https://w3id.org/cwl/cwl#CommandInputSchema"); - vocab.put("CommandLineBindable", "https://w3id.org/cwl/cwl#CommandLineBindable"); - vocab.put("CommandLineBinding", "https://w3id.org/cwl/cwl#CommandLineBinding"); - vocab.put("CommandLineTool", "CommandLineTool"); - vocab.put("CommandOutputArraySchema", "https://w3id.org/cwl/cwl#CommandOutputArraySchema"); - vocab.put("CommandOutputBinding", "https://w3id.org/cwl/cwl#CommandOutputBinding"); - vocab.put("CommandOutputEnumSchema", "https://w3id.org/cwl/cwl#CommandOutputEnumSchema"); - vocab.put("CommandOutputParameter", "https://w3id.org/cwl/cwl#CommandOutputParameter"); - vocab.put("CommandOutputRecordField", "https://w3id.org/cwl/cwl#CommandOutputRecordField"); - vocab.put("CommandOutputRecordSchema", "https://w3id.org/cwl/cwl#CommandOutputRecordSchema"); - vocab.put("Directory", "Directory"); - vocab.put("Dirent", "https://w3id.org/cwl/cwl#Dirent"); - vocab.put("DockerRequirement", "DockerRequirement"); - vocab.put("Documented", "https://w3id.org/cwl/salad#Documented"); - vocab.put("EnumSchema", "https://w3id.org/cwl/salad#EnumSchema"); - vocab.put("EnvVarRequirement", "EnvVarRequirement"); - vocab.put("EnvironmentDef", "https://w3id.org/cwl/cwl#EnvironmentDef"); - vocab.put("Expression", "https://w3id.org/cwl/cwl#Expression"); - vocab.put("ExpressionPlaceholder", "https://w3id.org/cwl/cwl#ExpressionPlaceholder"); - vocab.put("ExpressionTool", "ExpressionTool"); - vocab.put("ExpressionToolOutputParameter", "https://w3id.org/cwl/cwl#ExpressionToolOutputParameter"); - vocab.put("FieldBase", "https://w3id.org/cwl/cwl#FieldBase"); - vocab.put("File", "File"); - vocab.put("IOSchema", "https://w3id.org/cwl/cwl#IOSchema"); - vocab.put("Identified", "https://w3id.org/cwl/cwl#Identified"); - vocab.put("IdentifierRequired", "https://w3id.org/cwl/cwl#IdentifierRequired"); - vocab.put("InitialWorkDirRequirement", "InitialWorkDirRequirement"); - vocab.put("InlineJavascriptRequirement", "InlineJavascriptRequirement"); - vocab.put("InplaceUpdateRequirement", "InplaceUpdateRequirement"); - vocab.put("InputArraySchema", "https://w3id.org/cwl/cwl#InputArraySchema"); - vocab.put("InputBinding", "https://w3id.org/cwl/cwl#InputBinding"); - vocab.put("InputEnumSchema", "https://w3id.org/cwl/cwl#InputEnumSchema"); - vocab.put("InputFormat", "https://w3id.org/cwl/cwl#InputFormat"); - vocab.put("InputParameter", "https://w3id.org/cwl/cwl#InputParameter"); - vocab.put("InputRecordField", "https://w3id.org/cwl/cwl#InputRecordField"); - vocab.put("InputRecordSchema", "https://w3id.org/cwl/cwl#InputRecordSchema"); - vocab.put("InputSchema", "https://w3id.org/cwl/cwl#InputSchema"); - vocab.put("Labeled", "https://w3id.org/cwl/cwl#Labeled"); - vocab.put("LinkMergeMethod", "https://w3id.org/cwl/cwl#LinkMergeMethod"); - vocab.put("LoadContents", "https://w3id.org/cwl/cwl#LoadContents"); - vocab.put("LoadListingEnum", "https://w3id.org/cwl/cwl#LoadListingEnum"); - vocab.put("LoadListingRequirement", "LoadListingRequirement"); - vocab.put("Loop", "http://commonwl.org/cwltool#Loop"); - vocab.put("LoopInput", "http://commonwl.org/cwltool#LoopInput"); - vocab.put("MPIRequirement", "http://commonwl.org/cwltool#MPIRequirement"); - vocab.put("MapSchema", "https://w3id.org/cwl/salad#MapSchema"); - vocab.put("MultipleInputFeatureRequirement", "MultipleInputFeatureRequirement"); - vocab.put("NetworkAccess", "NetworkAccess"); - vocab.put("Operation", "Operation"); - vocab.put("OperationInputParameter", "https://w3id.org/cwl/cwl#OperationInputParameter"); - vocab.put("OperationOutputParameter", "https://w3id.org/cwl/cwl#OperationOutputParameter"); - vocab.put("OutputArraySchema", "https://w3id.org/cwl/cwl#OutputArraySchema"); - vocab.put("OutputEnumSchema", "https://w3id.org/cwl/cwl#OutputEnumSchema"); - vocab.put("OutputFormat", "https://w3id.org/cwl/cwl#OutputFormat"); - vocab.put("OutputParameter", "https://w3id.org/cwl/cwl#OutputParameter"); - vocab.put("OutputRecordField", "https://w3id.org/cwl/cwl#OutputRecordField"); - vocab.put("OutputRecordSchema", "https://w3id.org/cwl/cwl#OutputRecordSchema"); - vocab.put("OutputSchema", "https://w3id.org/cwl/cwl#OutputSchema"); - vocab.put("Parameter", "https://w3id.org/cwl/cwl#Parameter"); - vocab.put("PickValueMethod", "https://w3id.org/cwl/cwl#PickValueMethod"); - vocab.put("PrimitiveType", "https://w3id.org/cwl/salad#PrimitiveType"); - vocab.put("Process", "https://w3id.org/cwl/cwl#Process"); - vocab.put("ProcessGenerator", "http://commonwl.org/cwltool#ProcessGenerator"); - vocab.put("ProcessRequirement", "https://w3id.org/cwl/cwl#ProcessRequirement"); - vocab.put("RecordField", "https://w3id.org/cwl/salad#RecordField"); - vocab.put("RecordSchema", "https://w3id.org/cwl/salad#RecordSchema"); - vocab.put("ResourceRequirement", "ResourceRequirement"); - vocab.put("ScatterFeatureRequirement", "ScatterFeatureRequirement"); - vocab.put("ScatterMethod", "https://w3id.org/cwl/cwl#ScatterMethod"); - vocab.put("SchemaDefRequirement", "SchemaDefRequirement"); - vocab.put("SecondaryFileSchema", "https://w3id.org/cwl/cwl#SecondaryFileSchema"); - vocab.put("Secrets", "http://commonwl.org/cwltool#Secrets"); - vocab.put("ShellCommandRequirement", "ShellCommandRequirement"); - vocab.put("ShmSize", "http://commonwl.org/cwltool#ShmSize"); - vocab.put("Sink", "https://w3id.org/cwl/cwl#Sink"); - vocab.put("SoftwarePackage", "https://w3id.org/cwl/cwl#SoftwarePackage"); - vocab.put("SoftwareRequirement", "SoftwareRequirement"); - vocab.put("StepInputExpressionRequirement", "StepInputExpressionRequirement"); - vocab.put("SubworkflowFeatureRequirement", "SubworkflowFeatureRequirement"); - vocab.put("ToolTimeLimit", "ToolTimeLimit"); - vocab.put("UnionSchema", "https://w3id.org/cwl/salad#UnionSchema"); - vocab.put("WorkReuse", "WorkReuse"); - vocab.put("Workflow", "Workflow"); - vocab.put("WorkflowInputParameter", "https://w3id.org/cwl/cwl#WorkflowInputParameter"); - vocab.put("WorkflowOutputParameter", "https://w3id.org/cwl/cwl#WorkflowOutputParameter"); - vocab.put("WorkflowStep", "https://w3id.org/cwl/cwl#WorkflowStep"); - vocab.put("WorkflowStepInput", "https://w3id.org/cwl/cwl#WorkflowStepInput"); - vocab.put("WorkflowStepOutput", "https://w3id.org/cwl/cwl#WorkflowStepOutput"); - vocab.put("all", "all"); - vocab.put("all_non_null", "https://w3id.org/cwl/cwl#PickValueMethod/all_non_null"); - vocab.put("array", "array"); - vocab.put("boolean", "http://www.w3.org/2001/XMLSchema#boolean"); - vocab.put("deep_listing", "https://w3id.org/cwl/cwl#LoadListingEnum/deep_listing"); - vocab.put("dotproduct", "https://w3id.org/cwl/cwl#ScatterMethod/dotproduct"); - vocab.put("double", "http://www.w3.org/2001/XMLSchema#double"); - vocab.put("draft-2", "https://w3id.org/cwl/cwl#draft-2"); - vocab.put("draft-3", "https://w3id.org/cwl/cwl#draft-3"); - vocab.put("draft-3.dev1", "https://w3id.org/cwl/cwl#draft-3.dev1"); - vocab.put("draft-3.dev2", "https://w3id.org/cwl/cwl#draft-3.dev2"); - vocab.put("draft-3.dev3", "https://w3id.org/cwl/cwl#draft-3.dev3"); - vocab.put("draft-3.dev4", "https://w3id.org/cwl/cwl#draft-3.dev4"); - vocab.put("draft-3.dev5", "https://w3id.org/cwl/cwl#draft-3.dev5"); - vocab.put("draft-4.dev1", "https://w3id.org/cwl/cwl#draft-4.dev1"); - vocab.put("draft-4.dev2", "https://w3id.org/cwl/cwl#draft-4.dev2"); - vocab.put("draft-4.dev3", "https://w3id.org/cwl/cwl#draft-4.dev3"); - vocab.put("enum", "enum"); - vocab.put("first_non_null", "https://w3id.org/cwl/cwl#PickValueMethod/first_non_null"); - vocab.put("flat_crossproduct", "https://w3id.org/cwl/cwl#ScatterMethod/flat_crossproduct"); - vocab.put("float", "http://www.w3.org/2001/XMLSchema#float"); - vocab.put("int", "http://www.w3.org/2001/XMLSchema#int"); - vocab.put("last", "last"); - vocab.put("long", "http://www.w3.org/2001/XMLSchema#long"); - vocab.put("map", "map"); - vocab.put("merge_flattened", "https://w3id.org/cwl/cwl#LinkMergeMethod/merge_flattened"); - vocab.put("merge_nested", "https://w3id.org/cwl/cwl#LinkMergeMethod/merge_nested"); - vocab.put("nested_crossproduct", "https://w3id.org/cwl/cwl#ScatterMethod/nested_crossproduct"); - vocab.put("no_listing", "https://w3id.org/cwl/cwl#LoadListingEnum/no_listing"); - vocab.put("null", "https://w3id.org/cwl/salad#null"); - vocab.put("record", "record"); - vocab.put("shallow_listing", "https://w3id.org/cwl/cwl#LoadListingEnum/shallow_listing"); - vocab.put("stderr", "https://w3id.org/cwl/cwl#stderr"); - vocab.put("stdin", "https://w3id.org/cwl/cwl#stdin"); - vocab.put("stdout", "https://w3id.org/cwl/cwl#stdout"); - vocab.put("string", "http://www.w3.org/2001/XMLSchema#string"); - vocab.put("the_only_non_null", "https://w3id.org/cwl/cwl#PickValueMethod/the_only_non_null"); - vocab.put("union", "union"); - vocab.put("v1.0", "https://w3id.org/cwl/cwl#v1.0"); - vocab.put("v1.0.dev4", "https://w3id.org/cwl/cwl#v1.0.dev4"); - vocab.put("v1.1", "https://w3id.org/cwl/cwl#v1.1"); - vocab.put("v1.1.0-dev1", "https://w3id.org/cwl/cwl#v1.1.0-dev1"); - vocab.put("v1.2", "https://w3id.org/cwl/cwl#v1.2"); - vocab.put("v1.2.0-dev1", "https://w3id.org/cwl/cwl#v1.2.0-dev1"); - vocab.put("v1.2.0-dev2", "https://w3id.org/cwl/cwl#v1.2.0-dev2"); - vocab.put("v1.2.0-dev3", "https://w3id.org/cwl/cwl#v1.2.0-dev3"); - vocab.put("v1.2.0-dev4", "https://w3id.org/cwl/cwl#v1.2.0-dev4"); - vocab.put("v1.2.0-dev5", "https://w3id.org/cwl/cwl#v1.2.0-dev5"); - - - rvocab.put("https://w3id.org/cwl/salad#Any", "Any"); - rvocab.put("https://w3id.org/cwl/salad#ArraySchema", "ArraySchema"); - rvocab.put("http://commonwl.org/cwltool#CUDARequirement", "CUDARequirement"); - rvocab.put("https://w3id.org/cwl/cwl#CWLArraySchema", "CWLArraySchema"); - rvocab.put("https://w3id.org/cwl/cwl#CWLInputFile", "CWLInputFile"); - rvocab.put("https://w3id.org/cwl/cwl#CWLObjectType", "CWLObjectType"); - rvocab.put("https://w3id.org/cwl/cwl#CWLRecordField", "CWLRecordField"); - rvocab.put("https://w3id.org/cwl/cwl#CWLRecordSchema", "CWLRecordSchema"); - rvocab.put("https://w3id.org/cwl/cwl#CWLType", "CWLType"); - rvocab.put("https://w3id.org/cwl/cwl#CWLVersion", "CWLVersion"); - rvocab.put("https://w3id.org/cwl/cwl#CommandInputArraySchema", "CommandInputArraySchema"); - rvocab.put("https://w3id.org/cwl/cwl#CommandInputEnumSchema", "CommandInputEnumSchema"); - rvocab.put("https://w3id.org/cwl/cwl#CommandInputParameter", "CommandInputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#CommandInputRecordField", "CommandInputRecordField"); - rvocab.put("https://w3id.org/cwl/cwl#CommandInputRecordSchema", "CommandInputRecordSchema"); - rvocab.put("https://w3id.org/cwl/cwl#CommandInputSchema", "CommandInputSchema"); - rvocab.put("https://w3id.org/cwl/cwl#CommandLineBindable", "CommandLineBindable"); - rvocab.put("https://w3id.org/cwl/cwl#CommandLineBinding", "CommandLineBinding"); - rvocab.put("CommandLineTool", "CommandLineTool"); - rvocab.put("https://w3id.org/cwl/cwl#CommandOutputArraySchema", "CommandOutputArraySchema"); - rvocab.put("https://w3id.org/cwl/cwl#CommandOutputBinding", "CommandOutputBinding"); - rvocab.put("https://w3id.org/cwl/cwl#CommandOutputEnumSchema", "CommandOutputEnumSchema"); - rvocab.put("https://w3id.org/cwl/cwl#CommandOutputParameter", "CommandOutputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#CommandOutputRecordField", "CommandOutputRecordField"); - rvocab.put("https://w3id.org/cwl/cwl#CommandOutputRecordSchema", "CommandOutputRecordSchema"); - rvocab.put("Directory", "Directory"); - rvocab.put("https://w3id.org/cwl/cwl#Dirent", "Dirent"); - rvocab.put("DockerRequirement", "DockerRequirement"); - rvocab.put("https://w3id.org/cwl/salad#Documented", "Documented"); - rvocab.put("https://w3id.org/cwl/salad#EnumSchema", "EnumSchema"); - rvocab.put("EnvVarRequirement", "EnvVarRequirement"); - rvocab.put("https://w3id.org/cwl/cwl#EnvironmentDef", "EnvironmentDef"); - rvocab.put("https://w3id.org/cwl/cwl#Expression", "Expression"); - rvocab.put("https://w3id.org/cwl/cwl#ExpressionPlaceholder", "ExpressionPlaceholder"); - rvocab.put("ExpressionTool", "ExpressionTool"); - rvocab.put("https://w3id.org/cwl/cwl#ExpressionToolOutputParameter", "ExpressionToolOutputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#FieldBase", "FieldBase"); - rvocab.put("File", "File"); - rvocab.put("https://w3id.org/cwl/cwl#IOSchema", "IOSchema"); - rvocab.put("https://w3id.org/cwl/cwl#Identified", "Identified"); - rvocab.put("https://w3id.org/cwl/cwl#IdentifierRequired", "IdentifierRequired"); - rvocab.put("InitialWorkDirRequirement", "InitialWorkDirRequirement"); - rvocab.put("InlineJavascriptRequirement", "InlineJavascriptRequirement"); - rvocab.put("InplaceUpdateRequirement", "InplaceUpdateRequirement"); - rvocab.put("https://w3id.org/cwl/cwl#InputArraySchema", "InputArraySchema"); - rvocab.put("https://w3id.org/cwl/cwl#InputBinding", "InputBinding"); - rvocab.put("https://w3id.org/cwl/cwl#InputEnumSchema", "InputEnumSchema"); - rvocab.put("https://w3id.org/cwl/cwl#InputFormat", "InputFormat"); - rvocab.put("https://w3id.org/cwl/cwl#InputParameter", "InputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#InputRecordField", "InputRecordField"); - rvocab.put("https://w3id.org/cwl/cwl#InputRecordSchema", "InputRecordSchema"); - rvocab.put("https://w3id.org/cwl/cwl#InputSchema", "InputSchema"); - rvocab.put("https://w3id.org/cwl/cwl#Labeled", "Labeled"); - rvocab.put("https://w3id.org/cwl/cwl#LinkMergeMethod", "LinkMergeMethod"); - rvocab.put("https://w3id.org/cwl/cwl#LoadContents", "LoadContents"); - rvocab.put("https://w3id.org/cwl/cwl#LoadListingEnum", "LoadListingEnum"); - rvocab.put("LoadListingRequirement", "LoadListingRequirement"); - rvocab.put("http://commonwl.org/cwltool#Loop", "Loop"); - rvocab.put("http://commonwl.org/cwltool#LoopInput", "LoopInput"); - rvocab.put("http://commonwl.org/cwltool#MPIRequirement", "MPIRequirement"); - rvocab.put("https://w3id.org/cwl/salad#MapSchema", "MapSchema"); - rvocab.put("MultipleInputFeatureRequirement", "MultipleInputFeatureRequirement"); - rvocab.put("NetworkAccess", "NetworkAccess"); - rvocab.put("Operation", "Operation"); - rvocab.put("https://w3id.org/cwl/cwl#OperationInputParameter", "OperationInputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#OperationOutputParameter", "OperationOutputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#OutputArraySchema", "OutputArraySchema"); - rvocab.put("https://w3id.org/cwl/cwl#OutputEnumSchema", "OutputEnumSchema"); - rvocab.put("https://w3id.org/cwl/cwl#OutputFormat", "OutputFormat"); - rvocab.put("https://w3id.org/cwl/cwl#OutputParameter", "OutputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#OutputRecordField", "OutputRecordField"); - rvocab.put("https://w3id.org/cwl/cwl#OutputRecordSchema", "OutputRecordSchema"); - rvocab.put("https://w3id.org/cwl/cwl#OutputSchema", "OutputSchema"); - rvocab.put("https://w3id.org/cwl/cwl#Parameter", "Parameter"); - rvocab.put("https://w3id.org/cwl/cwl#PickValueMethod", "PickValueMethod"); - rvocab.put("https://w3id.org/cwl/salad#PrimitiveType", "PrimitiveType"); - rvocab.put("https://w3id.org/cwl/cwl#Process", "Process"); - rvocab.put("http://commonwl.org/cwltool#ProcessGenerator", "ProcessGenerator"); - rvocab.put("https://w3id.org/cwl/cwl#ProcessRequirement", "ProcessRequirement"); - rvocab.put("https://w3id.org/cwl/salad#RecordField", "RecordField"); - rvocab.put("https://w3id.org/cwl/salad#RecordSchema", "RecordSchema"); - rvocab.put("ResourceRequirement", "ResourceRequirement"); - rvocab.put("ScatterFeatureRequirement", "ScatterFeatureRequirement"); - rvocab.put("https://w3id.org/cwl/cwl#ScatterMethod", "ScatterMethod"); - rvocab.put("SchemaDefRequirement", "SchemaDefRequirement"); - rvocab.put("https://w3id.org/cwl/cwl#SecondaryFileSchema", "SecondaryFileSchema"); - rvocab.put("http://commonwl.org/cwltool#Secrets", "Secrets"); - rvocab.put("ShellCommandRequirement", "ShellCommandRequirement"); - rvocab.put("http://commonwl.org/cwltool#ShmSize", "ShmSize"); - rvocab.put("https://w3id.org/cwl/cwl#Sink", "Sink"); - rvocab.put("https://w3id.org/cwl/cwl#SoftwarePackage", "SoftwarePackage"); - rvocab.put("SoftwareRequirement", "SoftwareRequirement"); - rvocab.put("StepInputExpressionRequirement", "StepInputExpressionRequirement"); - rvocab.put("SubworkflowFeatureRequirement", "SubworkflowFeatureRequirement"); - rvocab.put("ToolTimeLimit", "ToolTimeLimit"); - rvocab.put("https://w3id.org/cwl/salad#UnionSchema", "UnionSchema"); - rvocab.put("WorkReuse", "WorkReuse"); - rvocab.put("Workflow", "Workflow"); - rvocab.put("https://w3id.org/cwl/cwl#WorkflowInputParameter", "WorkflowInputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#WorkflowOutputParameter", "WorkflowOutputParameter"); - rvocab.put("https://w3id.org/cwl/cwl#WorkflowStep", "WorkflowStep"); - rvocab.put("https://w3id.org/cwl/cwl#WorkflowStepInput", "WorkflowStepInput"); - rvocab.put("https://w3id.org/cwl/cwl#WorkflowStepOutput", "WorkflowStepOutput"); - rvocab.put("all", "all"); - rvocab.put("https://w3id.org/cwl/cwl#PickValueMethod/all_non_null", "all_non_null"); - rvocab.put("array", "array"); - rvocab.put("http://www.w3.org/2001/XMLSchema#boolean", "boolean"); - rvocab.put("https://w3id.org/cwl/cwl#LoadListingEnum/deep_listing", "deep_listing"); - rvocab.put("https://w3id.org/cwl/cwl#ScatterMethod/dotproduct", "dotproduct"); - rvocab.put("http://www.w3.org/2001/XMLSchema#double", "double"); - rvocab.put("https://w3id.org/cwl/cwl#draft-2", "draft-2"); - rvocab.put("https://w3id.org/cwl/cwl#draft-3", "draft-3"); - rvocab.put("https://w3id.org/cwl/cwl#draft-3.dev1", "draft-3.dev1"); - rvocab.put("https://w3id.org/cwl/cwl#draft-3.dev2", "draft-3.dev2"); - rvocab.put("https://w3id.org/cwl/cwl#draft-3.dev3", "draft-3.dev3"); - rvocab.put("https://w3id.org/cwl/cwl#draft-3.dev4", "draft-3.dev4"); - rvocab.put("https://w3id.org/cwl/cwl#draft-3.dev5", "draft-3.dev5"); - rvocab.put("https://w3id.org/cwl/cwl#draft-4.dev1", "draft-4.dev1"); - rvocab.put("https://w3id.org/cwl/cwl#draft-4.dev2", "draft-4.dev2"); - rvocab.put("https://w3id.org/cwl/cwl#draft-4.dev3", "draft-4.dev3"); - rvocab.put("enum", "enum"); - rvocab.put("https://w3id.org/cwl/cwl#PickValueMethod/first_non_null", "first_non_null"); - rvocab.put("https://w3id.org/cwl/cwl#ScatterMethod/flat_crossproduct", "flat_crossproduct"); - rvocab.put("http://www.w3.org/2001/XMLSchema#float", "float"); - rvocab.put("http://www.w3.org/2001/XMLSchema#int", "int"); - rvocab.put("last", "last"); - rvocab.put("http://www.w3.org/2001/XMLSchema#long", "long"); - rvocab.put("map", "map"); - rvocab.put("https://w3id.org/cwl/cwl#LinkMergeMethod/merge_flattened", "merge_flattened"); - rvocab.put("https://w3id.org/cwl/cwl#LinkMergeMethod/merge_nested", "merge_nested"); - rvocab.put("https://w3id.org/cwl/cwl#ScatterMethod/nested_crossproduct", "nested_crossproduct"); - rvocab.put("https://w3id.org/cwl/cwl#LoadListingEnum/no_listing", "no_listing"); - rvocab.put("https://w3id.org/cwl/salad#null", "null"); - rvocab.put("record", "record"); - rvocab.put("https://w3id.org/cwl/cwl#LoadListingEnum/shallow_listing", "shallow_listing"); - rvocab.put("https://w3id.org/cwl/cwl#stderr", "stderr"); - rvocab.put("https://w3id.org/cwl/cwl#stdin", "stdin"); - rvocab.put("https://w3id.org/cwl/cwl#stdout", "stdout"); - rvocab.put("http://www.w3.org/2001/XMLSchema#string", "string"); - rvocab.put("https://w3id.org/cwl/cwl#PickValueMethod/the_only_non_null", "the_only_non_null"); - rvocab.put("union", "union"); - rvocab.put("https://w3id.org/cwl/cwl#v1.0", "v1.0"); - rvocab.put("https://w3id.org/cwl/cwl#v1.0.dev4", "v1.0.dev4"); - rvocab.put("https://w3id.org/cwl/cwl#v1.1", "v1.1"); - rvocab.put("https://w3id.org/cwl/cwl#v1.1.0-dev1", "v1.1.0-dev1"); - rvocab.put("https://w3id.org/cwl/cwl#v1.2", "v1.2"); - rvocab.put("https://w3id.org/cwl/cwl#v1.2.0-dev1", "v1.2.0-dev1"); - rvocab.put("https://w3id.org/cwl/cwl#v1.2.0-dev2", "v1.2.0-dev2"); - rvocab.put("https://w3id.org/cwl/cwl#v1.2.0-dev3", "v1.2.0-dev3"); - rvocab.put("https://w3id.org/cwl/cwl#v1.2.0-dev4", "v1.2.0-dev4"); - rvocab.put("https://w3id.org/cwl/cwl#v1.2.0-dev5", "v1.2.0-dev5"); - - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/DefaultFetcher.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/DefaultFetcher.java deleted file mode 100644 index 46e4ed83..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/DefaultFetcher.java +++ /dev/null @@ -1,48 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.io.IOException; -import java.net.URI; -import java.util.Arrays; -import java.util.Scanner; - -public class DefaultFetcher implements Fetcher { - - public String urlJoin(final String baseUrl, final String url) { - if (url.startsWith("_:")) { - return url; - } - - final URI baseUri = Uris.toUri(baseUrl); - final URI uri = Uris.toUri(url); - if (baseUri.getScheme() != null - && !baseUri.getScheme().equals("file") - && "file".equals(uri.getScheme())) { - throw new ValidationException( - String.format( - "Not resolving potential remote exploit %s from base %s".format(url, baseUrl))); - } - String result = baseUri.resolve(uri).toString(); - if (result.startsWith("file:")) { - // Well this is gross - needed for http as well? - result = "file://" + result.substring("file:".length()); - } - return result; - } - - public String fetchText(final String url) { - final URI uri = Uris.toUri(url); - final String scheme = uri.getScheme(); - if (Arrays.asList("http", "https", "file").contains(scheme)) { - Scanner scanner; - try { - scanner = new Scanner(uri.toURL().openStream(), "UTF-8").useDelimiter("\\A"); - } catch (IOException e) { - throw new ValidationException("Error fetching %s: %s.".format(url, e)); - } - String result = scanner.next(); - scanner.close(); - return result; - } - throw new ValidationException("Unsupported scheme in URL: %s".format(url)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/EnumLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/EnumLoader.java deleted file mode 100644 index d93d67fe..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/EnumLoader.java +++ /dev/null @@ -1,33 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.lang.reflect.Method; -import java.lang.ReflectiveOperationException; -import java.util.Arrays; -import java.util.List; - -public class EnumLoader implements Loader{ - private final Class symbolEnumClass; - - public EnumLoader(final Class symbolEnumClass) { - this.symbolEnumClass = symbolEnumClass; - } - - public T load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - final String docString = Loader.validateOfJavaType(String.class, doc); - try { - final Method m = symbolEnumClass.getMethod("fromDocumentVal", String.class); - final T val = (T) m.invoke(null, docString); - return val; - } catch (final ReflectiveOperationException e) { - final Throwable cause = e.getCause(); - if (cause instanceof RuntimeException) { - throw (RuntimeException) cause; - } - throw new RuntimeException(e); - } - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/ExpressionLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/ExpressionLoader.java deleted file mode 100644 index 10cd2cdf..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/ExpressionLoader.java +++ /dev/null @@ -1,19 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -public class ExpressionLoader implements Loader { - - public ExpressionLoader() { - } - - public String load( - final Object doc_, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - if (doc_ instanceof String) { - return (String) doc_; - } else { - throw new ValidationException("Expected a string."); - } - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Fetcher.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Fetcher.java deleted file mode 100644 index 7b6ae32b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Fetcher.java +++ /dev/null @@ -1,8 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -public interface Fetcher { - - public abstract String urlJoin(final String baseUrl, final String url); - - public abstract String fetchText(final String url); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/IdMapLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/IdMapLoader.java deleted file mode 100644 index d561cf0b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/IdMapLoader.java +++ /dev/null @@ -1,51 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.TreeSet; - -public class IdMapLoader implements Loader { - private final Loader innerLoader; - private final String mapSubject; - private final String mapPredicate; - - public IdMapLoader( - final Loader innerLoader, final String mapSubject, final String mapPredicate) { - this.innerLoader = innerLoader; - this.mapSubject = mapSubject; - this.mapPredicate = mapPredicate; - } - - public T load( - final Object doc_, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - Object doc = doc_; - if (doc instanceof Map) { - final Map docMap = (Map) doc; - final List asList = new ArrayList(); - for (final String key : docMap.keySet()) { - final Object el = docMap.get(key); - if (el instanceof Map) { - final Map v2 = new HashMap((Map) el); - v2.put(this.mapSubject, key); - asList.add(v2); - } else { - if (this.mapPredicate != null) { - final Map v3 = new HashMap(); - v3.put(this.mapPredicate, el); - v3.put(this.mapSubject, key); - asList.add(v3); - } else { - throw new ValidationException("No mapPredicate"); - } - } - } - doc = asList; - } - return this.innerLoader.load(doc, baseUri, loadingOptions); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Loader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Loader.java deleted file mode 100644 index 01f45d30..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Loader.java +++ /dev/null @@ -1,125 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -public interface Loader { - - T load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot); - - default T load(final Object doc, final String baseUri, final LoadingOptions loadingOptions) { - return load(doc, baseUri, loadingOptions, null); - } - - default T documentLoad( - final String doc, final String baseUri, final LoadingOptions loadingOptions) { - return load(doc, baseUri, loadingOptions); - } - - default T documentLoad( - final Map doc_, final String baseUri_, final LoadingOptions loadingOptions_) { - Map doc = doc_; - LoadingOptions loadingOptions = loadingOptions_; - if (doc.containsKey("$namespaces")) { - final Map namespaces = (Map) doc.get("$namespaces"); - loadingOptions = - new LoadingOptionsBuilder().copiedFrom(loadingOptions).setNamespaces(namespaces).build(); - doc = copyWithoutKey(doc, "$namespaces"); - } - String baseUri = baseUri_; - if (doc.containsKey("$base")) { - baseUri = (String) doc.get("$base"); - } - if (doc.containsKey("$graph")) { - return load(doc.get("$graph"), baseUri, loadingOptions); - } else { - return load(doc, baseUri, loadingOptions, baseUri); - } - } - - default T documentLoad( - final List doc, final String baseUri, final LoadingOptions loadingOptions) { - return load(doc, baseUri, loadingOptions); - } - - default T documentLoadByUrl(final String url, final LoadingOptions loadingOptions) { - if (loadingOptions.idx.containsKey(url)) { - Object result = loadingOptions.idx.get(url); - if (result instanceof String) { - return documentLoad((String) result, url, loadingOptions); - } else if (result instanceof Map) { - return documentLoad((Map) result, url, loadingOptions); - } - return load(result, url, loadingOptions); - } - - final String text = loadingOptions.fetcher.fetchText(url); - try { - Map resultMap = YamlUtils.mapFromString(text); - loadingOptions.idx.put(url, resultMap); - final LoadingOptionsBuilder urlLoadingOptions = - new LoadingOptionsBuilder().copiedFrom(loadingOptions).setFileUri(url); - return documentLoad(resultMap, url, urlLoadingOptions.build()); - } catch (ClassCastException e) { - List resultList = YamlUtils.listFromString(text); - loadingOptions.idx.put(url, resultList); - final LoadingOptionsBuilder urlLoadingOptions = - new LoadingOptionsBuilder().copiedFrom(loadingOptions).setFileUri(url); - return documentLoad(resultList, url, urlLoadingOptions.build()); - } - } - - default T loadField( - final Object val_, final String baseUri, final LoadingOptions loadingOptions) { - Object val = val_; - if (val instanceof Map) { - Map valMap = (Map) val; - if (valMap.containsKey("$import")) { - if (loadingOptions.fileUri == null) { - throw new ValidationException("Cannot load $import without fileuri"); - } - return documentLoadByUrl( - loadingOptions.fetcher.urlJoin(loadingOptions.fileUri, (String) valMap.get("$import")), - loadingOptions); - } else if (valMap.containsKey("$include")) { - if (loadingOptions.fileUri == null) { - throw new ValidationException("Cannot load $import without fileuri"); - } - val = - loadingOptions.fetcher.fetchText( - loadingOptions.fetcher.urlJoin( - loadingOptions.fileUri, (String) valMap.get("$include"))); - } - } - return load(val, baseUri, loadingOptions); - } - - default Map copyWithoutKey(final Map doc, final String key) { - final Map result = new HashMap(); - for (final Map.Entry entry : doc.entrySet()) { - if (!entry.getKey().equals(key)) { - result.put(entry.getKey(), entry.getValue()); - } - } - return result; - } - - static T validateOfJavaType(final Class clazz, final Object doc) { - if (!clazz.isInstance(doc)) { - String className = "null"; - if (doc != null) { - className = doc.getClass().getName(); - } - final String message = - String.format( - "Expected object with Java type of %s but got %s", clazz.getName(), className); - throw new ValidationException(message); - } - return (T) doc; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/LoaderInstances.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/LoaderInstances.java deleted file mode 100644 index f3bad476..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/LoaderInstances.java +++ /dev/null @@ -1,347 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.List; -import org.commonwl.cwlsdk.cwl1_2.*; - -public class LoaderInstances { - public static Loader StringInstance = new PrimitiveLoader(String.class); - public static Loader IntegerInstance = new PrimitiveLoader(Integer.class); - public static Loader LongInstance = new PrimitiveLoader(Long.class); - public static Loader DoubleInstance = new PrimitiveLoader(Double.class); - public static Loader BooleanInstance = new PrimitiveLoader(Boolean.class); - public static Loader NullInstance = new NullLoader(); - public static Loader AnyInstance = new AnyLoader(); - public static Loader Documented = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.Documented.class, null, null); - public static Loader PrimitiveType = new EnumLoader(PrimitiveType.class); - public static Loader Any = new EnumLoader(Any.class); - public static Loader RecordField = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.RecordFieldImpl.class, null, null); - public static Loader RecordSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.RecordSchemaImpl.class, null, null); - public static Loader EnumSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.EnumSchemaImpl.class, null, null); - public static Loader ArraySchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.ArraySchemaImpl.class, null, null); - public static Loader MapSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.MapSchemaImpl.class, null, null); - public static Loader UnionSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.UnionSchemaImpl.class, null, null); - public static Loader CWLType = new EnumLoader(CWLType.class); - public static Loader CWLArraySchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CWLArraySchemaImpl.class, null, null); - public static Loader CWLRecordField = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CWLRecordFieldImpl.class, null, null); - public static Loader CWLRecordSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CWLRecordSchemaImpl.class, null, null); - public static Loader File = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.FileImpl.class, null, null); - public static Loader Directory = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.DirectoryImpl.class, null, null); - public static Loader CWLObjectType = new UnionLoader(new Loader[] {}); - public static Loader> optional_CWLObjectType = new OptionalLoader(CWLObjectType); - public static Loader>> array_of_optional_CWLObjectType = new ArrayLoader(optional_CWLObjectType); - public static Loader>> map_of_optional_CWLObjectType = new MapLoader(optional_CWLObjectType, null, null); - public static Loader InlineJavascriptRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.InlineJavascriptRequirementImpl.class, null, null); - public static Loader SchemaDefRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.SchemaDefRequirementImpl.class, null, null); - public static Loader LoadListingRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.LoadListingRequirementImpl.class, null, null); - public static Loader DockerRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.DockerRequirementImpl.class, null, null); - public static Loader SoftwareRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.SoftwareRequirementImpl.class, null, null); - public static Loader InitialWorkDirRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.InitialWorkDirRequirementImpl.class, null, null); - public static Loader EnvVarRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.EnvVarRequirementImpl.class, null, null); - public static Loader ShellCommandRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.ShellCommandRequirementImpl.class, null, null); - public static Loader ResourceRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.ResourceRequirementImpl.class, null, null); - public static Loader WorkReuse = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.WorkReuseImpl.class, null, null); - public static Loader NetworkAccess = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.NetworkAccessImpl.class, null, null); - public static Loader InplaceUpdateRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.InplaceUpdateRequirementImpl.class, null, null); - public static Loader ToolTimeLimit = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.ToolTimeLimitImpl.class, null, null); - public static Loader SubworkflowFeatureRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.SubworkflowFeatureRequirementImpl.class, null, null); - public static Loader ScatterFeatureRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.ScatterFeatureRequirementImpl.class, null, null); - public static Loader MultipleInputFeatureRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.MultipleInputFeatureRequirementImpl.class, null, null); - public static Loader StepInputExpressionRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.StepInputExpressionRequirementImpl.class, null, null); - public static Loader Secrets = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.SecretsImpl.class, null, null); - public static Loader MPIRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.MPIRequirementImpl.class, null, null); - public static Loader CUDARequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CUDARequirementImpl.class, null, null); - public static Loader Loop = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.LoopImpl.class, null, null); - public static Loader ShmSize = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.ShmSizeImpl.class, null, null); - public static Loader union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize = new UnionLoader(new Loader[] { InlineJavascriptRequirement, SchemaDefRequirement, LoadListingRequirement, DockerRequirement, SoftwareRequirement, InitialWorkDirRequirement, EnvVarRequirement, ShellCommandRequirement, ResourceRequirement, WorkReuse, NetworkAccess, InplaceUpdateRequirement, ToolTimeLimit, SubworkflowFeatureRequirement, ScatterFeatureRequirement, MultipleInputFeatureRequirement, StepInputExpressionRequirement, Secrets, MPIRequirement, CUDARequirement, Loop, ShmSize }); - public static Loader> array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize = new ArrayLoader(union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize); - public static Loader union_of_NullInstance_or_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_CWLObjectType = new UnionLoader(new Loader[] { NullInstance, array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize, CWLObjectType }); - public static Loader> map_of_union_of_NullInstance_or_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_CWLObjectType = new MapLoader(union_of_NullInstance_or_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_CWLObjectType, "@list", true); - public static Loader CWLVersion = new EnumLoader(CWLVersion.class); - public static Loader Labeled = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.Labeled.class, null, null); - public static Loader Identified = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.Identified.class, null, null); - public static Loader IdentifierRequired = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.IdentifierRequired.class, null, null); - public static Loader LoadListingEnum = new EnumLoader(LoadListingEnum.class); - public static Loader LoadContents = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.LoadContents.class, null, null); - public static Loader FieldBase = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.FieldBase.class, null, null); - public static Loader InputFormat = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.InputFormat.class, null, null); - public static Loader OutputFormat = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.OutputFormat.class, null, null); - public static Loader Parameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.Parameter.class, null, null); - public static Loader Expression = new EnumLoader(Expression.class); - public static Loader InputBinding = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.InputBindingImpl.class, null, null); - public static Loader IOSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.IOSchema.class, null, null); - public static Loader InputSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.InputSchema.class, null, null); - public static Loader OutputSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.OutputSchema.class, null, null); - public static Loader InputRecordField = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.InputRecordFieldImpl.class, null, null); - public static Loader InputRecordSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.InputRecordSchemaImpl.class, null, null); - public static Loader InputEnumSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.InputEnumSchemaImpl.class, null, null); - public static Loader InputArraySchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.InputArraySchemaImpl.class, null, null); - public static Loader OutputRecordField = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.OutputRecordFieldImpl.class, null, null); - public static Loader OutputRecordSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.OutputRecordSchemaImpl.class, null, null); - public static Loader OutputEnumSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.OutputEnumSchemaImpl.class, null, null); - public static Loader OutputArraySchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.OutputArraySchemaImpl.class, null, null); - public static Loader InputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.InputParameter.class, null, null); - public static Loader OutputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.OutputParameter.class, null, null); - public static Loader ProcessRequirement = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.ProcessRequirement.class, null, null); - public static Loader Process = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.Process.class, null, null); - public static Loader CommandInputSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandInputSchema.class, null, null); - public static Loader SecondaryFileSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.SecondaryFileSchemaImpl.class, null, null); - public static Loader EnvironmentDef = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.EnvironmentDefImpl.class, null, null); - public static Loader CommandLineBinding = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandLineBindingImpl.class, null, null); - public static Loader CommandOutputBinding = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandOutputBindingImpl.class, null, null); - public static Loader CommandLineBindable = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandLineBindable.class, null, null); - public static Loader CommandInputRecordField = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandInputRecordFieldImpl.class, null, null); - public static Loader CommandInputRecordSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandInputRecordSchemaImpl.class, null, null); - public static Loader CommandInputEnumSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandInputEnumSchemaImpl.class, null, null); - public static Loader CommandInputArraySchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandInputArraySchemaImpl.class, null, null); - public static Loader CommandOutputRecordField = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandOutputRecordFieldImpl.class, null, null); - public static Loader CommandOutputRecordSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandOutputRecordSchemaImpl.class, null, null); - public static Loader CommandOutputEnumSchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandOutputEnumSchemaImpl.class, null, null); - public static Loader CommandOutputArraySchema = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandOutputArraySchemaImpl.class, null, null); - public static Loader CommandInputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandInputParameterImpl.class, null, null); - public static Loader CommandOutputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandOutputParameterImpl.class, null, null); - public static Loader stdin = new EnumLoader(stdin.class); - public static Loader stdout = new EnumLoader(stdout.class); - public static Loader stderr = new EnumLoader(stderr.class); - public static Loader CommandLineTool = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.CommandLineToolImpl.class, null, null); - public static Loader SoftwarePackage = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.SoftwarePackageImpl.class, null, null); - public static Loader Dirent = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.DirentImpl.class, null, null); - public static Loader ExpressionToolOutputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.ExpressionToolOutputParameterImpl.class, null, null); - public static Loader WorkflowInputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.WorkflowInputParameterImpl.class, null, null); - public static Loader ExpressionTool = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.ExpressionToolImpl.class, null, null); - public static Loader LinkMergeMethod = new EnumLoader(LinkMergeMethod.class); - public static Loader PickValueMethod = new EnumLoader(PickValueMethod.class); - public static Loader WorkflowOutputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.WorkflowOutputParameterImpl.class, null, null); - public static Loader Sink = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.Sink.class, null, null); - public static Loader WorkflowStepInput = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.WorkflowStepInputImpl.class, null, null); - public static Loader WorkflowStepOutput = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.WorkflowStepOutputImpl.class, null, null); - public static Loader ScatterMethod = new EnumLoader(ScatterMethod.class); - public static Loader WorkflowStep = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.WorkflowStepImpl.class, null, null); - public static Loader Workflow = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.WorkflowImpl.class, null, null); - public static Loader OperationInputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.OperationInputParameterImpl.class, null, null); - public static Loader OperationOutputParameter = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.OperationOutputParameterImpl.class, null, null); - public static Loader Operation = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.OperationImpl.class, null, null); - public static Loader ProcessGenerator = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.ProcessGeneratorImpl.class, null, null); - public static Loader LoopInput = new RecordLoader(org.commonwl.cwlsdk.cwl1_2.LoopInputImpl.class, null, null); - public static Loader> array_of_StringInstance = new ArrayLoader(StringInstance); - public static Loader union_of_NullInstance_or_StringInstance_or_array_of_StringInstance = new UnionLoader(new Loader[] { NullInstance, StringInstance, array_of_StringInstance }); - public static Loader uri_StringInstance_True_False_None_None = new UriLoader(StringInstance, true, false, null, null); - public static Loader union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance = new UnionLoader(new Loader[] { PrimitiveType, RecordSchema, EnumSchema, ArraySchema, MapSchema, UnionSchema, StringInstance }); - public static Loader> array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance = new ArrayLoader(union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance); - public static Loader union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance = new UnionLoader(new Loader[] { PrimitiveType, RecordSchema, EnumSchema, ArraySchema, MapSchema, UnionSchema, StringInstance, array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance }); - public static Loader typedsl_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_2 = new TypeDslLoader(union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance, 2); - public static Loader> array_of_RecordField = new ArrayLoader(RecordField); - public static Loader>> optional_array_of_RecordField = new OptionalLoader(array_of_RecordField); - public static Loader>> idmap_fields_optional_array_of_RecordField = new IdMapLoader(optional_array_of_RecordField, "name", "type"); - public static Loader Record_name = new EnumLoader(Record_name.class); - public static Loader typedsl_Record_name_2 = new TypeDslLoader(Record_name, 2); - public static Loader> optional_StringInstance = new OptionalLoader(StringInstance); - public static Loader> uri_optional_StringInstance_True_False_None_None = new UriLoader(optional_StringInstance, true, false, null, null); - public static Loader> uri_array_of_StringInstance_True_False_None_None = new UriLoader(array_of_StringInstance, true, false, null, null); - public static Loader Enum_name = new EnumLoader(Enum_name.class); - public static Loader typedsl_Enum_name_2 = new TypeDslLoader(Enum_name, 2); - public static Loader uri_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_False_True_2_None = new UriLoader(union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_RecordSchema_or_EnumSchema_or_ArraySchema_or_MapSchema_or_UnionSchema_or_StringInstance, false, true, 2, null); - public static Loader Array_name = new EnumLoader(Array_name.class); - public static Loader typedsl_Array_name_2 = new TypeDslLoader(Array_name, 2); - public static Loader Map_name = new EnumLoader(Map_name.class); - public static Loader typedsl_Map_name_2 = new TypeDslLoader(Map_name, 2); - public static Loader Union_name = new EnumLoader(Union_name.class); - public static Loader typedsl_Union_name_2 = new TypeDslLoader(Union_name, 2); - public static Loader union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance = new UnionLoader(new Loader[] { PrimitiveType, CWLRecordSchema, EnumSchema, CWLArraySchema, StringInstance }); - public static Loader> array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance = new ArrayLoader(union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance); - public static Loader union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance = new UnionLoader(new Loader[] { PrimitiveType, CWLRecordSchema, EnumSchema, CWLArraySchema, StringInstance, array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance }); - public static Loader uri_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_False_True_2_None = new UriLoader(union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance, false, true, 2, null); - public static Loader typedsl_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance_or_array_of_union_of_PrimitiveType_or_CWLRecordSchema_or_EnumSchema_or_CWLArraySchema_or_StringInstance, 2); - public static Loader> array_of_CWLRecordField = new ArrayLoader(CWLRecordField); - public static Loader>> optional_array_of_CWLRecordField = new OptionalLoader(array_of_CWLRecordField); - public static Loader>> idmap_fields_optional_array_of_CWLRecordField = new IdMapLoader(optional_array_of_CWLRecordField, "name", "type"); - public static Loader File_class = new EnumLoader(File_class.class); - public static Loader uri_File_class_False_True_None_None = new UriLoader(File_class, false, true, null, null); - public static Loader> uri_optional_StringInstance_False_False_None_None = new UriLoader(optional_StringInstance, false, false, null, null); - public static Loader union_of_NullInstance_or_IntegerInstance_or_LongInstance = new UnionLoader(new Loader[] { NullInstance, IntegerInstance, LongInstance }); - public static Loader union_of_File_or_Directory = new UnionLoader(new Loader[] { File, Directory }); - public static Loader> array_of_union_of_File_or_Directory = new ArrayLoader(union_of_File_or_Directory); - public static Loader>> optional_array_of_union_of_File_or_Directory = new OptionalLoader(array_of_union_of_File_or_Directory); - public static Loader>> secondaryfilesdsl_optional_array_of_union_of_File_or_Directory = new SecondaryFilesDslLoader(optional_array_of_union_of_File_or_Directory); - public static Loader> uri_optional_StringInstance_True_False_None_True = new UriLoader(optional_StringInstance, true, false, null, true); - public static Loader Directory_class = new EnumLoader(Directory_class.class); - public static Loader uri_Directory_class_False_True_None_None = new UriLoader(Directory_class, false, true, null, null); - public static Loader> optional_BooleanInstance = new OptionalLoader(BooleanInstance); - public static Loader> optional_LoadListingEnum = new OptionalLoader(LoadListingEnum); - public static Loader> array_of_SecondaryFileSchema = new ArrayLoader(SecondaryFileSchema); - public static Loader union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema = new UnionLoader(new Loader[] { NullInstance, SecondaryFileSchema, array_of_SecondaryFileSchema }); - public static Loader secondaryfilesdsl_union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema = new SecondaryFilesDslLoader(union_of_NullInstance_or_SecondaryFileSchema_or_array_of_SecondaryFileSchema); - public static Loader ExpressionLoader = new ExpressionLoader(); - public static Loader union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { NullInstance, StringInstance, array_of_StringInstance, ExpressionLoader }); - public static Loader uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader_True_False_None_True = new UriLoader(union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_or_ExpressionLoader, true, false, null, true); - public static Loader union_of_NullInstance_or_StringInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { NullInstance, StringInstance, ExpressionLoader }); - public static Loader uri_union_of_NullInstance_or_StringInstance_or_ExpressionLoader_True_False_None_True = new UriLoader(union_of_NullInstance_or_StringInstance_or_ExpressionLoader, true, false, null, true); - public static Loader union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, InputRecordSchema, InputEnumSchema, InputArraySchema, StringInstance }); - public static Loader> array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance = new ArrayLoader(union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance); - public static Loader union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, InputRecordSchema, InputEnumSchema, InputArraySchema, StringInstance, array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance }); - public static Loader typedsl_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance, 2); - public static Loader> array_of_InputRecordField = new ArrayLoader(InputRecordField); - public static Loader>> optional_array_of_InputRecordField = new OptionalLoader(array_of_InputRecordField); - public static Loader>> idmap_fields_optional_array_of_InputRecordField = new IdMapLoader(optional_array_of_InputRecordField, "name", "type"); - public static Loader uri_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_False_True_2_None = new UriLoader(union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_InputRecordSchema_or_InputEnumSchema_or_InputArraySchema_or_StringInstance, false, true, 2, null); - public static Loader union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, OutputRecordSchema, OutputEnumSchema, OutputArraySchema, StringInstance }); - public static Loader> array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance = new ArrayLoader(union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance); - public static Loader union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, OutputRecordSchema, OutputEnumSchema, OutputArraySchema, StringInstance, array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance }); - public static Loader typedsl_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance, 2); - public static Loader> array_of_OutputRecordField = new ArrayLoader(OutputRecordField); - public static Loader>> optional_array_of_OutputRecordField = new OptionalLoader(array_of_OutputRecordField); - public static Loader>> idmap_fields_optional_array_of_OutputRecordField = new IdMapLoader(optional_array_of_OutputRecordField, "name", "type"); - public static Loader uri_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_False_True_2_None = new UriLoader(union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_OutputRecordSchema_or_OutputEnumSchema_or_OutputArraySchema_or_StringInstance, false, true, 2, null); - public static Loader union_of_CommandInputParameter_or_WorkflowInputParameter_or_OperationInputParameter = new UnionLoader(new Loader[] { CommandInputParameter, WorkflowInputParameter, OperationInputParameter }); - public static Loader> array_of_union_of_CommandInputParameter_or_WorkflowInputParameter_or_OperationInputParameter = new ArrayLoader(union_of_CommandInputParameter_or_WorkflowInputParameter_or_OperationInputParameter); - public static Loader> idmap_inputs_array_of_union_of_CommandInputParameter_or_WorkflowInputParameter_or_OperationInputParameter = new IdMapLoader(array_of_union_of_CommandInputParameter_or_WorkflowInputParameter_or_OperationInputParameter, "id", "type"); - public static Loader union_of_CommandOutputParameter_or_ExpressionToolOutputParameter_or_WorkflowOutputParameter_or_OperationOutputParameter = new UnionLoader(new Loader[] { CommandOutputParameter, ExpressionToolOutputParameter, WorkflowOutputParameter, OperationOutputParameter }); - public static Loader> array_of_union_of_CommandOutputParameter_or_ExpressionToolOutputParameter_or_WorkflowOutputParameter_or_OperationOutputParameter = new ArrayLoader(union_of_CommandOutputParameter_or_ExpressionToolOutputParameter_or_WorkflowOutputParameter_or_OperationOutputParameter); - public static Loader> idmap_outputs_array_of_union_of_CommandOutputParameter_or_ExpressionToolOutputParameter_or_WorkflowOutputParameter_or_OperationOutputParameter = new IdMapLoader(array_of_union_of_CommandOutputParameter_or_ExpressionToolOutputParameter_or_WorkflowOutputParameter_or_OperationOutputParameter, "id", "type"); - public static Loader>> optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize = new OptionalLoader(array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize); - public static Loader>> idmap_requirements_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize = new IdMapLoader(optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize, "class", "None"); - public static Loader union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_AnyInstance = new UnionLoader(new Loader[] { InlineJavascriptRequirement, SchemaDefRequirement, LoadListingRequirement, DockerRequirement, SoftwareRequirement, InitialWorkDirRequirement, EnvVarRequirement, ShellCommandRequirement, ResourceRequirement, WorkReuse, NetworkAccess, InplaceUpdateRequirement, ToolTimeLimit, SubworkflowFeatureRequirement, ScatterFeatureRequirement, MultipleInputFeatureRequirement, StepInputExpressionRequirement, Secrets, MPIRequirement, CUDARequirement, Loop, ShmSize, AnyInstance }); - public static Loader> array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_AnyInstance = new ArrayLoader(union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_AnyInstance); - public static Loader>> optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_AnyInstance = new OptionalLoader(array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_AnyInstance); - public static Loader>> idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_AnyInstance = new IdMapLoader(optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_Secrets_or_MPIRequirement_or_CUDARequirement_or_Loop_or_ShmSize_or_AnyInstance, "class", "None"); - public static Loader> optional_CWLVersion = new OptionalLoader(CWLVersion); - public static Loader> uri_optional_CWLVersion_False_True_None_None = new UriLoader(optional_CWLVersion, false, true, null, null); - public static Loader>> optional_array_of_StringInstance = new OptionalLoader(array_of_StringInstance); - public static Loader>> uri_optional_array_of_StringInstance_True_False_None_None = new UriLoader(optional_array_of_StringInstance, true, false, null, null); - public static Loader InlineJavascriptRequirement_class = new EnumLoader(InlineJavascriptRequirement_class.class); - public static Loader uri_InlineJavascriptRequirement_class_False_True_None_None = new UriLoader(InlineJavascriptRequirement_class, false, true, null, null); - public static Loader SchemaDefRequirement_class = new EnumLoader(SchemaDefRequirement_class.class); - public static Loader uri_SchemaDefRequirement_class_False_True_None_None = new UriLoader(SchemaDefRequirement_class, false, true, null, null); - public static Loader union_of_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema = new UnionLoader(new Loader[] { CommandInputRecordSchema, CommandInputEnumSchema, CommandInputArraySchema }); - public static Loader> array_of_union_of_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema = new ArrayLoader(union_of_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema); - public static Loader union_of_StringInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { StringInstance, ExpressionLoader }); - public static Loader union_of_NullInstance_or_BooleanInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { NullInstance, BooleanInstance, ExpressionLoader }); - public static Loader LoadListingRequirement_class = new EnumLoader(LoadListingRequirement_class.class); - public static Loader uri_LoadListingRequirement_class_False_True_None_None = new UriLoader(LoadListingRequirement_class, false, true, null, null); - public static Loader union_of_NullInstance_or_IntegerInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { NullInstance, IntegerInstance, ExpressionLoader }); - public static Loader union_of_NullInstance_or_StringInstance_or_ExpressionLoader_or_array_of_StringInstance = new UnionLoader(new Loader[] { NullInstance, StringInstance, ExpressionLoader, array_of_StringInstance }); - public static Loader> optional_ExpressionLoader = new OptionalLoader(ExpressionLoader); - public static Loader> optional_CommandLineBinding = new OptionalLoader(CommandLineBinding); - public static Loader union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, CommandInputRecordSchema, CommandInputEnumSchema, CommandInputArraySchema, StringInstance }); - public static Loader> array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance = new ArrayLoader(union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance); - public static Loader union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, CommandInputRecordSchema, CommandInputEnumSchema, CommandInputArraySchema, StringInstance, array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance }); - public static Loader typedsl_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance, 2); - public static Loader> array_of_CommandInputRecordField = new ArrayLoader(CommandInputRecordField); - public static Loader>> optional_array_of_CommandInputRecordField = new OptionalLoader(array_of_CommandInputRecordField); - public static Loader>> idmap_fields_optional_array_of_CommandInputRecordField = new IdMapLoader(optional_array_of_CommandInputRecordField, "name", "type"); - public static Loader uri_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_False_True_2_None = new UriLoader(union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance, false, true, 2, null); - public static Loader union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, CommandOutputRecordSchema, CommandOutputEnumSchema, CommandOutputArraySchema, StringInstance }); - public static Loader> array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance = new ArrayLoader(union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance); - public static Loader union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, CommandOutputRecordSchema, CommandOutputEnumSchema, CommandOutputArraySchema, StringInstance, array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance }); - public static Loader typedsl_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance, 2); - public static Loader> optional_CommandOutputBinding = new OptionalLoader(CommandOutputBinding); - public static Loader> array_of_CommandOutputRecordField = new ArrayLoader(CommandOutputRecordField); - public static Loader>> optional_array_of_CommandOutputRecordField = new OptionalLoader(array_of_CommandOutputRecordField); - public static Loader>> idmap_fields_optional_array_of_CommandOutputRecordField = new IdMapLoader(optional_array_of_CommandOutputRecordField, "name", "type"); - public static Loader uri_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_False_True_2_None = new UriLoader(union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance, false, true, 2, null); - public static Loader union_of_CWLType_or_stdin_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, stdin, CommandInputRecordSchema, CommandInputEnumSchema, CommandInputArraySchema, StringInstance, array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance }); - public static Loader typedsl_union_of_CWLType_or_stdin_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_CWLType_or_stdin_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandInputRecordSchema_or_CommandInputEnumSchema_or_CommandInputArraySchema_or_StringInstance, 2); - public static Loader union_of_CWLType_or_stdout_or_stderr_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance = new UnionLoader(new Loader[] { CWLType, stdout, stderr, CommandOutputRecordSchema, CommandOutputEnumSchema, CommandOutputArraySchema, StringInstance, array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance }); - public static Loader typedsl_union_of_CWLType_or_stdout_or_stderr_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_2 = new TypeDslLoader(union_of_CWLType_or_stdout_or_stderr_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance_or_array_of_union_of_CWLType_or_CommandOutputRecordSchema_or_CommandOutputEnumSchema_or_CommandOutputArraySchema_or_StringInstance, 2); - public static Loader CommandLineTool_class = new EnumLoader(CommandLineTool_class.class); - public static Loader uri_CommandLineTool_class_False_True_None_None = new UriLoader(CommandLineTool_class, false, true, null, null); - public static Loader> array_of_CommandInputParameter = new ArrayLoader(CommandInputParameter); - public static Loader> idmap_inputs_array_of_CommandInputParameter = new IdMapLoader(array_of_CommandInputParameter, "id", "type"); - public static Loader> array_of_CommandOutputParameter = new ArrayLoader(CommandOutputParameter); - public static Loader> idmap_outputs_array_of_CommandOutputParameter = new IdMapLoader(array_of_CommandOutputParameter, "id", "type"); - public static Loader union_of_StringInstance_or_ExpressionLoader_or_CommandLineBinding = new UnionLoader(new Loader[] { StringInstance, ExpressionLoader, CommandLineBinding }); - public static Loader> array_of_union_of_StringInstance_or_ExpressionLoader_or_CommandLineBinding = new ArrayLoader(union_of_StringInstance_or_ExpressionLoader_or_CommandLineBinding); - public static Loader>> optional_array_of_union_of_StringInstance_or_ExpressionLoader_or_CommandLineBinding = new OptionalLoader(array_of_union_of_StringInstance_or_ExpressionLoader_or_CommandLineBinding); - public static Loader> array_of_IntegerInstance = new ArrayLoader(IntegerInstance); - public static Loader>> optional_array_of_IntegerInstance = new OptionalLoader(array_of_IntegerInstance); - public static Loader DockerRequirement_class = new EnumLoader(DockerRequirement_class.class); - public static Loader uri_DockerRequirement_class_False_True_None_None = new UriLoader(DockerRequirement_class, false, true, null, null); - public static Loader SoftwareRequirement_class = new EnumLoader(SoftwareRequirement_class.class); - public static Loader uri_SoftwareRequirement_class_False_True_None_None = new UriLoader(SoftwareRequirement_class, false, true, null, null); - public static Loader> array_of_SoftwarePackage = new ArrayLoader(SoftwarePackage); - public static Loader> idmap_packages_array_of_SoftwarePackage = new IdMapLoader(array_of_SoftwarePackage, "package", "specs"); - public static Loader>> uri_optional_array_of_StringInstance_False_False_None_True = new UriLoader(optional_array_of_StringInstance, false, false, null, true); - public static Loader InitialWorkDirRequirement_class = new EnumLoader(InitialWorkDirRequirement_class.class); - public static Loader uri_InitialWorkDirRequirement_class_False_True_None_None = new UriLoader(InitialWorkDirRequirement_class, false, true, null, null); - public static Loader union_of_NullInstance_or_Dirent_or_ExpressionLoader_or_File_or_Directory_or_array_of_union_of_File_or_Directory = new UnionLoader(new Loader[] { NullInstance, Dirent, ExpressionLoader, File, Directory, array_of_union_of_File_or_Directory }); - public static Loader> array_of_union_of_NullInstance_or_Dirent_or_ExpressionLoader_or_File_or_Directory_or_array_of_union_of_File_or_Directory = new ArrayLoader(union_of_NullInstance_or_Dirent_or_ExpressionLoader_or_File_or_Directory_or_array_of_union_of_File_or_Directory); - public static Loader union_of_ExpressionLoader_or_array_of_union_of_NullInstance_or_Dirent_or_ExpressionLoader_or_File_or_Directory_or_array_of_union_of_File_or_Directory = new UnionLoader(new Loader[] { ExpressionLoader, array_of_union_of_NullInstance_or_Dirent_or_ExpressionLoader_or_File_or_Directory_or_array_of_union_of_File_or_Directory }); - public static Loader EnvVarRequirement_class = new EnumLoader(EnvVarRequirement_class.class); - public static Loader uri_EnvVarRequirement_class_False_True_None_None = new UriLoader(EnvVarRequirement_class, false, true, null, null); - public static Loader> array_of_EnvironmentDef = new ArrayLoader(EnvironmentDef); - public static Loader> idmap_envDef_array_of_EnvironmentDef = new IdMapLoader(array_of_EnvironmentDef, "envName", "envValue"); - public static Loader ShellCommandRequirement_class = new EnumLoader(ShellCommandRequirement_class.class); - public static Loader uri_ShellCommandRequirement_class_False_True_None_None = new UriLoader(ShellCommandRequirement_class, false, true, null, null); - public static Loader ResourceRequirement_class = new EnumLoader(ResourceRequirement_class.class); - public static Loader uri_ResourceRequirement_class_False_True_None_None = new UriLoader(ResourceRequirement_class, false, true, null, null); - public static Loader union_of_NullInstance_or_IntegerInstance_or_LongInstance_or_DoubleInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { NullInstance, IntegerInstance, LongInstance, DoubleInstance, ExpressionLoader }); - public static Loader WorkReuse_class = new EnumLoader(WorkReuse_class.class); - public static Loader uri_WorkReuse_class_False_True_None_None = new UriLoader(WorkReuse_class, false, true, null, null); - public static Loader union_of_BooleanInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { BooleanInstance, ExpressionLoader }); - public static Loader NetworkAccess_class = new EnumLoader(NetworkAccess_class.class); - public static Loader uri_NetworkAccess_class_False_True_None_None = new UriLoader(NetworkAccess_class, false, true, null, null); - public static Loader InplaceUpdateRequirement_class = new EnumLoader(InplaceUpdateRequirement_class.class); - public static Loader uri_InplaceUpdateRequirement_class_False_True_None_None = new UriLoader(InplaceUpdateRequirement_class, false, true, null, null); - public static Loader ToolTimeLimit_class = new EnumLoader(ToolTimeLimit_class.class); - public static Loader uri_ToolTimeLimit_class_False_True_None_None = new UriLoader(ToolTimeLimit_class, false, true, null, null); - public static Loader union_of_IntegerInstance_or_LongInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { IntegerInstance, LongInstance, ExpressionLoader }); - public static Loader> optional_InputBinding = new OptionalLoader(InputBinding); - public static Loader ExpressionTool_class = new EnumLoader(ExpressionTool_class.class); - public static Loader uri_ExpressionTool_class_False_True_None_None = new UriLoader(ExpressionTool_class, false, true, null, null); - public static Loader> array_of_WorkflowInputParameter = new ArrayLoader(WorkflowInputParameter); - public static Loader> idmap_inputs_array_of_WorkflowInputParameter = new IdMapLoader(array_of_WorkflowInputParameter, "id", "type"); - public static Loader> array_of_ExpressionToolOutputParameter = new ArrayLoader(ExpressionToolOutputParameter); - public static Loader> idmap_outputs_array_of_ExpressionToolOutputParameter = new IdMapLoader(array_of_ExpressionToolOutputParameter, "id", "type"); - public static Loader uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_1_None = new UriLoader(union_of_NullInstance_or_StringInstance_or_array_of_StringInstance, false, false, 1, null); - public static Loader> optional_LinkMergeMethod = new OptionalLoader(LinkMergeMethod); - public static Loader> optional_PickValueMethod = new OptionalLoader(PickValueMethod); - public static Loader uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_2_None = new UriLoader(union_of_NullInstance_or_StringInstance_or_array_of_StringInstance, false, false, 2, null); - public static Loader> array_of_WorkflowStepInput = new ArrayLoader(WorkflowStepInput); - public static Loader> idmap_in_array_of_WorkflowStepInput = new IdMapLoader(array_of_WorkflowStepInput, "id", "source"); - public static Loader union_of_StringInstance_or_WorkflowStepOutput = new UnionLoader(new Loader[] { StringInstance, WorkflowStepOutput }); - public static Loader> array_of_union_of_StringInstance_or_WorkflowStepOutput = new ArrayLoader(union_of_StringInstance_or_WorkflowStepOutput); - public static Loader> uri_array_of_union_of_StringInstance_or_WorkflowStepOutput_True_False_None_None = new UriLoader(array_of_union_of_StringInstance_or_WorkflowStepOutput, true, false, null, null); - public static Loader> array_of_AnyInstance = new ArrayLoader(AnyInstance); - public static Loader>> optional_array_of_AnyInstance = new OptionalLoader(array_of_AnyInstance); - public static Loader>> idmap_hints_optional_array_of_AnyInstance = new IdMapLoader(optional_array_of_AnyInstance, "class", "None"); - public static Loader union_of_StringInstance_or_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator = new UnionLoader(new Loader[] { StringInstance, CommandLineTool, ExpressionTool, Workflow, Operation, ProcessGenerator }); - public static Loader uri_union_of_StringInstance_or_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator_False_False_None_None = new UriLoader(union_of_StringInstance_or_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator, false, false, null, null); - public static Loader uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_0_None = new UriLoader(union_of_NullInstance_or_StringInstance_or_array_of_StringInstance, false, false, 0, null); - public static Loader> optional_ScatterMethod = new OptionalLoader(ScatterMethod); - public static Loader> uri_optional_ScatterMethod_False_True_None_None = new UriLoader(optional_ScatterMethod, false, true, null, null); - public static Loader Workflow_class = new EnumLoader(Workflow_class.class); - public static Loader uri_Workflow_class_False_True_None_None = new UriLoader(Workflow_class, false, true, null, null); - public static Loader> array_of_WorkflowOutputParameter = new ArrayLoader(WorkflowOutputParameter); - public static Loader> idmap_outputs_array_of_WorkflowOutputParameter = new IdMapLoader(array_of_WorkflowOutputParameter, "id", "type"); - public static Loader> array_of_WorkflowStep = new ArrayLoader(WorkflowStep); - public static Loader> idmap_steps_array_of_WorkflowStep = new IdMapLoader(array_of_WorkflowStep, "id", "None"); - public static Loader SubworkflowFeatureRequirement_class = new EnumLoader(SubworkflowFeatureRequirement_class.class); - public static Loader uri_SubworkflowFeatureRequirement_class_False_True_None_None = new UriLoader(SubworkflowFeatureRequirement_class, false, true, null, null); - public static Loader ScatterFeatureRequirement_class = new EnumLoader(ScatterFeatureRequirement_class.class); - public static Loader uri_ScatterFeatureRequirement_class_False_True_None_None = new UriLoader(ScatterFeatureRequirement_class, false, true, null, null); - public static Loader MultipleInputFeatureRequirement_class = new EnumLoader(MultipleInputFeatureRequirement_class.class); - public static Loader uri_MultipleInputFeatureRequirement_class_False_True_None_None = new UriLoader(MultipleInputFeatureRequirement_class, false, true, null, null); - public static Loader StepInputExpressionRequirement_class = new EnumLoader(StepInputExpressionRequirement_class.class); - public static Loader uri_StepInputExpressionRequirement_class_False_True_None_None = new UriLoader(StepInputExpressionRequirement_class, false, true, null, null); - public static Loader Operation_class = new EnumLoader(Operation_class.class); - public static Loader uri_Operation_class_False_True_None_None = new UriLoader(Operation_class, false, true, null, null); - public static Loader> array_of_OperationInputParameter = new ArrayLoader(OperationInputParameter); - public static Loader> idmap_inputs_array_of_OperationInputParameter = new IdMapLoader(array_of_OperationInputParameter, "id", "type"); - public static Loader> array_of_OperationOutputParameter = new ArrayLoader(OperationOutputParameter); - public static Loader> idmap_outputs_array_of_OperationOutputParameter = new IdMapLoader(array_of_OperationOutputParameter, "id", "type"); - public static Loader uri_StringInstance_False_True_None_None = new UriLoader(StringInstance, false, true, null, null); - public static Loader> uri_array_of_StringInstance_False_False_0_None = new UriLoader(array_of_StringInstance, false, false, 0, null); - public static Loader union_of_IntegerInstance_or_ExpressionLoader = new UnionLoader(new Loader[] { IntegerInstance, ExpressionLoader }); - public static Loader union_of_StringInstance_or_array_of_StringInstance = new UnionLoader(new Loader[] { StringInstance, array_of_StringInstance }); - public static Loader> optional_AnyInstance = new OptionalLoader(AnyInstance); - public static Loader> array_of_LoopInput = new ArrayLoader(LoopInput); - public static Loader> idmap_loop_array_of_LoopInput = new IdMapLoader(array_of_LoopInput, "id", "loopSource"); - public static Loader LoopOutputModes = new EnumLoader(LoopOutputModes.class); - public static Loader union_of_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator = new UnionLoader(new Loader[] { CommandLineTool, ExpressionTool, Workflow, Operation, ProcessGenerator }); - public static Loader> array_of_union_of_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator = new ArrayLoader(union_of_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator); - public static Loader union_of_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator_or_array_of_union_of_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator = new UnionLoader(new Loader[] { CommandLineTool, ExpressionTool, Workflow, Operation, ProcessGenerator, array_of_union_of_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator }); - - static { - ((UnionLoader) CWLObjectType).addLoaders(new Loader[] { BooleanInstance, IntegerInstance, LongInstance, DoubleInstance, DoubleInstance, StringInstance, File, Directory, array_of_optional_CWLObjectType, map_of_optional_CWLObjectType }); - } - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/LoadingOptions.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/LoadingOptions.java deleted file mode 100644 index c4ae09fb..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/LoadingOptions.java +++ /dev/null @@ -1,129 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.net.URI; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Map; - -public class LoadingOptions { - Fetcher fetcher; - String fileUri; - Map namespaces; - List schemas; - Boolean noLinkCheck; - String container; - Map idx; - Map vocab; - Map rvocab; - - LoadingOptions( - final Fetcher fetcher, - final String fileUri, - final Map namespaces, - final List schemas, - final Boolean noLinkCheck, - final String container, - final Map idx) { - this.fetcher = fetcher; - this.fileUri = fileUri; - this.namespaces = namespaces; - this.schemas = schemas; - this.noLinkCheck = noLinkCheck; - this.container = container; - this.idx = idx; - - if (namespaces != null) { - this.vocab = (Map) ConstantMaps.vocab.clone(); - this.rvocab = (Map) ConstantMaps.rvocab.clone(); - for (Map.Entry namespaceEntry : namespaces.entrySet()) { - this.vocab.put(namespaceEntry.getKey(), namespaceEntry.getValue()); - this.rvocab.put(namespaceEntry.getValue(), namespaceEntry.getKey()); - } - } else { - this.vocab = (Map) ConstantMaps.vocab; - this.rvocab = (Map) ConstantMaps.rvocab; - } - } - - public String expandUrl( - String url_, - final String baseUrl, - final boolean scopedId, - final boolean vocabTerm, - final Integer scopedRef) { - // NOT CONVERTING this - doesn't match type declaration - // if not isinstance(url, str): - // return url - String url = url_; - if (url.equals("@id") || url.equals("@type")) { - return url; - } - - if (vocabTerm && this.vocab.containsKey(url)) { - return url; - } - - if (!this.vocab.isEmpty() && url.contains(":")) { - String prefix = url.split(":")[0]; - if (this.vocab.containsKey(prefix)) { - url = this.vocab.get(prefix) + url.substring(prefix.length() + 1); - } - } - - Uris.UriSplit split = Uris.split(url); - final String scheme = split.scheme; - final boolean hasFragment = stringHasContent(split.fragment); - if (scheme != null - && ((scheme.length() > 0 - && (scheme.equals("http") || scheme.equals("https") || scheme.equals("file"))) - || url.startsWith("$(") - || url.startsWith("${"))) { - // pass - } else if (scopedId && !hasFragment) { - final Uris.UriSplit splitbase = Uris.split(baseUrl); - final String frg; - if (stringHasContent(splitbase.fragment)) { - frg = splitbase.fragment + "/" + split.path; - } else { - frg = split.path; - } - String pt; - if (!splitbase.path.equals("")) { - pt = splitbase.path; - } else { - pt = "/"; - } - url = Uris.unsplit(splitbase.scheme, splitbase.netloc, pt, splitbase.query, frg); - } else if (scopedRef != null && !hasFragment) { - final Uris.UriSplit splitbase = Uris.split(baseUrl); - final ArrayList sp = new ArrayList(Arrays.asList(splitbase.fragment.split("/"))); - int n = scopedRef; - while (n > 0 && sp.size() > 0) { - sp.remove(sp.size()-1); - n -= 1; - } - sp.add(url); - final String fragment = String.join("/", sp); - url = Uris.unsplit(splitbase.scheme, splitbase.netloc, splitbase.path, splitbase.query, fragment); - } else { - url = this.fetcher.urlJoin(baseUrl, url); - } - - if (vocabTerm) { - split = Uris.split(url); - if (stringHasContent(split.scheme)) { - if (this.rvocab.containsKey(url)) { - return this.rvocab.get(url); - } - } else { - throw new ValidationException("Term '{}' not in vocabulary".format(url)); - } - } - return url; - } - - static boolean stringHasContent(final String s) { - return s != null && s.length() > 0; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/LoadingOptionsBuilder.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/LoadingOptionsBuilder.java deleted file mode 100644 index 9fbba692..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/LoadingOptionsBuilder.java +++ /dev/null @@ -1,82 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Optional; - -public class LoadingOptionsBuilder { - private Optional fetcher = Optional.empty(); - private Optional fileUri = Optional.empty(); - private Optional> namespaces = Optional.empty(); - private Optional> schemas = Optional.empty(); - private Optional copyFrom = Optional.empty(); - private Optional noLinkCheck = Optional.empty(); - private Optional container = Optional.empty(); - - public LoadingOptionsBuilder() {} - - public LoadingOptionsBuilder setFetcher(final Fetcher fetcher) { - this.fetcher = Optional.of(fetcher); - return this; - } - - public LoadingOptionsBuilder copiedFrom(final LoadingOptions copyFrom) { - this.copyFrom = Optional.of(copyFrom); - return this; - } - - public LoadingOptionsBuilder setFileUri(final String fileUri) { - this.fileUri = Optional.of(fileUri); - return this; - } - - public LoadingOptionsBuilder setNamespaces(final Map namespaces) { - this.namespaces = Optional.of(namespaces); - return this; - } - - public LoadingOptionsBuilder setNoLinkCheck(final Boolean noLinkCheck) { - this.noLinkCheck = Optional.of(noLinkCheck); - return this; - } - - public LoadingOptionsBuilder setContainer(final String container) { - this.container = Optional.of(container); - return this; - } - - public LoadingOptions build() { - Fetcher fetcher = this.fetcher.orElse(null); - String fileUri = this.fileUri.orElse(null); - List schemas = this.schemas.orElse(null); - Map namespaces = this.namespaces.orElse(null); - Boolean noLinkCheck = this.noLinkCheck.orElse(null); - String container = this.container.orElse(null); - Map idx = new HashMap(); - if (this.copyFrom.isPresent()) { - final LoadingOptions copyFrom = this.copyFrom.get(); - idx = copyFrom.idx; - if (fetcher == null) { - fetcher = copyFrom.fetcher; - } - if (fileUri == null) { - fileUri = copyFrom.fileUri; - } - if (namespaces == null) { - namespaces = copyFrom.namespaces; - schemas = copyFrom.schemas; // Bug in Python codegen? - } - if (noLinkCheck == null) { - noLinkCheck = copyFrom.noLinkCheck; - } - if (container == null) { - container = copyFrom.container; - } - } - if (fetcher == null) { - fetcher = new DefaultFetcher(); - } - return new LoadingOptions(fetcher, fileUri, namespaces, schemas, noLinkCheck, container, idx); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/MapLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/MapLoader.java deleted file mode 100644 index 26099592..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/MapLoader.java +++ /dev/null @@ -1,51 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -public class MapLoader implements Loader> { - private final Loader valueLoader; - private final String container; - private final Boolean noLinkCheck; - - public MapLoader(Loader valueLoader, final String container, final Boolean noLinkCheck) { - this.valueLoader = valueLoader; - this.container = container; - this.noLinkCheck = noLinkCheck; - } - - public Map load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - final Map docMap = (Map) Loader.validateOfJavaType(Map.class, doc); - LoadingOptions innerLoadingOptions = loadingOptions; - if (this.container != null || this.noLinkCheck != null) { - LoadingOptionsBuilder builder = new LoadingOptionsBuilder().copiedFrom(loadingOptions); - if (this.container != null) { - builder.setContainer(this.container); - } - if (this.noLinkCheck != null) { - builder.setNoLinkCheck(this.noLinkCheck); - } - innerLoadingOptions = builder.build(); - } - final Map r = new HashMap(); - final List errors = new ArrayList(); - for (final Map.Entry entry : docMap.entrySet()) { - try { - final Object loadedField = this.valueLoader.loadField(entry.getValue(), baseUri, innerLoadingOptions); - r.put(entry.getKey(), (T) loadedField); - } catch (final ValidationException e) { - errors.add(e); - } - } - if (!errors.isEmpty()) { - throw new ValidationException("", errors); - } - return r; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/NullLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/NullLoader.java deleted file mode 100644 index c9679b8b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/NullLoader.java +++ /dev/null @@ -1,15 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -public class NullLoader implements Loader { - - public Object load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - if (doc != null) { - throw new ValidationException("Expected null"); - } - return doc; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/OneOrListOf.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/OneOrListOf.java deleted file mode 100644 index d998ecf8..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/OneOrListOf.java +++ /dev/null @@ -1,48 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.List; -import java.util.Optional; - -public class OneOrListOf { - private Optional object; - private Optional> objects; - - private OneOrListOf(final T object, final List objects) { - this.object = Optional.ofNullable(object); - this.objects = Optional.ofNullable(objects); - } - - public static OneOrListOf oneOf(T object) { - return new OneOrListOf(object, null); - } - - public static OneOrListOf listOf(List objects) { - assert objects != null; - return new OneOrListOf(null, objects); - } - - public boolean isOne() { - return this.getOneOptional().isPresent(); - } - - public boolean isList() { - return this.getListOptional().isPresent(); - } - - public Optional getOneOptional() { - return this.object; - } - - public Optional> getListOptional() { - return this.objects; - } - - public T getOne() { - return this.getOneOptional().get(); - } - - public List getList() { - return this.getListOptional().get(); - } - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/OneOrListOfLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/OneOrListOfLoader.java deleted file mode 100644 index 054244fc..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/OneOrListOfLoader.java +++ /dev/null @@ -1,35 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.ArrayList; -import java.util.List; -import java.util.Optional; - - -public class OneOrListOfLoader implements Loader> { - private final Loader oneLoader; - private final Loader> listLoader; - - public OneOrListOfLoader(Loader oneLoader, Loader> listLoader) { - this.oneLoader = oneLoader; - this.listLoader = listLoader; - } - - public OneOrListOf load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - final List errors = new ArrayList(); - try { - return OneOrListOf.oneOf(this.oneLoader.load(doc, baseUri, loadingOptions, docRoot)); - } catch (ValidationException e) { - errors.add(e); - } - try { - return OneOrListOf.listOf(this.listLoader.load(doc, baseUri, loadingOptions, docRoot)); - } catch (ValidationException e) { - errors.add(e); - } - throw new ValidationException("Failed to one or list of of type", errors); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/OptionalLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/OptionalLoader.java deleted file mode 100644 index 824b7eac..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/OptionalLoader.java +++ /dev/null @@ -1,23 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.Optional; - - -public class OptionalLoader implements Loader> { - private final Loader itemLoader; - - public OptionalLoader(Loader itemLoader) { - this.itemLoader = itemLoader; - } - - public Optional load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - if(doc == null) { - return Optional.empty(); - } - return Optional.of(itemLoader.load(doc, baseUri, loadingOptions, docRoot)); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/PrimitiveLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/PrimitiveLoader.java deleted file mode 100644 index f1a47266..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/PrimitiveLoader.java +++ /dev/null @@ -1,17 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -public class PrimitiveLoader implements Loader { - private Class clazz; - - public PrimitiveLoader(Class clazz) { - this.clazz = clazz; - } - - public T load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - return Loader.validateOfJavaType(this.clazz, doc); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/RecordLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/RecordLoader.java deleted file mode 100644 index f364d471..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/RecordLoader.java +++ /dev/null @@ -1,51 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.lang.reflect.Constructor; -import java.lang.reflect.InvocationTargetException; - -public class RecordLoader implements Loader { - private final Class saveableClass; - private final String container; - private final Boolean noLinkCheck; - - public RecordLoader(final Class saveableClass, final String container, final Boolean noLinkCheck) { - this.saveableClass = saveableClass; - this.container = container; - this.noLinkCheck = noLinkCheck; - } - - public T load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - Loader.validateOfJavaType(java.util.Map.class, doc); - try { - final Constructor constructor = - this.saveableClass.getConstructor( - new Class[] {Object.class, String.class, LoadingOptions.class, String.class}); - LoadingOptions innerLoadingOptions = loadingOptions; - if (this.container != null || this.noLinkCheck != null) { - LoadingOptionsBuilder builder = new LoadingOptionsBuilder().copiedFrom(loadingOptions); - if (this.container != null) { - builder.setContainer(this.container); - } - if (this.noLinkCheck != null) { - builder.setNoLinkCheck(this.noLinkCheck); - } - innerLoadingOptions = builder.build(); - } - final T ret = constructor.newInstance(doc, baseUri, innerLoadingOptions, docRoot); - return ret; - } catch (InvocationTargetException e) { - final Throwable cause = e.getCause(); - if (cause instanceof RuntimeException) { - throw (RuntimeException) cause; - } - throw new RuntimeException(e.getCause()); - } catch (ReflectiveOperationException e) { - throw new RuntimeException(e); - } - } - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/RootLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/RootLoader.java deleted file mode 100644 index 4921c843..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/RootLoader.java +++ /dev/null @@ -1,105 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.io.File; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.Map; - -public class RootLoader { - public static Object loadDocument( - final Map doc, final String baseUri_, final LoadingOptions loadingOptions_) { - final String baseUri = ensureBaseUri(baseUri_); - LoadingOptions loadingOptions = loadingOptions_; - if (loadingOptions == null) { - loadingOptions = new LoadingOptionsBuilder().setFileUri(baseUri).build(); - } - return LoaderInstances.union_of_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator_or_array_of_union_of_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator.documentLoad(doc, baseUri, loadingOptions); - } - - public static Object loadDocument( - final Map doc, final String baseUri) { - return loadDocument(doc, baseUri, null); - } - - public static Object loadDocument(final Map doc) { - return loadDocument(doc, ensureBaseUri(null)); - } - - public static Object loadDocument(final Path path) { - return loadDocument(readPath(path), path.toUri().toString()); - } - - public static Object loadDocument(final Path path, String baseUri) { - return loadDocument(readPath(path), baseUri); - } - - public static Object loadDocument( - final Path path, LoadingOptions loadingOptions) { - return loadDocument(readPath(path), loadingOptions); - } - - public static Object loadDocument( -final Path path, String baseUri, LoadingOptions loadingOptions) { - return loadDocument(readPath(path), baseUri, loadingOptions); - } - - public static Object loadDocument(final File file) { - return loadDocument(file.toPath()); - } - - public static Object loadDocument(final File file, String baseUri) { - return loadDocument(file.toPath(), baseUri); - } - - public static Object loadDocument(final File file, LoadingOptions loadingOptions) { - return loadDocument(file.toPath(), loadingOptions); - } - - public static Object loadDocument( - final File file, String baseUri, LoadingOptions loadingOptions) { - return loadDocument(file.toPath(), baseUri, loadingOptions); - } - - public static Object loadDocument(final String doc) { - return loadDocument(doc, ensureBaseUri(null)); - } - - public static Object loadDocument(final String doc, final LoadingOptions loadingOptions) { - return loadDocument(doc, ensureBaseUri(null), loadingOptions); - } - - public static Object loadDocument(final String doc, final String uri) { - return loadDocument(doc, uri, null); - } - - public static Object loadDocument( - final String doc, final String uri_, final LoadingOptions loadingOptions_) { - final String uri = ensureBaseUri(uri_); - LoadingOptions loadingOptions = loadingOptions_; - if (loadingOptions == null) { - loadingOptions = new LoadingOptionsBuilder().setFileUri(uri).build(); - } - final Map result = YamlUtils.mapFromString(doc); - loadingOptions.idx.put(uri, result); - return loadDocument(result, uri, loadingOptions); - } - - static String readPath(final Path path) { - try { - return new String(Files.readAllBytes(path), "UTF8"); - } catch (final IOException e) { - throw new RuntimeException(e); - } - } - - static String ensureBaseUri(final String baseUri_) { - String baseUri = baseUri_; - if(baseUri == null) { - baseUri = Uris.fileUri(Paths.get(".").toAbsolutePath().normalize().toString()) + "/"; - } - return baseUri; - } - -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Saveable.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Saveable.java deleted file mode 100644 index afb775e4..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Saveable.java +++ /dev/null @@ -1,6 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -public interface Saveable { - // TODO: implement writable interface - // public abstract void save(boolean top, String baseUrl, boolean relativeUris); -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/SaveableImpl.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/SaveableImpl.java deleted file mode 100644 index 0b229c9e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/SaveableImpl.java +++ /dev/null @@ -1,5 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -public class SaveableImpl implements Saveable { - public SaveableImpl(Object doc, String baseUri, LoadingOptions loadingOptions, String docRoot) {} -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/SecondaryFilesDslLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/SecondaryFilesDslLoader.java deleted file mode 100644 index 8a560d4e..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/SecondaryFilesDslLoader.java +++ /dev/null @@ -1,86 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -public class SecondaryFilesDslLoader implements Loader { - private final Loader innerLoader; - - public SecondaryFilesDslLoader(final Loader innerLoader) { - this.innerLoader = innerLoader; - } - - - public T load( - final Object doc_, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - Object doc = doc_; - List> r = new ArrayList>(); - if (doc instanceof List) { - final List docList = (List) doc; - for (final Object d : docList) { - Map entry = new HashMap(); - if (d instanceof String) { - String dString = (String) d; - if (dString.endsWith("?")) { - entry.put("pattern", dString.substring(0, dString.length()-1)); - entry.put("required", false); - } else { - entry.put("pattern", dString); - } - r.add(entry); - } else if (d instanceof Map) { - @SuppressWarnings("unchecked") - Map dMap = new HashMap((Map) d); - if (dMap.containsKey("pattern")) { - entry.put("pattern", dMap.remove("pattern")); - } else { - throw new ValidationException("Missing 'pattern' in secondaryFiles specification entry."); - } - if (dMap.containsKey("required")) { - entry.put("required", dMap.remove("required")); - } - if (dMap.size() > 0) { - throw new ValidationException("Unallowed values in secondaryFiles specification entry."); - } - r.add(entry); - } else { - throw new ValidationException("Expected a string or sequence of (strings or mappings)."); - } - } - } else if (doc instanceof Map) { - Map entry = new HashMap(); - @SuppressWarnings("unchecked") - Map dMap = new HashMap((Map) doc); - if (dMap.containsKey("pattern")) { - entry.put("pattern", dMap.remove("pattern")); - } else { - throw new ValidationException("Missing 'pattern' in secondaryFiles specification entry."); - } - if (dMap.containsKey("required")) { - entry.put("required", dMap.remove("required")); - } - if (dMap.size() > 0) { - throw new ValidationException("Unallowed values in secondaryFiles specification entry."); - } - r.add(entry); - } else if (doc instanceof String) { - String dString = (String) doc; - Map entry = new HashMap(); - if (dString.endsWith("?")) { - entry.put("pattern", dString.substring(0, dString.length()-1)); - entry.put("required", false); - } else { - entry.put("pattern", dString); - } - r.add(entry); - } else { - throw new ValidationException("Expected a string or sequence of (strings or mappings)."); - } - return this.innerLoader.load(r, baseUri, loadingOptions, docRoot); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/TypeDslLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/TypeDslLoader.java deleted file mode 100644 index 0f32b48b..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/TypeDslLoader.java +++ /dev/null @@ -1,81 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.regex.Matcher; -import java.util.regex.Pattern; - -public class TypeDslLoader implements Loader { - private final Loader innerLoader; - private final Integer refScope; - private static final Pattern TYPE_DSL_REGEX = Pattern.compile("^([^\\[?]+)(\\[\\])?(\\?)?$"); - - public TypeDslLoader(final Loader innerLoader, final Integer refScope) { - this.innerLoader = innerLoader; - this.refScope = refScope; - } - - private Object resolve( - final String doc_, final String baseUri, final LoadingOptions loadingOptions) { - final Matcher m = TYPE_DSL_REGEX.matcher(doc_); - if (m.matches()) { - final String first = - loadingOptions.expandUrl(m.group(1), baseUri, false, true, this.refScope); - Object second = null; - Object third = null; - if (m.group(2) != null && m.group(2).length() > 0) { - HashMap resolvedMap = new HashMap(); - resolvedMap.put("type", "array"); - resolvedMap.put("items", first); - second = resolvedMap; - } - if (m.group(3) != null && m.group(3).length() > 0) { - third = Arrays.asList("null", second != null ? second : first); - } - if (third != null) { - return third; - } else { - return second != null ? second : first; - } - } else { - return doc_; - } - } - - public T load( - final Object doc_, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - Object doc = doc_; - if (doc instanceof List) { - final List docList = (List) doc; - final List r = new ArrayList(); - for (final Object d : docList) { - if (d instanceof String) { - Object resolved = this.resolve((String) d, baseUri, loadingOptions); - if (resolved instanceof List) { - List resolvedList = (List) resolved; - for (Object i : resolvedList) { - if (!r.contains(i)) { - r.add(i); - } - } - } else { - if (!r.contains(resolved)) { - r.add(resolved); - } - } - } else { - r.add(d); - } - } - doc = docList; - } else if (doc instanceof String) { - doc = this.resolve((String) doc, baseUri, loadingOptions); - } - return this.innerLoader.load(doc, baseUri, loadingOptions); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/UnionLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/UnionLoader.java deleted file mode 100644 index ec57efc9..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/UnionLoader.java +++ /dev/null @@ -1,41 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - -public class UnionLoader implements Loader { - private final ArrayList alternates; - - public UnionLoader(List alternates) { - this.alternates = new ArrayList(alternates); - } - - public UnionLoader(Loader[] alternates) { - this(Arrays.asList(alternates)); - } - - public void addLoaders(List loaders) { - this.alternates.addAll(loaders); - } - - public void addLoaders(Loader[] loaders) { - this.addLoaders(Arrays.asList(loaders)); - } - - public Object load( - final Object doc, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - final List errors = new ArrayList(); - for (final Loader loader : this.alternates) { - try { - return loader.load(doc, baseUri, loadingOptions, docRoot); - } catch (ValidationException e) { - errors.add(e); - } - } - throw new ValidationException("Failed to match union type", errors); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/UriLoader.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/UriLoader.java deleted file mode 100644 index c861396a..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/UriLoader.java +++ /dev/null @@ -1,59 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.ArrayList; -import java.util.List; - -public class UriLoader implements Loader { - private final Loader innerLoader; - private final boolean scopedId; - private final boolean vocabTerm; - private final Integer scopedRef; - private final Boolean noLinkCheck; - - public UriLoader( - final Loader innerLoader, - final boolean scopedId, - final boolean vocabTerm, - final Integer scopedRef, - final Boolean noLinkCheck) { - this.innerLoader = innerLoader; - this.scopedId = scopedId; - this.vocabTerm = vocabTerm; - this.scopedRef = scopedRef; - this.noLinkCheck = noLinkCheck; - } - - private Object expandUrl( - final Object object, final String baseUri, final LoadingOptions loadingOptions) { - if (object instanceof String) { - return loadingOptions.expandUrl( - (String) object, baseUri, this.scopedId, this.vocabTerm, this.scopedRef); - } else { - return object; - } - } - - public T load( - final Object doc_, - final String baseUri, - final LoadingOptions loadingOptions, - final String docRoot) { - LoadingOptions innerLoadingOptions = loadingOptions; - if (this.noLinkCheck != null) { - innerLoadingOptions = new LoadingOptionsBuilder().copiedFrom(loadingOptions).setNoLinkCheck(this.noLinkCheck).build(); - } - Object doc = doc_; - if (doc instanceof List) { - List docList = (List) doc; - List docWithExpansion = new ArrayList(); - for (final Object el : docList) { - docWithExpansion.add(this.expandUrl(el, baseUri, innerLoadingOptions)); - } - doc = docWithExpansion; - } - if (doc instanceof String) { - doc = this.expandUrl(doc, baseUri, innerLoadingOptions); - } - return this.innerLoader.load(doc, baseUri, innerLoadingOptions); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Uris.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Uris.java deleted file mode 100644 index 2aa12481..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Uris.java +++ /dev/null @@ -1,129 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.io.UnsupportedEncodingException; -import java.net.URI; -import java.net.URISyntaxException; -import java.nio.charset.StandardCharsets; - -public class Uris { - - // Emulate Python's urlsplit. - public static class UriSplit { - String scheme; - String netloc; - String path; - String query; - String fragment; - - public UriSplit(String scheme, String netloc, String path, String query, String fragment) { - this.scheme = scheme; - this.netloc = netloc; - this.path = path; - this.query = query; - this.fragment = fragment; - } - - public String toString() { - return String.format("UriSplit[%s,%s,%s,%s,%s]", this.scheme, this.netloc, this.path, this.query, - this.fragment); - } - - } - - public static String fileUri(final String path) { - return fileUri(path, false); - } - - public static String fileUri(final String path, final boolean splitFrag) { - if (path.equals("file://")) { - return path; - } - String frag; - String urlPath; - if (splitFrag) { - final String[] pathsp = path.split("#", 2); - // is quoting this? - urlPath = Uris.quote(pathsp[0]); - if (pathsp.length == 2) { - frag = "#" + Uris.quote(pathsp[1]); - } else { - frag = ""; - urlPath = Uris.quote(path); - } - } else { - urlPath = Uris.quote(path); - frag = ""; - } - if (urlPath.startsWith("//")) { - return "file:" + urlPath + frag; - } else { - return "file://" + urlPath + frag; - } - } - - public static UriSplit split(final String uriString) { - try { - final URI uri = new URI(uriString); - return new Uris.UriSplit(uri.getScheme(), uri.getAuthority(), uri.getPath(), uri.getQuery(), - uri.getFragment()); - } catch (URISyntaxException e) { - return new Uris.UriSplit(null, null, uriString, null, null); - } - } - - public static String unsplit(final String scheme, final String netloc, final String path, final String query, - final String fragment) { - try { - return new URI(scheme, netloc, path, query, fragment).toString(); - } catch (URISyntaxException e) { - if (scheme == null && path.startsWith("_:")) { - String uri = path; - if (fragment != null && fragment.length() > 0) { - uri += "#" + fragment; - } - return fragment; - } - throw new RuntimeException(e); - } - } - - public static URI toUri(final String url) { - try { - return new URI(url); - } catch (URISyntaxException e) { - throw new RuntimeException(e); - } - } - - public static String quote(final String uri) { - try { - return java.net.URLDecoder.decode(uri, StandardCharsets.UTF_8.name()); - } catch (UnsupportedEncodingException e) { - throw new RuntimeException(e); - } - } - - public static String unquote(final String uri) { - try { - return java.net.URLEncoder.encode(uri, StandardCharsets.UTF_8.name()); - } catch (UnsupportedEncodingException e) { - throw new RuntimeException(e); - } - } - - public static String shortname(final String input_id) { - try { - final URI uri = new URI(input_id); - final String fragment = uri.getFragment(); - if (fragment != null) { - String[] fragment_elements = fragment.split("/"); - return fragment_elements[fragment_elements.length - 1]; - } else { - String[] path_elements = uri.getPath().split("/"); - return path_elements[path_elements.length - 1]; - } - } catch (URISyntaxException e) { - return input_id; - } - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/ValidationException.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/ValidationException.java deleted file mode 100644 index 0893e1e1..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/ValidationException.java +++ /dev/null @@ -1,80 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - -public class ValidationException extends RuntimeException { - private final List children; - private String bullet = ""; - private String currentMessage; - - public ValidationException(final String message) { - this(message, (List) null); - } - - public ValidationException(final String message, final ValidationException child) { - this(message, Arrays.asList(child)); - } - - public ValidationException(final String message, final List children_) { - super(message); - this.currentMessage = message; - final List children = new ArrayList(); - if (children_ != null) { - for (final ValidationException child : children_) { - children.addAll(child.simplify()); - } - } - this.children = children; - } - - public ValidationException withBullet(final String bullet) { - this.bullet = bullet; - return this; - } - - public List simplify() { - if (getMessage().length() > 0) { - return Arrays.asList(this); - } else { - return this.children; - } - } - - public String summary(final int level, final boolean withBullet) { - final int indentPerLevel = 2; - final String spaces = new String(new char[level * indentPerLevel]).replace("\0", " "); - final String bullet; - if (this.bullet.length() > 0 && withBullet) { - bullet = this.bullet; - } else { - bullet = ""; - } - return spaces + bullet + this.currentMessage; - } - - public String prettyStr(final Integer level_) { - Integer level = level_; - if (level == null) { - level = 0; - } - final List parts = new ArrayList(); - int nextLevel; - if (this.currentMessage != null && this.currentMessage.length() > 0) { - parts.add(this.summary(level, true)); - nextLevel = level + 1; - } else { - nextLevel = level; - } - for (final ValidationException child : this.children) { - parts.add(child.prettyStr(nextLevel)); - } - final String ret = String.join("\n", parts); - return ret; - } - - public String getMessage() { - return this.prettyStr(null); - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Validator.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Validator.java deleted file mode 100644 index eea66445..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Validator.java +++ /dev/null @@ -1,24 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.io.File; -import org.snakeyaml.engine.v2.api.Dump; -import org.snakeyaml.engine.v2.api.DumpSettings; -import org.snakeyaml.engine.v2.common.ScalarStyle; - -import com.fasterxml.jackson.annotation.JsonInclude.Include; -import com.fasterxml.jackson.databind.ObjectMapper; - -public class Validator { - public static void main(final String[] args) throws Exception { - if (args.length != 1) { - throw new Exception("No argument supplied to validate."); - } - // TODO: allow URLs and such. - final File uri = new File(args[0]); - Object doc = RootLoader.loadDocument(uri); - ObjectMapper mapper = new ObjectMapper(); - mapper.setSerializationInclusion(Include.NON_NULL).writerWithDefaultPrettyPrinter().writeValue(System.out, doc); - System.out.println(); - - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/YamlUtils.java b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/YamlUtils.java deleted file mode 100644 index 343c2405..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/YamlUtils.java +++ /dev/null @@ -1,31 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Objects; -import java.util.regex.Pattern; - -import org.snakeyaml.engine.v2.api.Load; -import org.snakeyaml.engine.v2.api.LoadSettings; -import org.snakeyaml.engine.v2.nodes.Tag; -import org.snakeyaml.engine.v2.resolver.ScalarResolver; -import org.snakeyaml.engine.v2.schema.CoreSchema; - -public class YamlUtils { - - public static Map mapFromString(final String text) { - LoadSettings settings = LoadSettings.builder().setSchema(new CoreSchema()).build(); - Load load = new Load(settings); - final Map result = (Map) load.loadFromString(text); - return result; - } - - public static List listFromString(final String text) { - LoadSettings settings = LoadSettings.builder().setSchema(new CoreSchema()).build(); - Load load = new Load(settings); - final List result = (List) load.loadFromString(text); - return result; - } -} diff --git a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/package.html b/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/package.html deleted file mode 100644 index fb58a00d..00000000 --- a/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/package.html +++ /dev/null @@ -1,3 +0,0 @@ - -This package contains utilities for working the SchemaSalad generated code for the org.commonwl.cwlsdk.cwl1_2 package. - diff --git a/src/main/javadoc/overview.html b/src/main/javadoc/overview.html deleted file mode 100644 index 71853196..00000000 --- a/src/main/javadoc/overview.html +++ /dev/null @@ -1,4 +0,0 @@ - - This project contains Java objects and utilities auto-generated by Schema Salad - for parsing documents corresponding to the https://w3id.org/cwl/cwl# schema. - diff --git a/src/main/resources/META-INF/MANIFEST.MF b/src/main/resources/META-INF/MANIFEST.MF deleted file mode 100644 index 47659aa6..00000000 --- a/src/main/resources/META-INF/MANIFEST.MF +++ /dev/null @@ -1,2 +0,0 @@ -Manifest-Version: 1.0 -Main-Class: org.commonwl.cwlsdk.cwl1_2.utils.Validator diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/AnonymousRecordTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/AnonymousRecordTest.java deleted file mode 100644 index 74ea0163..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/AnonymousRecordTest.java +++ /dev/null @@ -1,11 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -public class AnonymousRecordTest { - - @org.junit.Test - public void test_record_with_anonymous_type_record() throws Exception { - java.net.URL url = getClass().getResource("record-in-format.cwl.json"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/DefaultFetcherTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/DefaultFetcherTest.java deleted file mode 100644 index b4aa7e06..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/DefaultFetcherTest.java +++ /dev/null @@ -1,37 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import org.junit.Assert; -import org.junit.Test; - -public class DefaultFetcherTest { - @Test - public void testUnderscoreJoin() { - final DefaultFetcher fetcher = new DefaultFetcher(); - Assert.assertEquals(fetcher.urlJoin("http://googl.com/", "_:/moo"), "_:/moo"); - } - - @Test - public void testUnixJoin() { - final DefaultFetcher fetcher = new DefaultFetcher(); - String url; - - url = fetcher.urlJoin("file:///home/fred/foo.cwl", "soup.cwl"); - Assert.assertEquals(url, "file:///home/fred/soup.cwl"); - - url = fetcher.urlJoin("file:///home/fred/foo.cwl", "../alice/soup.cwl"); - Assert.assertEquals(url, "file:///home/alice/soup.cwl"); - // relative from root - url = fetcher.urlJoin("file:///home/fred/foo.cwl", "/baz/soup.cwl"); - Assert.assertEquals(url, "file:///baz/soup.cwl"); - - url = fetcher.urlJoin("file:///home/fred/foo.cwl", "http://example.com/bar/soup.cwl"); - Assert.assertEquals(url, "http://example.com/bar/soup.cwl"); - - url = fetcher.urlJoin("http://example.com/fred/foo.cwl", "soup.cwl"); - Assert.assertEquals(url, "http://example.com/fred/soup.cwl"); - - // Root-relative -- here relative to http host, not file:/// - url = fetcher.urlJoin("http://example.com/fred/foo.cwl", "/bar/soup.cwl"); - Assert.assertEquals(url, "http://example.com/bar/soup.cwl"); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/ExamplesTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/ExamplesTest.java deleted file mode 100644 index b3a906f2..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/ExamplesTest.java +++ /dev/null @@ -1,5429 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -public class ExamplesTest { - - @org.junit.Test - public void testvalid_stage_unprovided_fileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-unprovided-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stage_unprovided_fileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-unprovided-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stage_unprovided_fileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-unprovided-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_linkfileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_linkfile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_linkfileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_linkfile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_linkfileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_linkfile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wc_tool_shortcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wc-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wc_tool_shortcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wc-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wc_tool_shortcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wc-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_output_arrays_int_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_output_arrays_int_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_output_arrays_int_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat3_from_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat3_from_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat3_from_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_pass_unconnectedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_pass-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_pass_unconnectedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_pass-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_pass_unconnectedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_pass-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_output_arrays_intByString() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-int.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_output_arrays_intByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-int.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_output_arrays_intByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-int.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines7_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines7-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines7_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines7-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines7_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines7-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_symlink_legalByString() throws Exception { - java.net.URL url = getClass().getResource("valid_symlink-legal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_symlink_legalByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_symlink-legal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_symlink_legalByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_symlink-legal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_any_type_compatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_any-type-compat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_any_type_compatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_any-type-compat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_any_type_compatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_any-type-compat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_docker_output_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-output-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_docker_output_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-output-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_docker_output_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-output-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_output_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-output-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_output_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-output-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_output_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-output-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_wf3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_outputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_outputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_outputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wf_loadContents2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wf_loadContents2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wf_loadContents2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimit2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimit2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimit2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_anon_enum_inside_array_inside_schemadefByString() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array_inside_schemadef.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_anon_enum_inside_array_inside_schemadefByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array_inside_schemadef.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_anon_enum_inside_array_inside_schemadefByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array_inside_schemadef.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_imported_hintByString() throws Exception { - java.net.URL url = getClass().getResource("valid_imported-hint.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_imported_hintByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_imported-hint.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_imported_hintByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_imported-hint.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimit3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimit3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimit3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wf_loadContents4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wf_loadContents4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wf_loadContents4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_docker_array_secondaryfilesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-array-secondaryfiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_docker_array_secondaryfilesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-array-secondaryfiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_docker_array_secondaryfilesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-array-secondaryfiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wc2_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wc2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wc2_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wc2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wc2_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wc2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stderrByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stderrByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stderrByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wf_loadContents3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wf_loadContents3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wf_loadContents3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_schemadef_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_schemadef_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_schemadef_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stderr_mediumcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stderr_mediumcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stderr_mediumcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwdr_entryByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr-entry.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwdr_entryByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr-entry.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwdr_entryByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr-entry.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines17_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines17-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines17_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines17-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines17_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines17-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_updatedir_inplaceByString() throws Exception { - java.net.URL url = getClass().getResource("valid_updatedir_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_updatedir_inplaceByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_updatedir_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_updatedir_inplaceByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_updatedir_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_sum_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_sum-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_sum_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_sum-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_sum_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_sum-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines2_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines2_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines2_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines14_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines14-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines14_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines14-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines14_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines14-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_wf3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_wf3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_wf3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines6_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines6-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines6_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines6-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines6_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines6-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_vf_concatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_vf-concat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_vf_concatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_vf-concat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_vf_concatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_vf-concat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_deep1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_deep1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_deep1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_deep1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_deep1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_deep1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_js_expr_req_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_js-expr-req-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_js_expr_req_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_js-expr-req-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_js_expr_req_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_js-expr-req-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_wf5ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf5ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf5ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_recursive_input_directoryByString() throws Exception { - java.net.URL url = getClass().getResource("valid_recursive-input-directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_recursive_input_directoryByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_recursive-input-directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_recursive_input_directoryByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_recursive-input-directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines9_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines9-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines9_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines9-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines9_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines9-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_formattest3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_formattest3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_formattest3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat3_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat3_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat3_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_writable_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_writable-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_writable_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_writable-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_writable_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_writable-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_null_expression2_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_null_expression2_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_null_expression2_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_no_outputs_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_no-outputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_no_outputs_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_no-outputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_no_outputs_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_no-outputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines3_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines3_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines3_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_wf4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines11_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines11_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines11_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwdr_with_nested_dirsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr_with_nested_dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwdr_with_nested_dirsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr_with_nested_dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwdr_with_nested_dirsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr_with_nested_dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines1_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines1-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines1_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines1-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines1_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines1-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_tool_defaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_tool_defaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_tool_defaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_glob_path_errorByString() throws Exception { - java.net.URL url = getClass().getResource("valid_glob-path-error.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_glob_path_errorByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_glob-path-error.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_glob_path_errorByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_glob-path-error.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_fail_unspecified_inputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_fail-unspecified-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_fail_unspecified_inputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_fail-unspecified-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_fail_unspecified_inputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_fail-unspecified-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_inline_jsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_inline-js.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_inline_jsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_inline-js.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_inline_jsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_inline-js.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines16_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines16-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines16_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines16-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines16_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines16-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wc_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wc-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wc_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wc-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wc_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wc-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_steplevel_resreqByString() throws Exception { - java.net.URL url = getClass().getResource("valid_steplevel-resreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_steplevel_resreqByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_steplevel-resreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_steplevel_resreqByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_steplevel-resreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_int_default_tool_and_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-default-tool-and-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_int_default_tool_and_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-default-tool-and-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_int_default_tool_and_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-default-tool-and-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_nested_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_nested-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_nested_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_nested-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_nested_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_nested-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_no_inputs_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_no-inputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_no_inputs_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_no-inputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_no_inputs_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_no-inputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stderr_shortcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stderr_shortcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stderr_shortcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_in_secondaryFiles_missing_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles-missing-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_in_secondaryFiles_missing_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles-missing-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_in_secondaryFiles_missing_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles-missing-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_networkaccess2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_networkaccess2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_networkaccess2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_networkaccess2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_networkaccess2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_networkaccess2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_mkdirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_mkdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_mkdirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_mkdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_mkdirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_mkdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_valueFrom_constantByString() throws Exception { - java.net.URL url = getClass().getResource("valid_valueFrom-constant.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_valueFrom_constantByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_valueFrom-constant.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_valueFrom_constantByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_valueFrom-constant.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_test_cwl_out2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_test-cwl-out2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_test_cwl_out2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_test-cwl-out2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_test_cwl_out2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_test-cwl-out2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_metadataByString() throws Exception { - java.net.URL url = getClass().getResource("valid_metadata.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_metadataByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_metadata.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_metadataByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_metadata.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines9_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines9-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines9_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines9-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines9_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines9-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_any_wf_1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-any-wf-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_any_wf_1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-any-wf-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_any_wf_1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-any-wf-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_file_default_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-file-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_file_default_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-file-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_file_default_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-file-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_empty_array_inputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_empty-array-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_empty_array_inputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_empty-array-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_empty_array_inputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_empty-array-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_inpdir_update_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_inpdir_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_inpdir_update_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_inpdir_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_inpdir_update_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_inpdir_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wc3_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wc3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wc3_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wc3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wc3_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wc3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dir7ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir7.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dir7ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir7.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dir7ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir7.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_binding_testByString() throws Exception { - java.net.URL url = getClass().getResource("valid_binding-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_binding_testByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_binding-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_binding_testByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_binding-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines5_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines5_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines5_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_networkaccessByString() throws Exception { - java.net.URL url = getClass().getResource("valid_networkaccess.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_networkaccessByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_networkaccess.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_networkaccessByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_networkaccess.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat3_tool_dockerByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat3_tool_dockerByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat3_tool_dockerByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_optional_outputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_optional-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_optional_outputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_optional-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_optional_outputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_optional-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines8_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines8-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines8_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines8-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines8_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines8-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_wf2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_touchByString() throws Exception { - java.net.URL url = getClass().getResource("valid_touch.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_touchByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_touch.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_touchByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_touch.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat1_testcliByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat1-testcli.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat1_testcliByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat1-testcli.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat1_testcliByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat1-testcli.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dir2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dir2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dir2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_any_1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-any-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_any_1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-any-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_any_1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-any-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_revtoolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_revtool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_revtoolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_revtool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_revtoolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_revtool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_bool_empty_inputbindingByString() throws Exception { - java.net.URL url = getClass().getResource("valid_bool-empty-inputbinding.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_bool_empty_inputbindingByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_bool-empty-inputbinding.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_bool_empty_inputbindingByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_bool-empty-inputbinding.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_tool1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_tool1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_tool1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimit3_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimit3_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimit3_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_anon_enum_inside_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_anon_enum_inside_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_anon_enum_inside_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_no_outputs_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_no-outputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_no_outputs_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_no-outputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_no_outputs_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_no-outputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_wf_defaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-wf-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_wf_defaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-wf-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_wf_defaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-wf-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_int_optional_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-optional-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_int_optional_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-optional-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_int_optional_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-optional-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat3_tool_shortcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat3_tool_shortcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat3_tool_shortcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines11_extra_step_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-extra-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines11_extra_step_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-extra-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines11_extra_step_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-extra-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_sum_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_sum-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_sum_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_sum-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_sum_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_sum-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stage_file_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stage_file_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stage_file_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_initialworkdir_glob_fullpathByString() throws Exception { - java.net.URL url = getClass().getResource("valid_initialworkdir-glob-fullpath.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_initialworkdir_glob_fullpathByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_initialworkdir-glob-fullpath.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_initialworkdir_glob_fullpathByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_initialworkdir-glob-fullpath.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines11_null_step_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-null-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines11_null_step_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-null-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines11_null_step_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-null-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_position_exprByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-position-expr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_position_exprByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-position-expr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_position_exprByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-position-expr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_wf4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_wf4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_wf4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_wf2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_wf2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_wf2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_no_inputs_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_no-inputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_no_inputs_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_no-inputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_no_inputs_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_no-inputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_wf2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_wf2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_wf2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_glob_expr_listByString() throws Exception { - java.net.URL url = getClass().getResource("valid_glob-expr-list.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_glob_expr_listByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_glob-expr-list.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_glob_expr_listByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_glob-expr-list.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_runtime_paths_distinctByString() throws Exception { - java.net.URL url = getClass().getResource("valid_runtime-paths-distinct.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_runtime_paths_distinctByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_runtime-paths-distinct.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_runtime_paths_distinctByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_runtime-paths-distinct.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_wf1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_inputs_wf1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-inputs-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_inputs_wf1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-inputs-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_inputs_wf1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-inputs-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines10_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines10-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines10_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines10-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines10_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines10-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_glob_directoryByString() throws Exception { - java.net.URL url = getClass().getResource("valid_glob_directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_glob_directoryByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_glob_directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_glob_directoryByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_glob_directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_import_schema_defByString() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_import_schema_defByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_import_schema_defByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_docker_run_cmdByString() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-run-cmd.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_docker_run_cmdByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-run-cmd.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_docker_run_cmdByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-run-cmd.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_glob_testByString() throws Exception { - java.net.URL url = getClass().getResource("valid_glob_test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_glob_testByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_glob_test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_glob_testByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_glob_test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_basename_fields_testByString() throws Exception { - java.net.URL url = getClass().getResource("valid_basename-fields-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_basename_fields_testByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_basename-fields-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_basename_fields_testByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_basename-fields-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_tool_packed2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-packed2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_tool_packed2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-packed2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_tool_packed2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-packed2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wf_loadContentsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wf_loadContentsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wf_loadContentsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_in_secondaryFilesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_in_secondaryFilesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_in_secondaryFilesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_writable_dir_dockerByString() throws Exception { - java.net.URL url = getClass().getResource("valid_writable-dir-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_writable_dir_dockerByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_writable-dir-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_writable_dir_dockerByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_writable-dir-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_tool2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_tool2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_tool2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_searchByString() throws Exception { - java.net.URL url = getClass().getResource("valid_search.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_searchByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_search.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_searchByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_search.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_tool_packedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_tool_packedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_tool_packedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines11_null_step_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-null-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines11_null_step_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-null-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines11_null_step_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-null-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines1_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines1-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines1_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines1-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines1_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines1-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stage_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stage_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stage_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_envvar3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_envvar3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_envvar3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_renameByString() throws Exception { - java.net.URL url = getClass().getResource("valid_rename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_renameByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_rename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_renameByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_rename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_wf1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_wf1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_wf1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines12_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines12-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines12_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines12-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines12_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines12-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_union_input_default_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-union-input-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_union_input_default_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-union-input-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_union_input_default_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-union-input-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines13_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines13-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines13_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines13-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines13_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines13-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_shallow1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_shallow1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_shallow1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_shallow1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_shallow1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_shallow1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_wf6ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf6ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf6ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreqByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreqByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreqByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat5_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat5-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat5_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat5-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat5_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat5-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimitByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimitByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimitByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_none1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_none1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_none1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_none2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_none2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_none2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines11_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines11_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines11_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stagefileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stagefile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stagefileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stagefile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stagefileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stagefile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stage_file_array_basename_and_entrynameByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array_basename_and_entryname.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stage_file_array_basename_and_entrynameByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array_basename_and_entryname.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stage_file_array_basename_and_entrynameByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array_basename_and_entryname.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_shellchar2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_shellchar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_shellchar2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_shellchar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_shellchar2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_shellchar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_out_secondaryFilesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-out-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_out_secondaryFilesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-out-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_out_secondaryFilesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-out-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_inp_update_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_inp_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_inp_update_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_inp_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_inp_update_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_inp_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_bwa_mem_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_bwa-mem-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_bwa_mem_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_bwa-mem-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_bwa_mem_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_bwa-mem-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat3_tool_mediumcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat3_tool_mediumcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat3_tool_mediumcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_tool3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_tool3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_tool3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimit2_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimit2_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimit2_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_revsort_packedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_revsort_packedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_revsort_packedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_null_definedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_null-defined.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_null_definedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_null-defined.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_null_definedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_null-defined.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_none3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_none3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_none3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_wf3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_wf3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_wf3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_int_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_int_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_int_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_file_literal_exByString() throws Exception { - java.net.URL url = getClass().getResource("valid_file-literal-ex.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_file_literal_exByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_file-literal-ex.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_file_literal_exByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_file-literal-ex.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_revsortByString() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_revsortByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_revsortByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_tmap_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_tmap-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_tmap_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_tmap-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_tmap_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_tmap-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_tool4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_tool4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_tool4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stage_array_dirsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-array-dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stage_array_dirsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-array-dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stage_array_dirsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-array-dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_formattestByString() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_formattestByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_formattestByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreq_workflow_stepdefaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-stepdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreq_workflow_stepdefaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-stepdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreq_workflow_stepdefaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-stepdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_size_expression_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_size-expression-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_size_expression_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_size-expression-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_size_expression_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_size-expression-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_out_formatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-out-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_out_formatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-out-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_out_formatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-out-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wc4_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wc4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wc4_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wc4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wc4_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wc4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_step_valuefrom5_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_step_valuefrom5_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_step_valuefrom5_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_file_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-file-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_file_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-file-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_file_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-file-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_step_valuefrom_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_step_valuefrom_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_step_valuefrom_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_output_arrays_file_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-file-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_output_arrays_file_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-file-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_output_arrays_file_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-file-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat_from_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat_from_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat_from_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_fail_unconnectedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_fail-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_fail_unconnectedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_fail-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_fail_unconnectedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_fail-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_symlink_illegalByString() throws Exception { - java.net.URL url = getClass().getResource("valid_symlink-illegal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_symlink_illegalByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_symlink-illegal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_symlink_illegalByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_symlink-illegal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimit4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimit4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimit4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_step_valuefrom2_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_step_valuefrom2_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_step_valuefrom2_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valueFrom_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valueFrom-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valueFrom_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valueFrom-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valueFrom_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valueFrom-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_initialworkdirrequirement_docker_outByString() throws Exception { - java.net.URL url = getClass().getResource("valid_initialworkdirrequirement-docker-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_initialworkdirrequirement_docker_outByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_initialworkdirrequirement-docker-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_initialworkdirrequirement_docker_outByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_initialworkdirrequirement-docker-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_sd_secondaryFilesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-sd-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_sd_secondaryFilesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-sd-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_sd_secondaryFilesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-sd-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_formattest2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_formattest2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_formattest2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_shallow2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_shallow2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_shallow2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_shallow2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_shallow2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_shallow2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_in_secondaryFiles_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_in_secondaryFiles_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_in_secondaryFiles_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_shellcharByString() throws Exception { - java.net.URL url = getClass().getResource("valid_shellchar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_shellcharByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_shellchar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_shellcharByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_shellchar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_step_valuefrom4_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_step_valuefrom4_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_step_valuefrom4_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_template_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_template-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_template_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_template-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_template_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_template-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_schemadef_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_schemadef_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_schemadef_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreq_workflowByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreq_workflowByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreq_workflowByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dir3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dir3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dir3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreq_workflow_inputdefaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-inputdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreq_workflow_inputdefaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-inputdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreq_workflow_inputdefaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-inputdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_null_expression1_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression1-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_null_expression1_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression1-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_null_expression1_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression1-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_envvar2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_envvar2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_envvar2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_conflict_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_conflict-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_conflict_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_conflict-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_conflict_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_conflict-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreq_workflow_tooldefaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-tooldefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreq_workflow_tooldefaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-tooldefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreq_workflow_tooldefaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-tooldefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_test_cwl_outByString() throws Exception { - java.net.URL url = getClass().getResource("valid_test-cwl-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_test_cwl_outByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_test-cwl-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_test_cwl_outByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_test-cwl-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreq_defaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreq_defaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreq_defaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_in_formatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_in_formatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_in_formatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_exitcodeByString() throws Exception { - java.net.URL url = getClass().getResource("valid_exitcode.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_exitcodeByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_exitcode.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_exitcodeByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_exitcode.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_sorttoolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_sorttool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_sorttoolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_sorttool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_sorttoolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_sorttool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_import_schema_def_packedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def_packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_import_schema_def_packedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def_packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_import_schema_def_packedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def_packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines4_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines4_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines4_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dir6ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dir6ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dir6ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreq_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreq_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreq_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_int_default_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_int_default_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_int_default_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines18_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines18-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines18_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines18-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines18_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines18-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dir4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dir4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dir4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat3_nodockerByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-nodocker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat3_nodockerByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-nodocker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat3_nodockerByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-nodocker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_params2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_params2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_params2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_params2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_params2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_params2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_envvarByString() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_envvarByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_envvarByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines15_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines15-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines15_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines15-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines15_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines15-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines8_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines8-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines8_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines8-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines8_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines8-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_default_pathByString() throws Exception { - java.net.URL url = getClass().getResource("valid_default_path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_default_pathByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_default_path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_default_pathByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_default_path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_file_or_filesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-file-or-files.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_file_or_filesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-file-or-files.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_file_or_filesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-file-or-files.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_paramsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_params.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_paramsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_params.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_paramsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_params.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_initialwork_pathByString() throws Exception { - java.net.URL url = getClass().getResource("valid_initialwork-path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_initialwork_pathByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_initialwork-path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_initialwork_pathByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_initialwork-path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_parseInt_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_parseInt-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_parseInt_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_parseInt-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_parseInt_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_parseInt-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_step_valuefrom3_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_step_valuefrom3_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_step_valuefrom3_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_namerootByString() throws Exception { - java.net.URL url = getClass().getResource("valid_nameroot.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_namerootByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_nameroot.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_namerootByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_nameroot.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_exit_successByString() throws Exception { - java.net.URL url = getClass().getResource("valid_exit-success.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_exit_successByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_exit-success.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_exit_successByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_exit-success.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stage_file_array_basenameByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array_basename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stage_file_array_basenameByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array_basename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stage_file_array_basenameByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array_basename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_wf1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_wf1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_wf1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat4_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat4_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat4_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_null_expression3_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_null_expression3_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_null_expression3_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimit5ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimit5ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimit5ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_optional_numerical_output_0ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_optional-numerical-output-0.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_optional_numerical_output_0ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_optional-numerical-output-0.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_optional_numerical_output_0ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_optional-numerical-output-0.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_updateval_inplaceByString() throws Exception { - java.net.URL url = getClass().getResource("valid_updateval_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_updateval_inplaceByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_updateval_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_updateval_inplaceByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_updateval_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines11_extra_step_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-extra-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines11_extra_step_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-extra-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines11_extra_step_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-extra-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dir5ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dir5ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dir5ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_deep2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_deep2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_deep2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_deep2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_deep2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_deep2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/PackedWorkflowClassTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/PackedWorkflowClassTest.java deleted file mode 100644 index 0fe3582f..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/PackedWorkflowClassTest.java +++ /dev/null @@ -1,41 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.net.URISyntaxException; -import java.nio.file.Paths; -import java.util.List; -import org.junit.Assert; -import org.junit.Test; -import org.commonwl.cwlsdk.cwl1_1.Process; -import org.commonwl.cwlsdk.cwl1_1.Workflow; -import org.commonwl.cwlsdk.cwl1_1.WorkflowStep; -import org.commonwl.cwlsdk.cwl1_1.WorkflowStepInput; - -public class PackedWorkflowClassTest { - List doc; - - @SuppressWarnings("unchecked") - public PackedWorkflowClassTest() throws URISyntaxException { - super(); - this.doc = - (List) - RootLoader.loadDocument( - Paths.get(getClass().getResource("valid_scatter-wf4.cwl").toURI())); - } - - @Test - public void className() { - Workflow workflow = (Workflow) doc.get(1); - Assert.assertEquals("WorkflowImpl", workflow.getClass().getSimpleName()); - } - - @Test - public void workflowStepInputSources() { - Workflow workflow = (Workflow) doc.get(1); - String workflow_id = workflow.getId().get(); - WorkflowStep step1 = (WorkflowStep) workflow.getSteps().get(0); - List inputs = step1.getIn(); - WorkflowStepInput step1_input1 = (WorkflowStepInput) inputs.get(0); - Assert.assertEquals(workflow_id + "/step1/echo_in1", step1_input1.getId().get()); - Assert.assertEquals(workflow_id + "/inp1", step1_input1.getSource()); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/RequirementsClassTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/RequirementsClassTest.java deleted file mode 100644 index 22db1541..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/RequirementsClassTest.java +++ /dev/null @@ -1,53 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.net.URISyntaxException; -import org.junit.Assert; -import org.junit.Test; -import org.commonwl.cwlsdk.cwl1_1.CWLVersion; -import org.commonwl.cwlsdk.cwl1_1.InlineJavascriptRequirement; -import org.commonwl.cwlsdk.cwl1_1.Process; - -public class RequirementsClassTest { - Process doc; - - public RequirementsClassTest() throws URISyntaxException { - super(); - this.doc = - (Process) - RootLoader.loadDocument( - java.nio.file.Paths.get( - getClass().getResource("valid_writable-dir-docker.cwl").toURI())); - } - - @Test - public void className() { - Assert.assertEquals("CommandLineToolImpl", doc.getClass().getSimpleName()); - } - - @Test - public void version() { - java.util.Optional version = doc.getCwlVersion(); - Assert.assertTrue(version.isPresent()); - Assert.assertEquals(CWLVersion.V1_1, version.get()); - } - - @Test - public void hints() { - java.util.Optional> hints = doc.getHints(); - Assert.assertTrue(hints.isPresent()); - java.util.List hintList = hints.get(); - Assert.assertEquals(1, hintList.size()); - } - - @Test - public void reqs() { - java.util.Optional> reqs = doc.getRequirements(); - Assert.assertTrue(reqs.isPresent()); - java.util.List reqList = reqs.get(); - Assert.assertEquals(2, reqList.size()); - InlineJavascriptRequirement reqOne = (InlineJavascriptRequirement) reqList.get(0); - Assert.assertEquals("InlineJavascriptRequirementImpl", reqOne.getClass().getSimpleName()); - Assert.assertNotEquals( - "InlineJavascriptRequirementImpl", reqList.get(1).getClass().getSimpleName()); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/SchemaDefTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/SchemaDefTest.java deleted file mode 100644 index ad953da6..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/SchemaDefTest.java +++ /dev/null @@ -1,42 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.List; -import org.junit.Assert; -import org.commonwl.cwlsdk.cwl1_1.InputRecordSchema; -import org.commonwl.cwlsdk.cwl1_1.Process; -import org.commonwl.cwlsdk.cwl1_1.SchemaDefRequirement; - -public class SchemaDefTest { - - @org.junit.Test - public void testvalid_anon_enum_inside_array_inside_schemadef() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array_inside_schemadef.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - Process doc = (Process) RootLoader.loadDocument(resPath); - java.util.Optional> reqs = doc.getRequirements(); - Assert.assertTrue(reqs.isPresent()); - java.util.List reqList = reqs.get(); - Assert.assertEquals(reqList.size(), 1); - SchemaDefRequirement schemaReq = (SchemaDefRequirement) reqList.get(0); - List schemaTypes = schemaReq.getTypes(); - for (Object schemaType : schemaTypes) { - Assert.assertTrue(schemaType instanceof InputRecordSchema); - } - } - - @org.junit.Test - public void testvalid_record_sd_secondaryFiles() throws Exception { - java.net.URL url = getClass().getResource("valid_record-sd-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - Process doc = (Process) RootLoader.loadDocument(resPath); - java.util.Optional> reqs = doc.getRequirements(); - Assert.assertTrue(reqs.isPresent()); - java.util.List reqList = reqs.get(); - Assert.assertEquals(reqList.size(), 1); - SchemaDefRequirement schemaReq = (SchemaDefRequirement) reqList.get(0); - List schemaTypes = schemaReq.getTypes(); - for (Object schemaType : schemaTypes) { - Assert.assertTrue(schemaType instanceof InputRecordSchema); - } - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/SecondaryFilesTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/SecondaryFilesTest.java deleted file mode 100644 index c91c7601..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/SecondaryFilesTest.java +++ /dev/null @@ -1,47 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.net.URISyntaxException; -import java.nio.file.Paths; -import java.util.List; -import org.junit.Assert; -import org.junit.Test; -import org.commonwl.cwlsdk.cwl1_1.Process; -import org.commonwl.cwlsdk.cwl1_1.SecondaryFileSchema; -import org.commonwl.cwlsdk.cwl1_1.Workflow; -import org.commonwl.cwlsdk.cwl1_1.WorkflowInputParameter; - -public class SecondaryFilesTest { - List doc; - - @SuppressWarnings("unchecked") - public SecondaryFilesTest() throws URISyntaxException { - super(); - this.doc = - (List) - RootLoader.loadDocument(Paths.get(getClass().getResource("525.cwl").toURI())); - } - - @SuppressWarnings("unchecked") - @Test - public void workflowInputSecFiles() { - Workflow workflow = (Workflow) doc.get(0); - String workflow_id = workflow.getId().get(); - List inputs = workflow.getInputs(); - WorkflowInputParameter wf_file_input = (WorkflowInputParameter) inputs.get(1); - Assert.assertEquals(workflow_id + "/wf_file_input", wf_file_input.getId().get()); - List sec_files_l1 = - (List) wf_file_input.getSecondaryFiles(); - Assert.assertEquals(1, sec_files_l1.size()); - SecondaryFileSchema sec_files1 = sec_files_l1.get(0); - Assert.assertEquals(".also", sec_files1.getPattern()); - Assert.assertEquals(true, sec_files1.getRequired()); - WorkflowInputParameter wf_file_input_array = (WorkflowInputParameter) inputs.get(2); - Assert.assertEquals(workflow_id + "/wf_file_input_array", wf_file_input_array.getId().get()); - List sec_files_l2 = - (List) wf_file_input_array.getSecondaryFiles(); - Assert.assertEquals(1, sec_files_l2.size()); - SecondaryFileSchema sec_files2 = sec_files_l2.get(0); - Assert.assertEquals(".also", sec_files2.getPattern()); - Assert.assertEquals(true, sec_files2.getRequired()); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/ShortnameTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/ShortnameTest.java deleted file mode 100644 index 7494ceaf..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/ShortnameTest.java +++ /dev/null @@ -1,24 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import org.junit.Assert; -import org.junit.Test; - -public class ShortnameTest { - @Test - public void testShortname() { - Assert.assertEquals(Uris.shortname( - "file:/Users/jdidion/projects/cwlScala/target/test-classes/CommandLineTools/conformance/#anon_enum_inside_array_inside_schemadef.cwl/first/user_type_2/species/homo_sapiens"), - "homo_sapiens"); - Assert.assertEquals(Uris.shortname( - "file:///home/michael/cwljava/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCh37"), - "GRCh37"); - // Below are from https://w3id.org/cwl/v1.2/SchemaSalad.html#Short_names - Assert.assertEquals(Uris.shortname("http://example.com/foo"), "foo"); - Assert.assertEquals(Uris.shortname("http://example.com/#bar"), "bar"); - Assert.assertEquals(Uris.shortname("http://example.com/foo/bar"), "bar"); - Assert.assertEquals(Uris.shortname("http://example.com/foo#bar"), "bar"); - Assert.assertEquals(Uris.shortname("http://example.com/#foo/bar"), "bar"); - Assert.assertEquals(Uris.shortname("http://example.com/foo#bar/baz"), "baz"); - } - -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/WorkflowClassTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/WorkflowClassTest.java deleted file mode 100644 index 9116f3d3..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/WorkflowClassTest.java +++ /dev/null @@ -1,32 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.net.URISyntaxException; -import org.junit.Assert; -import org.junit.Test; -import org.commonwl.cwlsdk.cwl1_1.CWLVersion; -import org.commonwl.cwlsdk.cwl1_1.Process; - -public class WorkflowClassTest { - Process doc; - - public WorkflowClassTest() throws URISyntaxException { - super(); - this.doc = - (Process) - RootLoader.loadDocument( - java.nio.file.Paths.get( - getClass().getResource("valid_count-lines1-wf.cwl").toURI())); - } - - @Test - public void className() { - Assert.assertEquals("WorkflowImpl", doc.getClass().getSimpleName()); - } - - @Test - public void version() { - java.util.Optional version = doc.getCwlVersion(); - Assert.assertTrue(version.isPresent()); - Assert.assertEquals(CWLVersion.V1_1, version.get()); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/YamlUtilsTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/YamlUtilsTest.java deleted file mode 100644 index 8d865186..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_1/utils/YamlUtilsTest.java +++ /dev/null @@ -1,15 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_1.utils; - -import java.util.Map; -import org.junit.Assert; -import org.junit.Test; - -public class YamlUtilsTest { - @Test - public void testSimpleLoad() { - final String yamlStr = "moo: cow\nbark: dog\n"; - final Map loaded = YamlUtils.mapFromString(yamlStr); - Assert.assertEquals(loaded.get("moo"), "cow"); - Assert.assertEquals(loaded.get("bark"), "dog"); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/AnonymousRecordTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/AnonymousRecordTest.java deleted file mode 100644 index ca415c9e..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/AnonymousRecordTest.java +++ /dev/null @@ -1,11 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -public class AnonymousRecordTest { - - @org.junit.Test - public void test_record_with_anonymous_type_record() throws Exception { - java.net.URL url = getClass().getResource("record-in-format.cwl.json"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/DefaultFetcherTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/DefaultFetcherTest.java deleted file mode 100644 index 3dce32c7..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/DefaultFetcherTest.java +++ /dev/null @@ -1,37 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import org.junit.Assert; -import org.junit.Test; - -public class DefaultFetcherTest { - @Test - public void testUnderscoreJoin() { - final DefaultFetcher fetcher = new DefaultFetcher(); - Assert.assertEquals(fetcher.urlJoin("http://googl.com/", "_:/moo"), "_:/moo"); - } - - @Test - public void testUnixJoin() { - final DefaultFetcher fetcher = new DefaultFetcher(); - String url; - - url = fetcher.urlJoin("file:///home/fred/foo.cwl", "soup.cwl"); - Assert.assertEquals(url, "file:///home/fred/soup.cwl"); - - url = fetcher.urlJoin("file:///home/fred/foo.cwl", "../alice/soup.cwl"); - Assert.assertEquals(url, "file:///home/alice/soup.cwl"); - // relative from root - url = fetcher.urlJoin("file:///home/fred/foo.cwl", "/baz/soup.cwl"); - Assert.assertEquals(url, "file:///baz/soup.cwl"); - - url = fetcher.urlJoin("file:///home/fred/foo.cwl", "http://example.com/bar/soup.cwl"); - Assert.assertEquals(url, "http://example.com/bar/soup.cwl"); - - url = fetcher.urlJoin("http://example.com/fred/foo.cwl", "soup.cwl"); - Assert.assertEquals(url, "http://example.com/fred/soup.cwl"); - - // Root-relative -- here relative to http host, not file:/// - url = fetcher.urlJoin("http://example.com/fred/foo.cwl", "/bar/soup.cwl"); - Assert.assertEquals(url, "http://example.com/bar/soup.cwl"); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/ExamplesTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/ExamplesTest.java deleted file mode 100644 index 835b408f..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/ExamplesTest.java +++ /dev/null @@ -1,14573 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -public class ExamplesTest { - - @org.junit.Test - public void testvalid_stage_unprovided_fileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-unprovided-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stage_unprovided_fileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-unprovided-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stage_unprovided_fileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-unprovided-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_step_valuefrom3_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_step_valuefrom3_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_step_valuefrom3_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_stage_file_array_basenameByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage_file_array_basename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_stage_file_array_basenameByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage_file_array_basename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_stage_file_array_basenameByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage_file_array_basename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_record_in_secondaryFiles_missing_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-in-secondaryFiles-missing-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_record_in_secondaryFiles_missing_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-in-secondaryFiles-missing-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_record_in_secondaryFiles_missing_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-in-secondaryFiles-missing-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_linkfileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_linkfile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_linkfileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_linkfile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_linkfileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_linkfile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_fileobjs1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-fileobjs1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_fileobjs1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-fileobjs1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_fileobjs1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-fileobjs1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wc_tool_shortcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wc-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wc_tool_shortcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wc-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wc_tool_shortcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wc-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_outputevalByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record_outputeval.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_outputevalByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record_outputeval.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_outputevalByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record_outputeval.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_timelimit3_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_timelimit3_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_timelimit3_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_namerootByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_nameroot.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_namerootByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_nameroot.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_namerootByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_nameroot.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat3_tool_dockerByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-tool-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat3_tool_dockerByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-tool-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat3_tool_dockerByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-tool-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_output_arrays_int_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_output_arrays_int_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_output_arrays_int_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_013_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-013_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_013_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-013_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_013_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-013_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines15_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines15-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines15_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines15-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines15_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines15-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat3_from_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat3_from_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat3_from_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_pass_unconnectedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_pass-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_pass_unconnectedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_pass-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_pass_unconnectedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_pass-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat5_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat5-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat5_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat5-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat5_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat5-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_catByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_catByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_catByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_env_wf3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_env_wf3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_env_wf3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_output_arrays_intByString() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-int.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_output_arrays_intByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-int.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_output_arrays_intByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-int.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_initialworkdirrequirement_docker_outByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_initialworkdirrequirement-docker-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_initialworkdirrequirement_docker_outByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_initialworkdirrequirement-docker-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_initialworkdirrequirement_docker_outByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_initialworkdirrequirement-docker-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_writable_dir_dockerByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_writable-dir-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_writable_dir_dockerByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_writable-dir-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_writable_dir_dockerByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_writable-dir-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines7_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines7-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines7_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines7-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines7_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines7-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_formattestByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_formattest.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_formattestByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_formattest.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_formattestByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_formattest.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_passthrough3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-passthrough3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_passthrough3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-passthrough3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_passthrough3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-passthrough3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_007ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-007.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_007ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-007.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_007ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-007.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_scatter_wf2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_scatter_wf2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_scatter_wf2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_symlink_legalByString() throws Exception { - java.net.URL url = getClass().getResource("valid_symlink-legal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_symlink_legalByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_symlink-legal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_symlink_legalByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_symlink-legal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines1_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines1-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines1_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines1-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines1_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines1-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_any_type_compatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_any-type-compat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_any_type_compatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_any-type-compat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_any_type_compatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_any-type-compat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_record_outputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_record_outputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_record_outputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_docker_output_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-output-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_docker_output_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-output-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_docker_output_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-output-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_011ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-011.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_011ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-011.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_011ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-011.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_output_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-output-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_output_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-output-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_output_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-output-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwdr_entryByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwdr-entry.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwdr_entryByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwdr-entry.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwdr_entryByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwdr-entry.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_wf3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_outputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_outputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_outputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wf_loadContents2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wf_loadContents2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wf_loadContents2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimit2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimit2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimit2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_anon_enum_inside_array_inside_schemadefByString() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array_inside_schemadef.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_anon_enum_inside_array_inside_schemadefByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array_inside_schemadef.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_anon_enum_inside_array_inside_schemadefByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array_inside_schemadef.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_bool_empty_inputbindingByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bool-empty-inputbinding.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_bool_empty_inputbindingByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bool-empty-inputbinding.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_bool_empty_inputbindingByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bool-empty-inputbinding.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_imported_hintByString() throws Exception { - java.net.URL url = getClass().getResource("valid_imported-hint.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_imported_hintByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_imported-hint.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_imported_hintByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_imported-hint.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimit3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimit3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimit3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wf_loadContents4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wf_loadContents4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wf_loadContents4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_with_defaultsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-with-defaults.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_with_defaultsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-with-defaults.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_with_defaultsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-with-defaults.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_wf_loadContentsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_wf_loadContentsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_wf_loadContentsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_nested_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_nested-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_nested_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_nested-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_nested_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_nested-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_record_in_formatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-in-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_record_in_formatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-in-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_record_in_formatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-in-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_echo_tool_packed2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-tool-packed2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_echo_tool_packed2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-tool-packed2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_echo_tool_packed2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-tool-packed2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_docker_array_secondaryfilesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-array-secondaryfiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_docker_array_secondaryfilesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-array-secondaryfiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_docker_array_secondaryfilesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-array-secondaryfiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wc2_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wc2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wc2_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wc2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wc2_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wc2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_synth_fileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_synth-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_synth_fileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_synth-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_synth_fileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_synth-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_passthrough1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-passthrough1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_passthrough1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-passthrough1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_passthrough1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-passthrough1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_output_arrays_int_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_output-arrays-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_output_arrays_int_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_output-arrays-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_output_arrays_int_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_output-arrays-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_revtoolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_revtool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_revtoolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_revtool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_revtoolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_revtool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stderrByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stderrByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stderrByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_no_inputs_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_no-inputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_no_inputs_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_no-inputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_no_inputs_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_no-inputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines14_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines14-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines14_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines14-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines14_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines14-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_output_arrays_file_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_output-arrays-file-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_output_arrays_file_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_output-arrays-file-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_output_arrays_file_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_output-arrays-file-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wf_loadContents3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wf_loadContents3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wf_loadContents3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_fileobjs2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-fileobjs2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_fileobjs2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-fileobjs2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_fileobjs2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-fileobjs2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_wc3_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_wc3_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_wc3_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_echo_tool_packedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-tool-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_echo_tool_packedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-tool-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_echo_tool_packedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-tool-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_docker_run_cmdByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_docker-run-cmd.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_docker_run_cmdByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_docker-run-cmd.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_docker_run_cmdByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_docker-run-cmd.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_schemadef_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_schemadef_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_schemadef_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stderr_mediumcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stderr_mediumcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stderr_mediumcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_size_expression_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_size-expression-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_size_expression_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_size-expression-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_size_expression_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_size-expression-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_echo_wf_defaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-wf-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_echo_wf_defaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-wf-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_echo_wf_defaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-wf-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_io_int_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_io_int_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_io_int_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_any_type_compatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_any-type-compat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_any_type_compatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_any-type-compat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_any_type_compatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_any-type-compat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwdr_entryByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr-entry.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwdr_entryByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr-entry.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwdr_entryByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr-entry.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines17_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines17-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines17_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines17-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines17_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines17-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_sum_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_sum-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_sum_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_sum-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_sum_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_sum-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_004_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-004_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_004_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-004_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_004_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-004_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_updatedir_inplaceByString() throws Exception { - java.net.URL url = getClass().getResource("valid_updatedir_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_updatedir_inplaceByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_updatedir_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_updatedir_inplaceByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_updatedir_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_null_definedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_null-defined.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_null_definedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_null-defined.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_null_definedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_null-defined.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_writable_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_writable-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_writable_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_writable-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_writable_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_writable-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_formattest2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_formattest2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_formattest2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_formattest2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_formattest2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_formattest2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_passthrough2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_passthrough2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_passthrough2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_storage_floatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_storage_float.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_storage_floatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_storage_float.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_storage_floatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_storage_float.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf5ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf5ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf5ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_sum_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_sum-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_sum_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_sum-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_sum_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_sum-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_wc_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_wc_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_wc_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines2_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines2_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines2_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_listing_shallow1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_shallow1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_listing_shallow1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_shallow1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_listing_shallow1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_shallow1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wf_renByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wf_ren.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wf_renByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wf_ren.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wf_renByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wf_ren.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines14_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines14-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines14_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines14-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines14_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines14-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_binding_testByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_binding-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_binding_testByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_binding-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_binding_testByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_binding-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_009_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-009_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_009_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-009_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_009_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-009_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_null_expression1_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_null-expression1-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_null_expression1_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_null-expression1-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_null_expression1_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_null-expression1-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_wf3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_wf3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_wf3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_bash_line_continuation_with_expressionByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bash-line-continuation-with-expression.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_bash_line_continuation_with_expressionByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bash-line-continuation-with-expression.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_bash_line_continuation_with_expressionByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bash-line-continuation-with-expression.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines6_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines6-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines6_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines6-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines6_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines6-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_007ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-007.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_007ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-007.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_007ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-007.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_vf_concatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_vf-concat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_vf_concatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_vf-concat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_vf_concatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_vf-concat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_recursive_input_directoryByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_recursive-input-directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_recursive_input_directoryByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_recursive-input-directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_recursive_input_directoryByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_recursive-input-directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_002ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-002.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_002ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-002.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_002ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-002.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_deep1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_deep1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_deep1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_deep1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_deep1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_deep1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_js_quoteByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_js-quote.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_js_quoteByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_js-quote.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_js_quoteByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_js-quote.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_js_input_recordByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_js-input-record.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_js_input_recordByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_js-input-record.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_js_input_recordByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_js-input-record.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_wf5ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf5ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf5ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_recursive_input_directoryByString() throws Exception { - java.net.URL url = getClass().getResource("valid_recursive-input-directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_recursive_input_directoryByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_recursive-input-directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_recursive_input_directoryByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_recursive-input-directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines9_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines9-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines9_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines9-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines9_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines9-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_stderr_shortcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stderr-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_stderr_shortcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stderr-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_stderr_shortcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stderr-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_formattest3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_formattest3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_formattest3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_metadataByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_metadata.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_metadataByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_metadata.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_metadataByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_metadata.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_bash_dollar_quoteByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bash-dollar-quote.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_bash_dollar_quoteByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bash-dollar-quote.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_bash_dollar_quoteByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bash-dollar-quote.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_vf_concatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_vf-concat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_vf_concatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_vf-concat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_vf_concatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_vf-concat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_storage_floatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_storage_float.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_storage_floatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_storage_float.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_storage_floatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_storage_float.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines11_extra_step_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-extra-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines11_extra_step_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-extra-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines11_extra_step_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-extra-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_002_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-002_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_002_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-002_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_002_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-002_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_synth_fileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_synth-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_synth_fileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_synth-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_synth_fileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_synth-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_env_tool1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-tool1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_env_tool1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-tool1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_env_tool1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-tool1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat_tool_shortcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat_tool_shortcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat_tool_shortcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat3_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat3_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat3_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_operationByString() throws Exception { - java.net.URL url = getClass().getResource("valid_operation.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_operationByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_operation.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_operationByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_operation.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_listing_deep2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_deep2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_listing_deep2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_deep2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_listing_deep2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_deep2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_container_entryname1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-container-entryname1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_container_entryname1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-container-entryname1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_container_entryname1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-container-entryname1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_fooByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_foo.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_fooByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_foo.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_fooByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_foo.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_inline_jsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_inline-js.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_inline_jsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_inline-js.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_inline_jsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_inline-js.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cwloutput_nolimitByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cwloutput-nolimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cwloutput_nolimitByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cwloutput-nolimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cwloutput_nolimitByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cwloutput-nolimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_timelimit5ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_timelimit5ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_timelimit5ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_rename_inputsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_rename-inputs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_rename_inputsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_rename-inputs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_rename_inputsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_rename-inputs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_touchByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_touch.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_touchByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_touch.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_touchByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_touch.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_js_quoteByString() throws Exception { - java.net.URL url = getClass().getResource("valid_js-quote.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_js_quoteByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_js-quote.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_js_quoteByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_js-quote.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_scatter_wf1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_scatter_wf1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_scatter_wf1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dynresreq_workflow_tooldefaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-workflow-tooldefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dynresreq_workflow_tooldefaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-workflow-tooldefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dynresreq_workflow_tooldefaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-workflow-tooldefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_wc_tool_shortcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_wc_tool_shortcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_wc_tool_shortcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_writable_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_writable-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_writable_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_writable-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_writable_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_writable-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_colon_testByString() throws Exception { - java.net.URL url = getClass().getResource("valid_colon:test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_colon_testByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_colon:test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_colon_testByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_colon:test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_null_expression2_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_null_expression2_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_null_expression2_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_no_outputs_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_no-outputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_no_outputs_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_no-outputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_no_outputs_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_no-outputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines3_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines3_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines3_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_envvar3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_envvar3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_envvar3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_envvar3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_envvar3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_envvar3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_wf4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dynresreqByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dynresreqByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dynresreqByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines11_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines11_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines11_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwdr_with_nested_dirsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr_with_nested_dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwdr_with_nested_dirsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr_with_nested_dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwdr_with_nested_dirsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr_with_nested_dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines1_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines1-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines1_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines1-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines1_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines1-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_timelimitByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_timelimitByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_timelimitByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_env_tool3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-tool3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_env_tool3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-tool3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_env_tool3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-tool3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_tool_defaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_tool_defaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_tool_defaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines19_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines19-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines19_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines19-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines19_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines19-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_timelimit3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_timelimit3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_timelimit3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_003_1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-003.1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_003_1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-003.1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_003_1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-003.1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_no_outputs_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_no-outputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_no_outputs_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_no-outputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_no_outputs_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_no-outputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_004_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-004_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_004_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-004_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_004_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-004_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_glob_path_errorByString() throws Exception { - java.net.URL url = getClass().getResource("valid_glob-path-error.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_glob_path_errorByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_glob-path-error.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_glob_path_errorByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_glob-path-error.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_tmap_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_tmap-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_tmap_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_tmap-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_tmap_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_tmap-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat4_from_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat4-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat4_from_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat4-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat4_from_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat4-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_envvarByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_envvar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_envvarByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_envvar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_envvarByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_envvar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_fail_unspecified_inputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_fail-unspecified-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_fail_unspecified_inputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_fail-unspecified-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_fail_unspecified_inputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_fail-unspecified-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines17_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines17-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines17_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines17-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines17_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines17-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_optional_outputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_optional-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_optional_outputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_optional-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_optional_outputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_optional-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_inline_jsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_inline-js.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_inline_jsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_inline-js.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_inline_jsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_inline-js.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines16_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines16-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines16_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines16-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines16_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines16-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines1_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines1-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines1_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines1-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines1_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines1-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_schemadef_types_with_import_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_schemadef_types_with_import-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_schemadef_types_with_import_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_schemadef_types_with_import-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_schemadef_types_with_import_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_schemadef_types_with_import-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wc_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wc-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wc_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wc-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wc_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wc-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_jsondump2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_jsondump2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_jsondump2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_steplevel_resreqByString() throws Exception { - java.net.URL url = getClass().getResource("valid_steplevel-resreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_steplevel_resreqByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_steplevel-resreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_steplevel_resreqByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_steplevel-resreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_passthrough4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_passthrough4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_passthrough4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_jsondump3_nlByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump3-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_jsondump3_nlByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump3-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_jsondump3_nlByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump3-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_int_default_tool_and_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-default-tool-and-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_int_default_tool_and_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-default-tool-and-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_int_default_tool_and_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-default-tool-and-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_nested_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_nested-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_nested_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_nested-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_nested_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_nested-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_no_inputs_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_no-inputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_no_inputs_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_no-inputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_no_inputs_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_no-inputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwdr_with_nested_dirsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwdr_with_nested_dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwdr_with_nested_dirsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwdr_with_nested_dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwdr_with_nested_dirsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwdr_with_nested_dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stderr_shortcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stderr_shortcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stderr_shortcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stderr-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_007_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-007_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_007_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-007_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_007_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-007_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_record_output_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-output-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_record_output_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-output-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_record_output_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-output-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_in_secondaryFiles_missing_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles-missing-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_in_secondaryFiles_missing_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles-missing-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_in_secondaryFiles_missing_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles-missing-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_009ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-009.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_009ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-009.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_009ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-009.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_011_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-011_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_011_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-011_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_011_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-011_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_networkaccess2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_networkaccess2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_networkaccess2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_networkaccess2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_networkaccess2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_networkaccess2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_timelimit2_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_timelimit2_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_timelimit2_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_bash_line_continuation_with_expressionByString() throws Exception { - java.net.URL url = getClass().getResource("valid_bash-line-continuation-with-expression.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_bash_line_continuation_with_expressionByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_bash-line-continuation-with-expression.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_bash_line_continuation_with_expressionByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_bash-line-continuation-with-expression.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_mkdirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_mkdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_mkdirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_mkdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_mkdirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_mkdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_valueFrom_constantByString() throws Exception { - java.net.URL url = getClass().getResource("valid_valueFrom-constant.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_valueFrom_constantByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_valueFrom-constant.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_valueFrom_constantByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_valueFrom-constant.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_schemadef_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_schemadef-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_schemadef_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_schemadef-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_schemadef_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_schemadef-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_test_cwl_out2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_test-cwl-out2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_test_cwl_out2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_test-cwl-out2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_test_cwl_out2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_test-cwl-out2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf6ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf6ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf6ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_metadataByString() throws Exception { - java.net.URL url = getClass().getResource("valid_metadata.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_metadataByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_metadata.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_metadataByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_metadata.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines9_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines9-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines9_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines9-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines9_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines9-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_fooByString() throws Exception { - java.net.URL url = getClass().getResource("valid_foo.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_fooByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_foo.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_fooByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_foo.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_params2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_params2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_params2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_params2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_params2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_params2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines9_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines9-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines9_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines9-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines9_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines9-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_multiple_input_feature_requirementByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_multiple_input_feature_requirement.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_multiple_input_feature_requirementByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_multiple_input_feature_requirement.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_multiple_input_feature_requirementByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_multiple_input_feature_requirement.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_passthrough3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_passthrough3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_passthrough3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines7_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines7-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines7_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines7-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines7_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines7-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_any_wf_1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-any-wf-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_any_wf_1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-any-wf-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_any_wf_1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-any-wf-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_default_pathByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_default_path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_default_pathByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_default_path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_default_pathByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_default_path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_fail_unconnectedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_fail-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_fail_unconnectedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_fail-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_fail_unconnectedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_fail-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_actionByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_action.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_actionByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_action.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_actionByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_action.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_file_default_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-file-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_file_default_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-file-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_file_default_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-file-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_empty_array_inputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_empty-array-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_empty_array_inputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_empty-array-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_empty_array_inputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_empty-array-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_inpdir_update_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_inpdir_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_inpdir_update_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_inpdir_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_inpdir_update_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_inpdir_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dir3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dir3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dir3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat3_tool_mediumcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-tool-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat3_tool_mediumcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-tool-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat3_tool_mediumcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-tool-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wc3_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wc3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wc3_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wc3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wc3_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wc3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_env_wf2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_env_wf2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_env_wf2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dir7ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir7.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dir7ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir7.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dir7ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir7.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_binding_testByString() throws Exception { - java.net.URL url = getClass().getResource("valid_binding-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_binding_testByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_binding-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_binding_testByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_binding-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_revsort_packedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_revsort-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_revsort_packedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_revsort-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_revsort_packedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_revsort-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_paramsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_params.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_paramsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_params.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_paramsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_params.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_record_in_secondaryFilesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-in-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_record_in_secondaryFilesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-in-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_record_in_secondaryFilesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-in-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_record_orderByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-order.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_record_orderByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-order.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_record_orderByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-order.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines8_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines8-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines8_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines8-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines8_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines8-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_output_reference_workflow_inputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_output_reference_workflow_input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_output_reference_workflow_inputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_output_reference_workflow_input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_output_reference_workflow_inputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_output_reference_workflow_input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines5_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines5_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines5_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_pass_unconnectedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_pass-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_pass_unconnectedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_pass-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_pass_unconnectedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_pass-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_networkaccessByString() throws Exception { - java.net.URL url = getClass().getResource("valid_networkaccess.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_networkaccessByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_networkaccess.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_networkaccessByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_networkaccess.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines11_null_step_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-null-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines11_null_step_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-null-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines11_null_step_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-null-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines4_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines4_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines4_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_empty_array_inputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_empty-array-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_empty_array_inputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_empty-array-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_empty_array_inputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_empty-array-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_colon_test_outputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_colon_test_output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_colon_test_outputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_colon_test_output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_colon_test_outputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_colon_test_output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat3_tool_dockerByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat3_tool_dockerByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat3_tool_dockerByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_optional_outputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_optional-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_optional_outputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_optional-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_optional_outputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_optional-output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_record_in_secondaryFiles_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-in-secondaryFiles-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_record_in_secondaryFiles_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-in-secondaryFiles-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_record_in_secondaryFiles_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-in-secondaryFiles-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_anon_enum_inside_array_inside_schemadefByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_anon_enum_inside_array_inside_schemadef.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_anon_enum_inside_array_inside_schemadefByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_anon_enum_inside_array_inside_schemadef.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_anon_enum_inside_array_inside_schemadefByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_anon_enum_inside_array_inside_schemadef.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines8_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines8-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines8_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines8-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines8_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines8-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_wf2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_symlink_legalByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_symlink-legal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_symlink_legalByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_symlink-legal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_symlink_legalByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_symlink-legal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_touchByString() throws Exception { - java.net.URL url = getClass().getResource("valid_touch.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_touchByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_touch.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_touchByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_touch.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_listing_none3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_none3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_listing_none3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_none3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_listing_none3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_none3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat1_testcliByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat1-testcli.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat1_testcliByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat1-testcli.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat1_testcliByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat1-testcli.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_jsondump1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_jsondump1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_jsondump1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dir2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dir2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dir2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_any_1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-any-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_any_1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-any-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_any_1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-any-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_003_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-003_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_003_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-003_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_003_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-003_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_stage_array_dirsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage-array-dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_stage_array_dirsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage-array-dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_stage_array_dirsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage-array-dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_rename_outputsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_rename-outputs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_rename_outputsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_rename-outputs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_rename_outputsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_rename-outputs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_revtoolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_revtool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_revtoolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_revtool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_revtoolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_revtool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat_tool_shortcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat_tool_shortcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat_tool_shortcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_002_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-002_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_002_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-002_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_002_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-002_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_011ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-011.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_011ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-011.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_011ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-011.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_003_1_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-003.1_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_003_1_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-003.1_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_003_1_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-003.1_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_001ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-001.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_001ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-001.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_001ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-001.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines10_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines10-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines10_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines10-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines10_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines10-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_valid_schemadef_types_with_import_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_valid_schemadef_types_with_import-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_valid_schemadef_types_with_import_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_valid_schemadef_types_with_import-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_valid_schemadef_types_with_import_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_valid_schemadef_types_with_import-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_004ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-004.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_004ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-004.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_004ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-004.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_bool_empty_inputbindingByString() throws Exception { - java.net.URL url = getClass().getResource("valid_bool-empty-inputbinding.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_bool_empty_inputbindingByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_bool-empty-inputbinding.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_bool_empty_inputbindingByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_bool-empty-inputbinding.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_tool1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_tool1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_tool1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_import_schema_defByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_import_schema-def.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_import_schema_defByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_import_schema-def.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_import_schema_defByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_import_schema-def.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_io_any_1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-any-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_io_any_1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-any-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_io_any_1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-any-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_anon_enum_inside_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_anon_enum_inside_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_anon_enum_inside_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_anon_enum_inside_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_anon_enum_inside_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_anon_enum_inside_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimit3_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimit3_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimit3_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_container_entryname2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-container-entryname2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_container_entryname2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-container-entryname2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_container_entryname2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-container-entryname2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_colon_test_outputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_colon_test_output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_colon_test_outputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_colon_test_output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_colon_test_outputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_colon_test_output.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dir4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dir4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dir4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_anon_enum_inside_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_anon_enum_inside_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_anon_enum_inside_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_no_outputs_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_no-outputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_no_outputs_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_no-outputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_no_outputs_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_no-outputs-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_inp_update_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_inp_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_inp_update_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_inp_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_inp_update_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_inp_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_fileobjs2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-fileobjs2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_fileobjs2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-fileobjs2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_fileobjs2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-fileobjs2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines12_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines12-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines12_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines12-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines12_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines12-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_env_tool2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-tool2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_env_tool2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-tool2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_env_tool2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-tool2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_wf_defaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-wf-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_wf_defaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-wf-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_wf_defaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-wf-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dir7ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir7.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dir7ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir7.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dir7ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir7.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_int_optional_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-optional-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_int_optional_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-optional-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_int_optional_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-optional-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_001ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-001.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_001ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-001.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_001ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-001.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_sorttoolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_sorttool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_sorttoolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_sorttool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_sorttoolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_sorttool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat3_tool_shortcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat3_tool_shortcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat3_tool_shortcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_012_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-012_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_012_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-012_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_012_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-012_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_docker_array_secondaryfilesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_docker-array-secondaryfiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_docker_array_secondaryfilesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_docker-array-secondaryfiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_docker_array_secondaryfilesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_docker-array-secondaryfiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_013_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-013_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_013_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-013_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_013_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-013_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines9_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines9-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines9_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines9-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines9_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines9-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines11_extra_step_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-extra-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines11_extra_step_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-extra-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines11_extra_step_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-extra-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_listing_shallow2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_shallow2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_listing_shallow2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_shallow2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_listing_shallow2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_shallow2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_002ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-002.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_002ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-002.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_002ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-002.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_wf_loadContents2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_wf_loadContents2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_wf_loadContents2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_001_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-001_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_001_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-001_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_001_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-001_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_updatedir_inplaceByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_updatedir_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_updatedir_inplaceByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_updatedir_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_updatedir_inplaceByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_updatedir_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_sum_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_sum-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_sum_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_sum-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_sum_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_sum-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stage_file_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stage_file_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stage_file_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_checkByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_check.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_checkByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_check.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_checkByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_check.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_wf_loadContents3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_wf_loadContents3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_wf_loadContents3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_003ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-003.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_003ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-003.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_003ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-003.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_jsondump3_nlByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump3-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_jsondump3_nlByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump3-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_jsondump3_nlByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump3-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_initialworkdir_glob_fullpathByString() throws Exception { - java.net.URL url = getClass().getResource("valid_initialworkdir-glob-fullpath.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_initialworkdir_glob_fullpathByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_initialworkdir-glob-fullpath.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_initialworkdir_glob_fullpathByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_initialworkdir-glob-fullpath.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines11_null_step_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-null-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines11_null_step_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-null-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines11_null_step_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-null-step-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_container_entryname4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-container-entryname4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_container_entryname4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-container-entryname4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_container_entryname4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-container-entryname4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_position_exprByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-position-expr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_position_exprByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-position-expr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_position_exprByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-position-expr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_wf4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_wf4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_wf4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_shellchar2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_shellchar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_shellchar2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_shellchar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_shellchar2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_shellchar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_wf2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_wf2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_wf2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_null_expression3_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_null-expression3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_null_expression3_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_null-expression3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_null_expression3_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_null-expression3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_no_inputs_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_no-inputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_no_inputs_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_no-inputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_no_inputs_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_no-inputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_001_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-001_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_001_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-001_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_001_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-001_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_no_inputs_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_no-inputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_no_inputs_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_no-inputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_no_inputs_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_no-inputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_wf2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_wf2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_wf2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_013ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-013.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_013ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-013.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_013ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-013.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_runtime_outdirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_runtime-outdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_runtime_outdirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_runtime-outdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_runtime_outdirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_runtime-outdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_003ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-003.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_003ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-003.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_003ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-003.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_010ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-010.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_010ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-010.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_010ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-010.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_tool_v12ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_tool-v12.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_tool_v12ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_tool-v12.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_tool_v12ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_tool-v12.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_glob_expr_listByString() throws Exception { - java.net.URL url = getClass().getResource("valid_glob-expr-list.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_glob_expr_listByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_glob-expr-list.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_glob_expr_listByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_glob-expr-list.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_runtime_paths_distinctByString() throws Exception { - java.net.URL url = getClass().getResource("valid_runtime-paths-distinct.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_runtime_paths_distinctByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_runtime-paths-distinct.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_runtime_paths_distinctByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_runtime-paths-distinct.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_loadContents_limitByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_loadContents-limit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_loadContents_limitByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_loadContents-limit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_loadContents_limitByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_loadContents-limit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_wf1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_inputs_wf1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-inputs-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_inputs_wf1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-inputs-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_inputs_wf1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-inputs-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_007_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-007_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_007_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-007_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_007_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-007_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_scatter_wf4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_scatter_wf4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_scatter_wf4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines10_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines10-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines10_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines10-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines10_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines10-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_glob_directoryByString() throws Exception { - java.net.URL url = getClass().getResource("valid_glob_directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_glob_directoryByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_glob_directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_glob_directoryByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_glob_directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines11_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines11_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines11_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_import_schema_defByString() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_import_schema_defByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_import_schema_defByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_import_schema_def2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_import_schema-def2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_import_schema_def2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_import_schema-def2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_import_schema_def2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_import_schema-def2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_docker_run_cmdByString() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-run-cmd.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_docker_run_cmdByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-run-cmd.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_docker_run_cmdByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_docker-run-cmd.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_schemadef_types_with_import_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef_types_with_import-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_schemadef_types_with_import_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef_types_with_import-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_schemadef_types_with_import_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef_types_with_import-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_no_outputs_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_no-outputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_no_outputs_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_no-outputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_no_outputs_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_no-outputs-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_011_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-011_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_011_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-011_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_011_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-011_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_003_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-003_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_003_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-003_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_003_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-003_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_glob_testByString() throws Exception { - java.net.URL url = getClass().getResource("valid_glob_test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_glob_testByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_glob_test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_glob_testByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_glob_test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_bwa_mem_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bwa-mem-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_bwa_mem_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bwa-mem-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_bwa_mem_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bwa-mem-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_glob_expr_listByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_glob-expr-list.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_glob_expr_listByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_glob-expr-list.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_glob_expr_listByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_glob-expr-list.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_stage_file_array_basename_and_entrynameByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage_file_array_basename_and_entryname.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_stage_file_array_basename_and_entrynameByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage_file_array_basename_and_entryname.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_stage_file_array_basename_and_entrynameByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage_file_array_basename_and_entryname.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_runtime_outdirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_runtime-outdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_runtime_outdirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_runtime-outdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_runtime_outdirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_runtime-outdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_operationByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_operation.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_operationByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_operation.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_operationByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_operation.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_basename_fields_testByString() throws Exception { - java.net.URL url = getClass().getResource("valid_basename-fields-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_basename_fields_testByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_basename-fields-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_basename_fields_testByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_basename-fields-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_jsondump3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_jsondump3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_jsondump3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_jsondump1_nlByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump1-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_jsondump1_nlByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump1-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_jsondump1_nlByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump1-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_import_schema_def2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_import_schema_def2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_import_schema_def2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_tool_packed2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-packed2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_tool_packed2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-packed2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_tool_packed2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-packed2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_output_arrays_intByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_output-arrays-int.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_output_arrays_intByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_output-arrays-int.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_output_arrays_intByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_output-arrays-int.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_echo_position_exprByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-position-expr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_echo_position_exprByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-position-expr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_echo_position_exprByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-position-expr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wf_loadContentsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wf_loadContentsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wf_loadContentsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wf-loadContents.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_in_secondaryFilesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_in_secondaryFilesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_in_secondaryFilesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_writable_dir_dockerByString() throws Exception { - java.net.URL url = getClass().getResource("valid_writable-dir-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_writable_dir_dockerByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_writable-dir-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_writable_dir_dockerByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_writable-dir-docker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_tool2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_tool2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_tool2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_searchByString() throws Exception { - java.net.URL url = getClass().getResource("valid_search.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_searchByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_search.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_searchByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_search.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_params_input_length_non_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_params_input_length_non_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_params_input_length_non_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_params_input_length_non_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_params_input_length_non_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_params_input_length_non_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_tool_packedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_tool_packedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_tool_packedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_fail_unspecified_inputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_fail-unspecified-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_fail_unspecified_inputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_fail-unspecified-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_fail_unspecified_inputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_fail-unspecified-input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines8_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines8-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines8_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines8-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines8_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines8-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines11_null_step_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-null-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines11_null_step_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-null-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines11_null_step_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-null-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines1_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines1-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines1_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines1-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines1_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines1-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stage_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stage_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stage_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat1_testcliByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat1-testcli.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat1_testcliByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat1-testcli.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat1_testcliByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat1-testcli.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_params_input_length_non_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_params_input_length_non_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_params_input_length_non_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_params_input_length_non_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_params_input_length_non_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_params_input_length_non_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_step_valuefrom_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_step_valuefrom_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_step_valuefrom_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cwloutput_nolimitByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cwloutput-nolimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cwloutput_nolimitByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cwloutput-nolimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cwloutput_nolimitByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cwloutput-nolimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_echo_tool_defaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-tool-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_echo_tool_defaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-tool-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_echo_tool_defaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-tool-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_envvar3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_envvar3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_envvar3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_renameByString() throws Exception { - java.net.URL url = getClass().getResource("valid_rename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_renameByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_rename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_renameByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_rename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dynresreq_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dynresreq_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dynresreq_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_wf1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_wf1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_wf1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_container_entryname4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-container-entryname4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_container_entryname4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-container-entryname4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_container_entryname4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-container-entryname4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_012_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-012_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_012_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-012_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_012_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-012_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines13_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines13-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines13_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines13-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines13_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines13-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_record_outputeval_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record_outputeval_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_record_outputeval_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record_outputeval_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_record_outputeval_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record_outputeval_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_barByString() throws Exception { - java.net.URL url = getClass().getResource("valid_bar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_barByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_bar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_barByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_bar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines12_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines12-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines12_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines12-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines12_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines12-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dir2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dir2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dir2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines11_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines11_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines11_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines11_extra_step_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-extra-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines11_extra_step_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-extra-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines11_extra_step_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-extra-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_container_entryname1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-container-entryname1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_container_entryname1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-container-entryname1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_container_entryname1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-container-entryname1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_listing_none1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_none1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_listing_none1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_none1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_listing_none1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_none1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_003_1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-003.1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_003_1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-003.1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_003_1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-003.1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_union_input_default_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-union-input-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_union_input_default_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-union-input-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_union_input_default_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-union-input-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_nolimitByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-nolimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_nolimitByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-nolimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_nolimitByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-nolimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_006ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-006.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_006ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-006.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_006ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-006.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines13_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines13-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines13_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines13-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines13_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines13-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_shallow1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_shallow1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_shallow1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_shallow1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_shallow1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_shallow1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_colon_testByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_colon:test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_colon_testByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_colon:test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_colon_testByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_colon:test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valuefrom_wf6ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf6ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valuefrom_wf6ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valuefrom-wf6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreqByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreqByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreqByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat5_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat5-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat5_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat5-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat5_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat5-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_renameByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_rename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_renameByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_rename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_renameByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_rename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_container_entryname2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-container-entryname2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_container_entryname2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-container-entryname2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_container_entryname2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-container-entryname2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_bash_line_continuationByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bash-line-continuation.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_bash_line_continuationByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bash-line-continuation.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_bash_line_continuationByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bash-line-continuation.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_revsort_abstractByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_revsort-abstract.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_revsort_abstractByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_revsort-abstract.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_revsort_abstractByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_revsort-abstract.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_timelimit4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_timelimit4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_timelimit4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_wc4_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_wc4_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_wc4_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines3_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines3_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines3_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_symlink_illegalByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_symlink-illegal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_symlink_illegalByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_symlink-illegal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_symlink_illegalByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_symlink-illegal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_stderr_mediumcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stderr-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_stderr_mediumcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stderr-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_stderr_mediumcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stderr-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cores_floatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cores_float.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cores_floatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cores_float.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cores_floatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cores_float.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimitByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimitByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimitByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_null_expression2_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_null-expression2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_null_expression2_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_null-expression2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_null_expression2_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_null-expression2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_container_entryname3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-container-entryname3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_container_entryname3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-container-entryname3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_container_entryname3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-container-entryname3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_bash_dollar_quoteByString() throws Exception { - java.net.URL url = getClass().getResource("valid_bash-dollar-quote.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_bash_dollar_quoteByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_bash-dollar-quote.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_bash_dollar_quoteByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_bash-dollar-quote.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dir5ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dir5ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dir5ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat3_from_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat3_from_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat3_from_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_none1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_none1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_none1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_none2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_none2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_none2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_passthrough2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-passthrough2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_passthrough2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-passthrough2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_passthrough2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-passthrough2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines11_wf_noETByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines11_wf_noETByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines11_wf_noETByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-wf-noET.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stagefileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stagefile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stagefileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stagefile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stagefileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stagefile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_wc2_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_wc2_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_wc2_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wc2-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_basename_fields_testByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_basename-fields-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_basename_fields_testByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_basename-fields-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_basename_fields_testByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_basename-fields-test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stage_file_array_basename_and_entrynameByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array_basename_and_entryname.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stage_file_array_basename_and_entrynameByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array_basename_and_entryname.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stage_file_array_basename_and_entrynameByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array_basename_and_entryname.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_shellchar2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_shellchar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_shellchar2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_shellchar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_shellchar2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_shellchar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_out_secondaryFilesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-out-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_out_secondaryFilesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-out-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_out_secondaryFilesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-out-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_networkaccess2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_networkaccess2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_networkaccess2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_networkaccess2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_networkaccess2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_networkaccess2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_test_cwl_outByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_test-cwl-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_test_cwl_outByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_test-cwl-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_test_cwl_outByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_test-cwl-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cores_floatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cores_float.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cores_floatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cores_float.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cores_floatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cores_float.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_stderrByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stderr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_stderrByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stderr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_stderrByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stderr.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_glob_testByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_glob_test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_glob_testByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_glob_test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_glob_testByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_glob_test.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_inp_update_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_inp_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_inp_update_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_inp_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_inp_update_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_inp_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_bwa_mem_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_bwa-mem-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_bwa_mem_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_bwa-mem-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_bwa_mem_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_bwa-mem-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat3_tool_mediumcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat3_tool_mediumcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat3_tool_mediumcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-tool-mediumcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_glob_path_errorByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_glob-path-error.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_glob_path_errorByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_glob-path-error.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_glob_path_errorByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_glob-path-error.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dynresreq_workflow_inputdefaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-workflow-inputdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dynresreq_workflow_inputdefaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-workflow-inputdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dynresreq_workflow_inputdefaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-workflow-inputdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_loadContents_limitByString() throws Exception { - java.net.URL url = getClass().getResource("valid_loadContents-limit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_loadContents_limitByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_loadContents-limit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_loadContents_limitByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_loadContents-limit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_stage_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_stage_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_stage_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage-array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_output_reference_workflow_inputByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_output_reference_workflow_input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_output_reference_workflow_inputByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_output_reference_workflow_input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_output_reference_workflow_inputByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_output_reference_workflow_input.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_tool3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_tool3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_tool3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimit2_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimit2_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimit2_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_revsort_packedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_revsort_packedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_revsort_packedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort-packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_null_definedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_null-defined.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_null_definedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_null-defined.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_null_definedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_null-defined.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_initialworkdir_glob_fullpathByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_initialworkdir-glob-fullpath.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_initialworkdir_glob_fullpathByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_initialworkdir-glob-fullpath.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_initialworkdir_glob_fullpathByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_initialworkdir-glob-fullpath.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_none3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_none3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_none3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_none3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat3_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat3_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat3_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_wf_renByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf_ren.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_wf_renByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf_ren.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_wf_renByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf_ren.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_exitcodeByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_exitcode.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_exitcodeByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_exitcode.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_exitcodeByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_exitcode.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat3_nodockerByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-nodocker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat3_nodockerByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-nodocker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat3_nodockerByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-nodocker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_jsondump1_nlByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump1-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_jsondump1_nlByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump1-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_jsondump1_nlByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump1-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_jsondump2_nlByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump2-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_jsondump2_nlByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump2-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_jsondump2_nlByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump2-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwdr_dir_literal_real_fileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr_dir_literal_real_file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwdr_dir_literal_real_fileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr_dir_literal_real_file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwdr_dir_literal_real_fileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwdr_dir_literal_real_file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_wf3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_wf3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_wf3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_int_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_int_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_int_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_listing_deep1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_deep1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_listing_deep1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_deep1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_listing_deep1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_deep1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_009_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-009_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_009_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-009_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_009_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-009_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_006_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-006_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_006_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-006_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_006_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-006_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_file_literal_exByString() throws Exception { - java.net.URL url = getClass().getResource("valid_file-literal-ex.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_file_literal_exByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_file-literal-ex.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_file_literal_exByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_file-literal-ex.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_revsortByString() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_revsortByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_revsortByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_tmap_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_tmap-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_tmap_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_tmap-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_tmap_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_tmap-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_record_outputevalByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record_outputeval.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_record_outputevalByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record_outputeval.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_record_outputevalByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record_outputeval.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_012ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-012.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_012ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-012.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_012ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-012.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_010ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-010.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_010ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-010.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_010ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-010.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_record_out_formatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-out-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_record_out_formatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-out-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_record_out_formatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-out-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_io_union_input_default_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-union-input-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_io_union_input_default_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-union-input-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_io_union_input_default_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-union-input-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_env_tool4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_env_tool4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_env_tool4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_env-tool4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stage_array_dirsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-array-dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stage_array_dirsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-array-dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stage_array_dirsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stage-array-dirs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_inputs_wf1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-inputs-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_inputs_wf1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-inputs-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_inputs_wf1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-inputs-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_step_valuefrom4_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_step_valuefrom4_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_step_valuefrom4_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dir6ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dir6ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dir6ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dir6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_shellcharByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_shellchar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_shellcharByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_shellchar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_shellcharByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_shellchar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines2_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines2_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines2_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_formattestByString() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_formattestByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_formattestByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_stagefileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stagefile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_stagefileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stagefile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_stagefileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stagefile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_stage_file_arrayByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage_file_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_stage_file_arrayByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage_file_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_stage_file_arrayByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage_file_array.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreq_workflow_stepdefaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-stepdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreq_workflow_stepdefaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-stepdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreq_workflow_stepdefaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-stepdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_jsondump3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_jsondump3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_jsondump3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_io_int_default_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-int-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_io_int_default_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-int-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_io_int_default_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-int-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_size_expression_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_size-expression-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_size_expression_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_size-expression-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_size_expression_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_size-expression-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat4_from_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat4-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat4_from_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat4-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat4_from_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat4-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_out_formatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-out-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_out_formatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-out-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_out_formatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-out-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_revsort_abstractByString() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort-abstract.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_revsort_abstractByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort-abstract.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_revsort_abstractByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_revsort-abstract.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_009ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-009.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_009ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-009.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_009ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-009.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_nolimitByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-nolimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_nolimitByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-nolimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_nolimitByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-nolimit.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_wc4_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_wc4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_wc4_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_wc4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_wc4_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_wc4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_step_valuefrom5_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_step_valuefrom5_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_step_valuefrom5_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_file_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-file-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_file_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-file-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_file_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-file-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_step_valuefrom_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_step_valuefrom_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_step_valuefrom_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_output_arrays_file_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-file-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_output_arrays_file_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-file-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_output_arrays_file_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_output-arrays-file-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_echo_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_echo_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_echo_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat_from_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat_from_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat_from_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_fail_unconnectedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_fail-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_fail_unconnectedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_fail-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_fail_unconnectedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_fail-unconnected.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_symlink_illegalByString() throws Exception { - java.net.URL url = getClass().getResource("valid_symlink-illegal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_symlink_illegalByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_symlink-illegal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_symlink_illegalByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_symlink-illegal.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_actionByString() throws Exception { - java.net.URL url = getClass().getResource("valid_action.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_actionByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_action.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_actionByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_action.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimit4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimit4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimit4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_echo_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_echo_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_echo_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_echo-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_step_valuefrom2_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_step_valuefrom2_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_step_valuefrom2_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_valueFrom_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valueFrom-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_valueFrom_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valueFrom-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_valueFrom_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-valueFrom-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines18_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines18-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines18_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines18-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines18_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines18-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dynresreq_workflowByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-workflow.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dynresreq_workflowByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-workflow.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dynresreq_workflowByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-workflow.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_glob_directoryByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_glob_directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_glob_directoryByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_glob_directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_glob_directoryByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_glob_directory.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat_from_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat_from_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat_from_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat-from-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_io_int_optional_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-int-optional-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_io_int_optional_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-int-optional-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_io_int_optional_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-int-optional-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_revsortByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_revsort.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_revsortByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_revsort.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_revsortByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_revsort.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_passthrough4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-passthrough4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_passthrough4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-passthrough4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_passthrough4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-passthrough4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_initialworkdirrequirement_docker_outByString() throws Exception { - java.net.URL url = getClass().getResource("valid_initialworkdirrequirement-docker-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_initialworkdirrequirement_docker_outByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_initialworkdirrequirement-docker-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_initialworkdirrequirement_docker_outByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_initialworkdirrequirement-docker-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_sd_secondaryFilesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-sd-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_sd_secondaryFilesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-sd-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_sd_secondaryFilesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-sd-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_formattest2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_formattest2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_formattest2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_formattest2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_shallow2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_shallow2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_shallow2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_shallow2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_shallow2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_shallow2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_inpdir_update_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_inpdir_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_inpdir_update_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_inpdir_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_inpdir_update_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_inpdir_update_wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat4_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat4_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat4_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_004ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-004.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_004ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-004.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_004ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-004.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_in_secondaryFiles_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_in_secondaryFiles_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_in_secondaryFiles_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-secondaryFiles-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_shellcharByString() throws Exception { - java.net.URL url = getClass().getResource("valid_shellchar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_shellcharByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_shellchar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_shellcharByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_shellchar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_listing_none2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_none2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_listing_none2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_none2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_listing_none2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_listing_none2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_step_valuefrom4_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_step_valuefrom4_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_step_valuefrom4_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_exit_successByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_exit-success.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_exit_successByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_exit-success.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_exit_successByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_exit-success.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_template_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_template-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_template_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_template-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_template_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_template-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_initialwork_pathByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_initialwork-path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_initialwork_pathByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_initialwork-path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_initialwork_pathByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_initialwork-path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_valueFrom_constantByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_valueFrom-constant.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_valueFrom_constantByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_valueFrom-constant.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_valueFrom_constantByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_valueFrom-constant.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_env_wf1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_env_wf1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_env_wf1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_010_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-010_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_010_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-010_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_010_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-010_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_with_defaultsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-with-defaults.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_with_defaultsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-with-defaults.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_with_defaultsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-with-defaults.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_networkaccessByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_networkaccess.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_networkaccessByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_networkaccess.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_networkaccessByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_networkaccess.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_schemadef_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_schemadef_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_schemadef_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_schemadef-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreq_workflowByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreq_workflowByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreq_workflowByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dir3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dir3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dir3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreq_workflow_inputdefaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-inputdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreq_workflow_inputdefaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-inputdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreq_workflow_inputdefaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-inputdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines6_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines6-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines6_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines6-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines6_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines6-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_null_expression1_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression1-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_null_expression1_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression1-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_null_expression1_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression1-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_imported_hintByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_imported-hint.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_imported_hintByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_imported-hint.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_imported_hintByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_imported-hint.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_013ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-013.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_013ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-013.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_013ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-013.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_fileobjs1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-fileobjs1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_fileobjs1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-fileobjs1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_fileobjs1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-fileobjs1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_test_cwl_out2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_test-cwl-out2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_test_cwl_out2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_test-cwl-out2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_test_cwl_out2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_test-cwl-out2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines16_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines16-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines16_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines16-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines16_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines16-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_passthrough1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_passthrough1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_passthrough1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-passthrough1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_envvar2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_envvar2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_envvar2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_step_valuefrom2_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_step_valuefrom2_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_step_valuefrom2_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom2-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dynresreq_defaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dynresreq_defaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dynresreq_defaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_echo_file_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-file-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_echo_file_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-file-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_echo_file_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_echo-file-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_template_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_template-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_template_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_template-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_template_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_template-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stdout_chained_commandsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stdout_chained_commands.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stdout_chained_commandsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stdout_chained_commands.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stdout_chained_commandsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stdout_chained_commands.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_formattest3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_formattest3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_formattest3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_formattest3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_formattest3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_formattest3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_js_input_recordByString() throws Exception { - java.net.URL url = getClass().getResource("valid_js-input-record.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_js_input_recordByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_js-input-record.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_js_input_recordByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_js-input-record.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreq_workflow_tooldefaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-tooldefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreq_workflow_tooldefaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-tooldefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreq_workflow_tooldefaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-workflow-tooldefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_test_cwl_outByString() throws Exception { - java.net.URL url = getClass().getResource("valid_test-cwl-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_test_cwl_outByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_test-cwl-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_test_cwl_outByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_test-cwl-out.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_multiple_input_feature_requirementByString() throws Exception { - java.net.URL url = getClass().getResource("valid_multiple_input_feature_requirement.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_multiple_input_feature_requirementByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_multiple_input_feature_requirement.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_multiple_input_feature_requirementByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_multiple_input_feature_requirement.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreq_defaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreq_defaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreq_defaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-default.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_in_formatByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_in_formatByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_in_formatByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-in-format.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_import_schema_def_packedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_import_schema-def_packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_import_schema_def_packedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_import_schema-def_packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_import_schema_def_packedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_import_schema-def_packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_exitcodeByString() throws Exception { - java.net.URL url = getClass().getResource("valid_exitcode.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_exitcodeByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_exitcode.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_exitcodeByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_exitcode.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_container_entryname3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-container-entryname3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_container_entryname3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-container-entryname3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_container_entryname3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-container-entryname3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_file_literal_exByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_file-literal-ex.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_file_literal_exByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_file-literal-ex.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_file_literal_exByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_file-literal-ex.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_sorttoolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_sorttool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_sorttoolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_sorttool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_sorttoolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_sorttool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_import_schema_def_packedByString() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def_packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_import_schema_def_packedByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def_packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_import_schema_def_packedByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_import_schema-def_packed.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_linkfileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_linkfile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_linkfileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_linkfile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_linkfileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_linkfile.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat3_tool_shortcutByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat3_tool_shortcutByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat3_tool_shortcutByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat3-tool-shortcut.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines4_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines4_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines4_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines4-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_checkByString() throws Exception { - java.net.URL url = getClass().getResource("valid_check.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_checkByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_check.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_checkByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_check.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_updateval_inplaceByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_updateval_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_updateval_inplaceByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_updateval_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_updateval_inplaceByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_updateval_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dir6ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dir6ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dir6ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir6.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dynresreq_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dynresreq_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dynresreq_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dynresreq-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines11_null_step_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-null-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines11_null_step_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-null-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines11_null_step_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines11-null-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_006ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-006.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_006ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-006.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_006ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-006.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_rename_inputsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_rename-inputs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_rename_inputsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_rename-inputs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_rename_inputsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_rename-inputs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_step_valuefrom5_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_step_valuefrom5_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_step_valuefrom5_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_step-valuefrom5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_barByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_barByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_barByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_bar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_int_default_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_int_default_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_int_default_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-int-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_count_lines5_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_count_lines5_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_count_lines5_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_count-lines5-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_outputeval_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record_outputeval_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_outputeval_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record_outputeval_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_outputeval_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record_outputeval_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_scatter_valueFrom_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valueFrom-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_scatter_valueFrom_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valueFrom-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_scatter_valueFrom_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valueFrom-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines18_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines18-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines18_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines18-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines18_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines18-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwd_jsondump2_nlByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump2-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwd_jsondump2_nlByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump2-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwd_jsondump2_nlByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwd-jsondump2-nl.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_docker_output_dirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_docker-output-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_docker_output_dirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_docker-output-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_docker_output_dirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_docker-output-dir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines19_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines19-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines19_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines19-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines19_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines19-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dir4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dir4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dir4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cat_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cat_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cat_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cat-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat3_nodockerByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-nodocker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat3_nodockerByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-nodocker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat3_nodockerByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat3-nodocker.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_params2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_params2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_params2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_params2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_params2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_params2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_envvarByString() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_envvarByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_envvarByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_envvar.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_rename_outputsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_rename-outputs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_rename_outputsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_rename-outputs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_rename_outputsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_rename-outputs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_scatter_valuefrom_wf4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-valuefrom-wf4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines15_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines15-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines15_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines15-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines15_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines15-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_io_int_default_tool_and_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-int-default-tool-and-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_io_int_default_tool_and_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-int-default-tool-and-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_io_int_default_tool_and_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-int-default-tool-and-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_env_tool4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-tool4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_env_tool4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-tool4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_env_tool4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_env-tool4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_io_file_or_filesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-file-or-files.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_io_file_or_filesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-file-or-files.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_io_file_or_filesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-file-or-files.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_sum_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_sum-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_sum_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_sum-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_sum_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_sum-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_schemadef_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_schemadef-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_schemadef_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_schemadef-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_schemadef_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_schemadef-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_bash_line_continuationByString() throws Exception { - java.net.URL url = getClass().getResource("valid_bash-line-continuation.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_bash_line_continuationByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_bash-line-continuation.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_bash_line_continuationByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_bash-line-continuation.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_steplevel_resreqByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_steplevel-resreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_steplevel_resreqByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_steplevel-resreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_steplevel_resreqByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_steplevel-resreq.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_dynresreq_workflow_stepdefaultByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-workflow-stepdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_dynresreq_workflow_stepdefaultByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-workflow-stepdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_dynresreq_workflow_stepdefaultByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_dynresreq-workflow-stepdefault.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines8_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines8-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines8_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines8-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines8_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines8-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_record_orderByString() throws Exception { - java.net.URL url = getClass().getResource("valid_record-order.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_record_orderByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_record-order.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_record_orderByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_record-order.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_catByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_catByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_catByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_wf_loadContents4ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_wf_loadContents4ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_wf_loadContents4ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_wf-loadContents4.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_default_pathByString() throws Exception { - java.net.URL url = getClass().getResource("valid_default_path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_default_pathByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_default_path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_default_pathByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_default_path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_io_file_or_filesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_io-file-or-files.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_io_file_or_filesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_io-file-or-files.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_io_file_or_filesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_io-file-or-files.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_paramsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_params.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_paramsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_params.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_paramsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_params.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_optional_numerical_output_0ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_optional-numerical-output-0.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_optional_numerical_output_0ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_optional-numerical-output-0.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_optional_numerical_output_0ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_optional-numerical-output-0.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_initialwork_pathByString() throws Exception { - java.net.URL url = getClass().getResource("valid_initialwork-path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_initialwork_pathByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_initialwork-path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_initialwork_pathByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_initialwork-path.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_parseInt_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_parseInt-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_parseInt_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_parseInt-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_parseInt_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_parseInt-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_010_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-010_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_010_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-010_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_010_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-010_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_step_valuefrom3_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_step_valuefrom3_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_step_valuefrom3_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_step-valuefrom3-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_namerootByString() throws Exception { - java.net.URL url = getClass().getResource("valid_nameroot.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_namerootByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_nameroot.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_namerootByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_nameroot.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_exit_successByString() throws Exception { - java.net.URL url = getClass().getResource("valid_exit-success.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_exit_successByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_exit-success.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_exit_successByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_exit-success.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_stage_file_array_basenameByString() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array_basename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_stage_file_array_basenameByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array_basename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_stage_file_array_basenameByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_stage_file_array_basename.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_record_sd_secondaryFilesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-sd-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_record_sd_secondaryFilesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-sd-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_record_sd_secondaryFilesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-sd-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_tool_v12ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_tool-v12.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_tool_v12ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_tool-v12.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_tool_v12ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_tool-v12.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_scatter_wf3ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_scatter_wf3ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_scatter_wf3ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_scatter-wf3.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_jsondump2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_jsondump2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_jsondump2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_scatter_wf1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_scatter_wf1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_scatter_wf1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_scatter-wf1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cat4_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cat4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cat4_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cat4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cat4_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cat4-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_parseInt_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_parseInt-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_parseInt_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_parseInt-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_parseInt_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_parseInt-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_record_out_secondaryFilesByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-out-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_record_out_secondaryFilesByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-out-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_record_out_secondaryFilesByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_record-out-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_null_expression3_toolByString() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_null_expression3_toolByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_null_expression3_toolByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_null-expression3-tool.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_timelimit2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_timelimit2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_timelimit2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_timelimit2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_mkdirByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_mkdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_mkdirByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_mkdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_mkdirByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_mkdir.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_timelimit5ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_timelimit5ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_timelimit5ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_timelimit5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_stage_unprovided_fileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage-unprovided-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_stage_unprovided_fileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage-unprovided-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_stage_unprovided_fileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stage-unprovided-file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_cond_wf_012ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-012.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_012ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-012.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_cond_wf_012ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_cond-wf-012.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_optional_numerical_output_0ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_optional-numerical-output-0.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_optional_numerical_output_0ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_optional-numerical-output-0.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_optional_numerical_output_0ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_optional-numerical-output-0.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_stdout_chained_commandsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stdout_chained_commands.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_stdout_chained_commandsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stdout_chained_commands.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_stdout_chained_commandsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_stdout_chained_commands.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_updateval_inplaceByString() throws Exception { - java.net.URL url = getClass().getResource("valid_updateval_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_updateval_inplaceByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_updateval_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_updateval_inplaceByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_updateval_inplace.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_006_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-006_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_006_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-006_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_006_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-006_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_searchByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_search.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_searchByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_search.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_searchByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_search.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_io_file_default_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-file-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_io_file_default_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-file-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_io_file_default_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-file-default-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_count_lines11_extra_step_wfByString() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-extra-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_count_lines11_extra_step_wfByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-extra-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_count_lines11_extra_step_wfByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_count-lines11-extra-step-wf.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_cond_wf_003_1_nojsByString() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-003.1_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_cond_wf_003_1_nojsByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-003.1_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_cond_wf_003_1_nojsByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_cond-wf-003.1_nojs.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_io_any_wf_1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-any-wf-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_io_any_wf_1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-any-wf-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_io_any_wf_1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_io-any-wf-1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_iwd_jsondump1ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_iwd_jsondump1ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_iwd_jsondump1ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_iwd-jsondump1.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_iwdr_dir_literal_real_fileByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwdr_dir_literal_real_file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_iwdr_dir_literal_real_fileByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwdr_dir_literal_real_file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_iwdr_dir_literal_real_fileByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_iwdr_dir_literal_real_file.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_runtime_paths_distinctByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_runtime-paths-distinct.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_runtime_paths_distinctByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_runtime-paths-distinct.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_runtime_paths_distinctByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_runtime-paths-distinct.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_dir5ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_dir5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_dir5ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_dir5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_dir5ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_dir5.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_packed_envvar2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_envvar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_packed_envvar2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_envvar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_packed_envvar2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_packed_envvar2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } - @org.junit.Test - public void testvalid_listing_deep2ByString() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_deep2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - RootLoader.loadDocument(yaml, url.toString()); - } - - @org.junit.Test - public void testvalid_listing_deep2ByPath() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_deep2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - RootLoader.loadDocument(resPath); - } - - @org.junit.Test - public void testvalid_listing_deep2ByMap() throws Exception { - java.net.URL url = getClass().getResource("valid_listing_deep2.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8"); - java.util.Map doc; - doc = (java.util.Map) YamlUtils.mapFromString(yaml); - RootLoader.loadDocument(doc, url.toString()); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/PackedWorkflowClassTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/PackedWorkflowClassTest.java deleted file mode 100644 index 1fff5929..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/PackedWorkflowClassTest.java +++ /dev/null @@ -1,41 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.net.URISyntaxException; -import java.nio.file.Paths; -import java.util.List; -import org.junit.Assert; -import org.junit.Test; -import org.commonwl.cwlsdk.cwl1_2.Process; -import org.commonwl.cwlsdk.cwl1_2.Workflow; -import org.commonwl.cwlsdk.cwl1_2.WorkflowStep; -import org.commonwl.cwlsdk.cwl1_2.WorkflowStepInput; - -public class PackedWorkflowClassTest { - List doc; - - @SuppressWarnings("unchecked") - public PackedWorkflowClassTest() throws URISyntaxException { - super(); - this.doc = - (List) - RootLoader.loadDocument( - Paths.get(getClass().getResource("valid_scatter-wf4.cwl").toURI())); - } - - @Test - public void className() { - Workflow workflow = (Workflow) doc.get(1); - Assert.assertEquals("WorkflowImpl", workflow.getClass().getSimpleName()); - } - - @Test - public void workflowStepInputSources() { - Workflow workflow = (Workflow) doc.get(1); - String workflow_id = workflow.getId().get(); - WorkflowStep step1 = (WorkflowStep) workflow.getSteps().get(0); - List inputs = step1.getIn(); - WorkflowStepInput step1_input1 = (WorkflowStepInput) inputs.get(0); - Assert.assertEquals(workflow_id + "/step1/echo_in1", step1_input1.getId()); - Assert.assertEquals(workflow_id + "/inp1", step1_input1.getSource()); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/RequirementsClassTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/RequirementsClassTest.java deleted file mode 100644 index 9d1b40e7..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/RequirementsClassTest.java +++ /dev/null @@ -1,53 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.net.URISyntaxException; -import org.junit.Assert; -import org.junit.Test; -import org.commonwl.cwlsdk.cwl1_2.CWLVersion; -import org.commonwl.cwlsdk.cwl1_2.InlineJavascriptRequirement; -import org.commonwl.cwlsdk.cwl1_2.Process; - -public class RequirementsClassTest { - Process doc; - - public RequirementsClassTest() throws URISyntaxException { - super(); - this.doc = - (Process) - RootLoader.loadDocument( - java.nio.file.Paths.get( - getClass().getResource("valid_writable-dir-docker.cwl").toURI())); - } - - @Test - public void className() { - Assert.assertEquals("CommandLineToolImpl", doc.getClass().getSimpleName()); - } - - @Test - public void version() { - java.util.Optional version = doc.getCwlVersion(); - Assert.assertTrue(version.isPresent()); - Assert.assertEquals(CWLVersion.V1_2, version.get()); - } - - @Test - public void hints() { - java.util.Optional> hints = doc.getHints(); - Assert.assertTrue(hints.isPresent()); - java.util.List hintList = hints.get(); - Assert.assertEquals(1, hintList.size()); - } - - @Test - public void reqs() { - java.util.Optional> reqs = doc.getRequirements(); - Assert.assertTrue(reqs.isPresent()); - java.util.List reqList = reqs.get(); - Assert.assertEquals(2, reqList.size()); - InlineJavascriptRequirement reqOne = (InlineJavascriptRequirement) reqList.get(0); - Assert.assertEquals("InlineJavascriptRequirementImpl", reqOne.getClass().getSimpleName()); - Assert.assertNotEquals( - "InlineJavascriptRequirementImpl", reqList.get(1).getClass().getSimpleName()); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/SchemaDefTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/SchemaDefTest.java deleted file mode 100644 index 14fc18bc..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/SchemaDefTest.java +++ /dev/null @@ -1,42 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.List; -import org.junit.Assert; -import org.commonwl.cwlsdk.cwl1_2.InputRecordSchema; -import org.commonwl.cwlsdk.cwl1_2.Process; -import org.commonwl.cwlsdk.cwl1_2.SchemaDefRequirement; - -public class SchemaDefTest { - - @org.junit.Test - public void testvalid_anon_enum_inside_array_inside_schemadef() throws Exception { - java.net.URL url = getClass().getResource("valid_anon_enum_inside_array_inside_schemadef.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - Process doc = (Process) RootLoader.loadDocument(resPath); - java.util.Optional> reqs = doc.getRequirements(); - Assert.assertTrue(reqs.isPresent()); - java.util.List reqList = reqs.get(); - Assert.assertEquals(reqList.size(), 1); - SchemaDefRequirement schemaReq = (SchemaDefRequirement) reqList.get(0); - List schemaTypes = schemaReq.getTypes(); - for (Object schemaType : schemaTypes) { - Assert.assertTrue(schemaType instanceof InputRecordSchema); - } - } - - @org.junit.Test - public void testvalid_record_sd_secondaryFiles() throws Exception { - java.net.URL url = getClass().getResource("valid_record-sd-secondaryFiles.cwl"); - java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI()); - Process doc = (Process) RootLoader.loadDocument(resPath); - java.util.Optional> reqs = doc.getRequirements(); - Assert.assertTrue(reqs.isPresent()); - java.util.List reqList = reqs.get(); - Assert.assertEquals(reqList.size(), 1); - SchemaDefRequirement schemaReq = (SchemaDefRequirement) reqList.get(0); - List schemaTypes = schemaReq.getTypes(); - for (Object schemaType : schemaTypes) { - Assert.assertTrue(schemaType instanceof InputRecordSchema); - } - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/SecondaryFilesTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/SecondaryFilesTest.java deleted file mode 100644 index 911112f7..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/SecondaryFilesTest.java +++ /dev/null @@ -1,47 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.net.URISyntaxException; -import java.nio.file.Paths; -import java.util.List; -import org.junit.Assert; -import org.junit.Test; -import org.commonwl.cwlsdk.cwl1_2.Process; -import org.commonwl.cwlsdk.cwl1_2.SecondaryFileSchema; -import org.commonwl.cwlsdk.cwl1_2.Workflow; -import org.commonwl.cwlsdk.cwl1_2.WorkflowInputParameter; - -public class SecondaryFilesTest { - List doc; - - @SuppressWarnings("unchecked") - public SecondaryFilesTest() throws URISyntaxException { - super(); - this.doc = - (List) - RootLoader.loadDocument(Paths.get(getClass().getResource("525.cwl").toURI())); - } - - @SuppressWarnings("unchecked") - @Test - public void workflowInputSecFiles() { - Workflow workflow = (Workflow) doc.get(0); - String workflow_id = workflow.getId().get(); - List inputs = workflow.getInputs(); - WorkflowInputParameter wf_file_input = (WorkflowInputParameter) inputs.get(1); - Assert.assertEquals(workflow_id + "/wf_file_input", wf_file_input.getId()); - List sec_files_l1 = - (List) wf_file_input.getSecondaryFiles(); - Assert.assertEquals(1, sec_files_l1.size()); - SecondaryFileSchema sec_files1 = sec_files_l1.get(0); - Assert.assertEquals(".also", sec_files1.getPattern()); - Assert.assertEquals(true, sec_files1.getRequired()); - WorkflowInputParameter wf_file_input_array = (WorkflowInputParameter) inputs.get(2); - Assert.assertEquals(workflow_id + "/wf_file_input_array", wf_file_input_array.getId()); - List sec_files_l2 = - (List) wf_file_input_array.getSecondaryFiles(); - Assert.assertEquals(1, sec_files_l2.size()); - SecondaryFileSchema sec_files2 = sec_files_l2.get(0); - Assert.assertEquals(".also", sec_files2.getPattern()); - Assert.assertEquals(true, sec_files2.getRequired()); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/ShortnameTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/ShortnameTest.java deleted file mode 100644 index 4a2e5081..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/ShortnameTest.java +++ /dev/null @@ -1,24 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import org.junit.Assert; -import org.junit.Test; - -public class ShortnameTest { - @Test - public void testShortname() { - Assert.assertEquals(Uris.shortname( - "file:/Users/jdidion/projects/cwlScala/target/test-classes/CommandLineTools/conformance/#anon_enum_inside_array_inside_schemadef.cwl/first/user_type_2/species/homo_sapiens"), - "homo_sapiens"); - Assert.assertEquals(Uris.shortname( - "file:///home/michael/cwljava/src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCh37"), - "GRCh37"); - // Below are from https://w3id.org/cwl/v1.2/SchemaSalad.html#Short_names - Assert.assertEquals(Uris.shortname("http://example.com/foo"), "foo"); - Assert.assertEquals(Uris.shortname("http://example.com/#bar"), "bar"); - Assert.assertEquals(Uris.shortname("http://example.com/foo/bar"), "bar"); - Assert.assertEquals(Uris.shortname("http://example.com/foo#bar"), "bar"); - Assert.assertEquals(Uris.shortname("http://example.com/#foo/bar"), "bar"); - Assert.assertEquals(Uris.shortname("http://example.com/foo#bar/baz"), "baz"); - } - -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/WorkflowClassTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/WorkflowClassTest.java deleted file mode 100644 index 765d7dbd..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/WorkflowClassTest.java +++ /dev/null @@ -1,32 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.net.URISyntaxException; -import org.junit.Assert; -import org.junit.Test; -import org.commonwl.cwlsdk.cwl1_2.CWLVersion; -import org.commonwl.cwlsdk.cwl1_2.Process; - -public class WorkflowClassTest { - Process doc; - - public WorkflowClassTest() throws URISyntaxException { - super(); - this.doc = - (Process) - RootLoader.loadDocument( - java.nio.file.Paths.get( - getClass().getResource("valid_count-lines1-wf.cwl").toURI())); - } - - @Test - public void className() { - Assert.assertEquals("WorkflowImpl", doc.getClass().getSimpleName()); - } - - @Test - public void version() { - java.util.Optional version = doc.getCwlVersion(); - Assert.assertTrue(version.isPresent()); - Assert.assertEquals(CWLVersion.V1_2, version.get()); - } -} diff --git a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/YamlUtilsTest.java b/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/YamlUtilsTest.java deleted file mode 100644 index e79469ca..00000000 --- a/src/test/java/org/commonwl/cwlsdk/cwl1_2/utils/YamlUtilsTest.java +++ /dev/null @@ -1,15 +0,0 @@ -package org.commonwl.cwlsdk.cwl1_2.utils; - -import java.util.Map; -import org.junit.Assert; -import org.junit.Test; - -public class YamlUtilsTest { - @Test - public void testSimpleLoad() { - final String yamlStr = "moo: cow\nbark: dog\n"; - final Map loaded = YamlUtils.mapFromString(yamlStr); - Assert.assertEquals(loaded.get("moo"), "cow"); - Assert.assertEquals(loaded.get("bark"), "dog"); - } -} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/525.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/525.cwl deleted file mode 100644 index 8706536d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/525.cwl +++ /dev/null @@ -1,118 +0,0 @@ -{ - "cwlVersion": "v1.1", - "$graph": [ - { - "id": "main", - "class": "Workflow", - "inputs": [ - { - "id": "command", - "type": "string" - }, - { - "id": "wf_file_input", - "type": "File", - "secondaryFiles": [ - { - "pattern": ".also", - "required": true - } - ] - }, - { - "id": "wf_file_input_array", - "type": { - "type": "array", - "items": "File" - }, - "secondaryFiles": [ - { - "pattern": ".also", - "required": true - } - ] - } - ], - "outputs": [ - { - "id": "the_answer", - "type": "string", - "outputSource": "run_tool/the_answer" - } - ], - "steps": [ - { - "id": "run_tool", - "run": "#cwl_secondary_files_workflow_tool", - "in": { - "command": "command", - "f": "wf_file_input", - "fs": "wf_file_input_array" - }, - "out": [ - { - "id": "the_answer" - } - ] - } - ] - }, - { - "id": "cwl_secondary_files_workflow_tool", - "class": "CommandLineTool", - "requirements": [ - { - "class": "InlineJavascriptRequirement" - } - ], - "hints": { - "DockerRequirement": { - "dockerPull": "debian:stretch-slim" - }, - "NetworkAccess": { - "networkAccess": true - }, - "LoadListingRequirement": { - "loadListing": "deep_listing" - } - }, - "inputs": [ - { - "id": "command", - "type": "string" - }, - { - "id": "f", - "type": "File", - "inputBinding": { - "position": 2 - } - }, - { - "id": "fs", - "type": { - "type": "array", - "items": "File", - "inputBinding": { - "position": 3 - } - } - } - ], - "outputs": { - "the_answer": { - "type": "string", - "outputBinding": { - "outputEval": "${ return \"\\$(\" + 42 + \")\"; }" - } - } - }, - "baseCommand": [], - "arguments": [ - "bash", - "-c", - "$(inputs.command)" - ] - } - ] -} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/capture_kit.yml b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/capture_kit.yml deleted file mode 100644 index 4323dd90..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/capture_kit.yml +++ /dev/null @@ -1,5 +0,0 @@ -- name: capture_kit - type: record - fields: - - name: bait - type: string diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/envvar.yml b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/envvar.yml deleted file mode 100644 index 097c3f27..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/envvar.yml +++ /dev/null @@ -1,4 +0,0 @@ -class: EnvVarRequirement -envDef: - - envName: "TEST_ENV" - envValue: "hello test env" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/params_inc.yml b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/params_inc.yml deleted file mode 100644 index 930d2e89..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/params_inc.yml +++ /dev/null @@ -1,120 +0,0 @@ - - id: t1 - type: Any - outputBinding: - outputEval: $(inputs) - - id: t2 - type: Any - outputBinding: - outputEval: $(inputs.bar) - - id: t3 - type: Any - outputBinding: - outputEval: $(inputs['bar']) - - id: t4 - type: Any - outputBinding: - outputEval: $(inputs["bar"]) - - - id: t5 - type: Any - outputBinding: - outputEval: $(inputs.bar.baz) - - id: t6 - type: Any - outputBinding: - outputEval: $(inputs['bar'].baz) - - id: t7 - type: Any - outputBinding: - outputEval: $(inputs['bar']["baz"]) - - id: t8 - type: Any - outputBinding: - outputEval: $(inputs.bar['baz']) - - - id: t9 - type: Any - outputBinding: - outputEval: $(inputs.bar['b az']) - - id: t10 - type: Any - outputBinding: - outputEval: $(inputs.bar['b\'az']) - - id: t11 - type: Any - outputBinding: - outputEval: $(inputs.bar["b'az"]) - - id: t12 - type: "null" - outputBinding: - outputEval: $(inputs.bar['b"az']) - - - id: t13 - type: Any - outputBinding: - outputEval: -$(inputs.bar.baz) - - id: t14 - type: Any - outputBinding: - outputEval: -$(inputs['bar'].baz) - - id: t15 - type: Any - outputBinding: - outputEval: -$(inputs['bar']["baz"]) - - id: t16 - type: Any - outputBinding: - outputEval: -$(inputs.bar['baz']) - - - id: t17 - type: Any - outputBinding: - outputEval: $(inputs.bar.baz) $(inputs.bar.baz) - - id: t18 - type: Any - outputBinding: - outputEval: $(inputs['bar'].baz) $(inputs['bar'].baz) - - id: t19 - type: Any - outputBinding: - outputEval: $(inputs['bar']["baz"]) $(inputs['bar']["baz"]) - - id: t20 - type: Any - outputBinding: - outputEval: $(inputs.bar['baz']) $(inputs.bar['baz']) - - - id: t21 - type: Any - outputBinding: - outputEval: $(inputs.bar['b az']) $(inputs.bar['b az']) - - id: t22 - type: Any - outputBinding: - outputEval: $(inputs.bar['b\'az']) $(inputs.bar['b\'az']) - - id: t23 - type: Any - outputBinding: - outputEval: $(inputs.bar["b'az"]) $(inputs.bar["b'az"]) - - id: t24 - type: Any - outputBinding: - outputEval: $(inputs.bar['b"az']) $(inputs.bar['b"az']) - - - id: t25 - type: Any - outputBinding: - outputEval: $(inputs.bar.buz[1]) - - id: t26 - type: Any - outputBinding: - outputEval: $(inputs.bar.buz[1]) $(inputs.bar.buz[1]) - - - id: t27 - type: "null" - outputBinding: - outputEval: $(null) - - - id: t28 - type: int - outputBinding: - outputEval: $(inputs.bar.buz.length) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/record-in-format.cwl.json b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/record-in-format.cwl.json deleted file mode 100644 index f680989a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/record-in-format.cwl.json +++ /dev/null @@ -1,37 +0,0 @@ -{ - "class": "CommandLineTool", - "inputs": [ - { - "type": { - "type": "record", - "fields": [ - { - "type": "File", - "format": "http://example.com/format1", - "name": "#main/record_input/f1" - }, - { - "type": { - "type": "array", - "items": "File" - }, - "format": "http://example.com/format2", - "name": "#main/record_input/f2" - } - ] - }, - "id": "#main/record_input" - }, - { - "type": "File", - "format": "http://example.com/format1", - "id": "#main/regular_input" - } - ], - "outputs": [], - "arguments": [ - "true" - ], - "id": "#main", - "cwlVersion": "v1.1" -} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/schemadef-type.yml b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/schemadef-type.yml deleted file mode 100644 index 45a82a75..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/schemadef-type.yml +++ /dev/null @@ -1,9 +0,0 @@ -class: SchemaDefRequirement -types: - - name: HelloType - type: record - fields: - - name: a - type: string - - name: b - type: string diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/underscore.js b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/underscore.js deleted file mode 100644 index 05bfdc0b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/underscore.js +++ /dev/null @@ -1,1416 +0,0 @@ -// Underscore.js 1.7.0 -// http://underscorejs.org -// (c) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors -// Underscore may be freely distributed under the MIT license. - -(function() { - - // Baseline setup - // -------------- - - // Establish the root object, `window` in the browser, or `exports` on the server. - var root = this; - - // Save the previous value of the `_` variable. - //var previousUnderscore = root._; - - // Save bytes in the minified (but not gzipped) version: - var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype; - - // Create quick reference variables for speed access to core prototypes. - var - push = ArrayProto.push, - slice = ArrayProto.slice, - concat = ArrayProto.concat, - toString = ObjProto.toString, - hasOwnProperty = ObjProto.hasOwnProperty; - - // All **ECMAScript 5** native function implementations that we hope to use - // are declared here. - var - nativeIsArray = Array.isArray, - nativeKeys = Object.keys, - nativeBind = FuncProto.bind; - - // Create a safe reference to the Underscore object for use below. - var _ = function(obj) { - if (obj instanceof _) return obj; - if (!(this instanceof _)) return new _(obj); - this._wrapped = obj; - }; - - // Export the Underscore object for **Node.js**, with - // backwards-compatibility for the old `require()` API. If we're in - // the browser, add `_` as a global object. - if (typeof exports !== 'undefined') { - if (typeof module !== 'undefined' && module.exports) { - exports = module.exports = _; - } - exports._ = _; - } else { - root._ = _; - } - - // Current version. - _.VERSION = '1.7.0'; - - // Internal function that returns an efficient (for current engines) version - // of the passed-in callback, to be repeatedly applied in other Underscore - // functions. - var createCallback = function(func, context, argCount) { - if (context === void 0) return func; - switch (argCount == null ? 3 : argCount) { - case 1: return function(value) { - return func.call(context, value); - }; - case 2: return function(value, other) { - return func.call(context, value, other); - }; - case 3: return function(value, index, collection) { - return func.call(context, value, index, collection); - }; - case 4: return function(accumulator, value, index, collection) { - return func.call(context, accumulator, value, index, collection); - }; - } - return function() { - return func.apply(context, arguments); - }; - }; - - // A mostly-internal function to generate callbacks that can be applied - // to each element in a collection, returning the desired result — either - // identity, an arbitrary callback, a property matcher, or a property accessor. - _.iteratee = function(value, context, argCount) { - if (value == null) return _.identity; - if (_.isFunction(value)) return createCallback(value, context, argCount); - if (_.isObject(value)) return _.matches(value); - return _.property(value); - }; - - // Collection Functions - // -------------------- - - // The cornerstone, an `each` implementation, aka `forEach`. - // Handles raw objects in addition to array-likes. Treats all - // sparse array-likes as if they were dense. - _.each = _.forEach = function(obj, iteratee, context) { - if (obj == null) return obj; - iteratee = createCallback(iteratee, context); - var i, length = obj.length; - if (length === +length) { - for (i = 0; i < length; i++) { - iteratee(obj[i], i, obj); - } - } else { - var keys = _.keys(obj); - for (i = 0, length = keys.length; i < length; i++) { - iteratee(obj[keys[i]], keys[i], obj); - } - } - return obj; - }; - - // Return the results of applying the iteratee to each element. - _.map = _.collect = function(obj, iteratee, context) { - if (obj == null) return []; - iteratee = _.iteratee(iteratee, context); - var keys = obj.length !== +obj.length && _.keys(obj), - length = (keys || obj).length, - results = Array(length), - currentKey; - for (var index = 0; index < length; index++) { - currentKey = keys ? keys[index] : index; - results[index] = iteratee(obj[currentKey], currentKey, obj); - } - return results; - }; - - var reduceError = 'Reduce of empty array with no initial value'; - - // **Reduce** builds up a single result from a list of values, aka `inject`, - // or `foldl`. - _.reduce = _.foldl = _.inject = function(obj, iteratee, memo, context) { - if (obj == null) obj = []; - iteratee = createCallback(iteratee, context, 4); - var keys = obj.length !== +obj.length && _.keys(obj), - length = (keys || obj).length, - index = 0, currentKey; - if (arguments.length < 3) { - if (!length) throw new TypeError(reduceError); - memo = obj[keys ? keys[index++] : index++]; - } - for (; index < length; index++) { - currentKey = keys ? keys[index] : index; - memo = iteratee(memo, obj[currentKey], currentKey, obj); - } - return memo; - }; - - // The right-associative version of reduce, also known as `foldr`. - _.reduceRight = _.foldr = function(obj, iteratee, memo, context) { - if (obj == null) obj = []; - iteratee = createCallback(iteratee, context, 4); - var keys = obj.length !== + obj.length && _.keys(obj), - index = (keys || obj).length, - currentKey; - if (arguments.length < 3) { - if (!index) throw new TypeError(reduceError); - memo = obj[keys ? keys[--index] : --index]; - } - while (index--) { - currentKey = keys ? keys[index] : index; - memo = iteratee(memo, obj[currentKey], currentKey, obj); - } - return memo; - }; - - // Return the first value which passes a truth test. Aliased as `detect`. - _.find = _.detect = function(obj, predicate, context) { - var result; - predicate = _.iteratee(predicate, context); - _.some(obj, function(value, index, list) { - if (predicate(value, index, list)) { - result = value; - return true; - } - }); - return result; - }; - - // Return all the elements that pass a truth test. - // Aliased as `select`. - _.filter = _.select = function(obj, predicate, context) { - var results = []; - if (obj == null) return results; - predicate = _.iteratee(predicate, context); - _.each(obj, function(value, index, list) { - if (predicate(value, index, list)) results.push(value); - }); - return results; - }; - - // Return all the elements for which a truth test fails. - _.reject = function(obj, predicate, context) { - return _.filter(obj, _.negate(_.iteratee(predicate)), context); - }; - - // Determine whether all of the elements match a truth test. - // Aliased as `all`. - _.every = _.all = function(obj, predicate, context) { - if (obj == null) return true; - predicate = _.iteratee(predicate, context); - var keys = obj.length !== +obj.length && _.keys(obj), - length = (keys || obj).length, - index, currentKey; - for (index = 0; index < length; index++) { - currentKey = keys ? keys[index] : index; - if (!predicate(obj[currentKey], currentKey, obj)) return false; - } - return true; - }; - - // Determine if at least one element in the object matches a truth test. - // Aliased as `any`. - _.some = _.any = function(obj, predicate, context) { - if (obj == null) return false; - predicate = _.iteratee(predicate, context); - var keys = obj.length !== +obj.length && _.keys(obj), - length = (keys || obj).length, - index, currentKey; - for (index = 0; index < length; index++) { - currentKey = keys ? keys[index] : index; - if (predicate(obj[currentKey], currentKey, obj)) return true; - } - return false; - }; - - // Determine if the array or object contains a given value (using `===`). - // Aliased as `include`. - _.contains = _.include = function(obj, target) { - if (obj == null) return false; - if (obj.length !== +obj.length) obj = _.values(obj); - return _.indexOf(obj, target) >= 0; - }; - - // Invoke a method (with arguments) on every item in a collection. - _.invoke = function(obj, method) { - var args = slice.call(arguments, 2); - var isFunc = _.isFunction(method); - return _.map(obj, function(value) { - return (isFunc ? method : value[method]).apply(value, args); - }); - }; - - // Convenience version of a common use case of `map`: fetching a property. - _.pluck = function(obj, key) { - return _.map(obj, _.property(key)); - }; - - // Convenience version of a common use case of `filter`: selecting only objects - // containing specific `key:value` pairs. - _.where = function(obj, attrs) { - return _.filter(obj, _.matches(attrs)); - }; - - // Convenience version of a common use case of `find`: getting the first object - // containing specific `key:value` pairs. - _.findWhere = function(obj, attrs) { - return _.find(obj, _.matches(attrs)); - }; - - // Return the maximum element (or element-based computation). - _.max = function(obj, iteratee, context) { - var result = -Infinity, lastComputed = -Infinity, - value, computed; - if (iteratee == null && obj != null) { - obj = obj.length === +obj.length ? obj : _.values(obj); - for (var i = 0, length = obj.length; i < length; i++) { - value = obj[i]; - if (value > result) { - result = value; - } - } - } else { - iteratee = _.iteratee(iteratee, context); - _.each(obj, function(value, index, list) { - computed = iteratee(value, index, list); - if (computed > lastComputed || computed === -Infinity && result === -Infinity) { - result = value; - lastComputed = computed; - } - }); - } - return result; - }; - - // Return the minimum element (or element-based computation). - _.min = function(obj, iteratee, context) { - var result = Infinity, lastComputed = Infinity, - value, computed; - if (iteratee == null && obj != null) { - obj = obj.length === +obj.length ? obj : _.values(obj); - for (var i = 0, length = obj.length; i < length; i++) { - value = obj[i]; - if (value < result) { - result = value; - } - } - } else { - iteratee = _.iteratee(iteratee, context); - _.each(obj, function(value, index, list) { - computed = iteratee(value, index, list); - if (computed < lastComputed || computed === Infinity && result === Infinity) { - result = value; - lastComputed = computed; - } - }); - } - return result; - }; - - // Shuffle a collection, using the modern version of the - // [Fisher-Yates shuffle](http://en.wikipedia.org/wiki/Fisher–Yates_shuffle). - _.shuffle = function(obj) { - var set = obj && obj.length === +obj.length ? obj : _.values(obj); - var length = set.length; - var shuffled = Array(length); - for (var index = 0, rand; index < length; index++) { - rand = _.random(0, index); - if (rand !== index) shuffled[index] = shuffled[rand]; - shuffled[rand] = set[index]; - } - return shuffled; - }; - - // Sample **n** random values from a collection. - // If **n** is not specified, returns a single random element. - // The internal `guard` argument allows it to work with `map`. - _.sample = function(obj, n, guard) { - if (n == null || guard) { - if (obj.length !== +obj.length) obj = _.values(obj); - return obj[_.random(obj.length - 1)]; - } - return _.shuffle(obj).slice(0, Math.max(0, n)); - }; - - // Sort the object's values by a criterion produced by an iteratee. - _.sortBy = function(obj, iteratee, context) { - iteratee = _.iteratee(iteratee, context); - return _.pluck(_.map(obj, function(value, index, list) { - return { - value: value, - index: index, - criteria: iteratee(value, index, list) - }; - }).sort(function(left, right) { - var a = left.criteria; - var b = right.criteria; - if (a !== b) { - if (a > b || a === void 0) return 1; - if (a < b || b === void 0) return -1; - } - return left.index - right.index; - }), 'value'); - }; - - // An internal function used for aggregate "group by" operations. - var group = function(behavior) { - return function(obj, iteratee, context) { - var result = {}; - iteratee = _.iteratee(iteratee, context); - _.each(obj, function(value, index) { - var key = iteratee(value, index, obj); - behavior(result, value, key); - }); - return result; - }; - }; - - // Groups the object's values by a criterion. Pass either a string attribute - // to group by, or a function that returns the criterion. - _.groupBy = group(function(result, value, key) { - if (_.has(result, key)) result[key].push(value); else result[key] = [value]; - }); - - // Indexes the object's values by a criterion, similar to `groupBy`, but for - // when you know that your index values will be unique. - _.indexBy = group(function(result, value, key) { - result[key] = value; - }); - - // Counts instances of an object that group by a certain criterion. Pass - // either a string attribute to count by, or a function that returns the - // criterion. - _.countBy = group(function(result, value, key) { - if (_.has(result, key)) result[key]++; else result[key] = 1; - }); - - // Use a comparator function to figure out the smallest index at which - // an object should be inserted so as to maintain order. Uses binary search. - _.sortedIndex = function(array, obj, iteratee, context) { - iteratee = _.iteratee(iteratee, context, 1); - var value = iteratee(obj); - var low = 0, high = array.length; - while (low < high) { - var mid = low + high >>> 1; - if (iteratee(array[mid]) < value) low = mid + 1; else high = mid; - } - return low; - }; - - // Safely create a real, live array from anything iterable. - _.toArray = function(obj) { - if (!obj) return []; - if (_.isArray(obj)) return slice.call(obj); - if (obj.length === +obj.length) return _.map(obj, _.identity); - return _.values(obj); - }; - - // Return the number of elements in an object. - _.size = function(obj) { - if (obj == null) return 0; - return obj.length === +obj.length ? obj.length : _.keys(obj).length; - }; - - // Split a collection into two arrays: one whose elements all satisfy the given - // predicate, and one whose elements all do not satisfy the predicate. - _.partition = function(obj, predicate, context) { - predicate = _.iteratee(predicate, context); - var pass = [], fail = []; - _.each(obj, function(value, key, obj) { - (predicate(value, key, obj) ? pass : fail).push(value); - }); - return [pass, fail]; - }; - - // Array Functions - // --------------- - - // Get the first element of an array. Passing **n** will return the first N - // values in the array. Aliased as `head` and `take`. The **guard** check - // allows it to work with `_.map`. - _.first = _.head = _.take = function(array, n, guard) { - if (array == null) return void 0; - if (n == null || guard) return array[0]; - if (n < 0) return []; - return slice.call(array, 0, n); - }; - - // Returns everything but the last entry of the array. Especially useful on - // the arguments object. Passing **n** will return all the values in - // the array, excluding the last N. The **guard** check allows it to work with - // `_.map`. - _.initial = function(array, n, guard) { - return slice.call(array, 0, Math.max(0, array.length - (n == null || guard ? 1 : n))); - }; - - // Get the last element of an array. Passing **n** will return the last N - // values in the array. The **guard** check allows it to work with `_.map`. - _.last = function(array, n, guard) { - if (array == null) return void 0; - if (n == null || guard) return array[array.length - 1]; - return slice.call(array, Math.max(array.length - n, 0)); - }; - - // Returns everything but the first entry of the array. Aliased as `tail` and `drop`. - // Especially useful on the arguments object. Passing an **n** will return - // the rest N values in the array. The **guard** - // check allows it to work with `_.map`. - _.rest = _.tail = _.drop = function(array, n, guard) { - return slice.call(array, n == null || guard ? 1 : n); - }; - - // Trim out all falsy values from an array. - _.compact = function(array) { - return _.filter(array, _.identity); - }; - - // Internal implementation of a recursive `flatten` function. - var flatten = function(input, shallow, strict, output) { - if (shallow && _.every(input, _.isArray)) { - return concat.apply(output, input); - } - for (var i = 0, length = input.length; i < length; i++) { - var value = input[i]; - if (!_.isArray(value) && !_.isArguments(value)) { - if (!strict) output.push(value); - } else if (shallow) { - push.apply(output, value); - } else { - flatten(value, shallow, strict, output); - } - } - return output; - }; - - // Flatten out an array, either recursively (by default), or just one level. - _.flatten = function(array, shallow) { - return flatten(array, shallow, false, []); - }; - - // Return a version of the array that does not contain the specified value(s). - _.without = function(array) { - return _.difference(array, slice.call(arguments, 1)); - }; - - // Produce a duplicate-free version of the array. If the array has already - // been sorted, you have the option of using a faster algorithm. - // Aliased as `unique`. - _.uniq = _.unique = function(array, isSorted, iteratee, context) { - if (array == null) return []; - if (!_.isBoolean(isSorted)) { - context = iteratee; - iteratee = isSorted; - isSorted = false; - } - if (iteratee != null) iteratee = _.iteratee(iteratee, context); - var result = []; - var seen = []; - for (var i = 0, length = array.length; i < length; i++) { - var value = array[i]; - if (isSorted) { - if (!i || seen !== value) result.push(value); - seen = value; - } else if (iteratee) { - var computed = iteratee(value, i, array); - if (_.indexOf(seen, computed) < 0) { - seen.push(computed); - result.push(value); - } - } else if (_.indexOf(result, value) < 0) { - result.push(value); - } - } - return result; - }; - - // Produce an array that contains the union: each distinct element from all of - // the passed-in arrays. - _.union = function() { - return _.uniq(flatten(arguments, true, true, [])); - }; - - // Produce an array that contains every item shared between all the - // passed-in arrays. - _.intersection = function(array) { - if (array == null) return []; - var result = []; - var argsLength = arguments.length; - for (var i = 0, length = array.length; i < length; i++) { - var item = array[i]; - if (_.contains(result, item)) continue; - for (var j = 1; j < argsLength; j++) { - if (!_.contains(arguments[j], item)) break; - } - if (j === argsLength) result.push(item); - } - return result; - }; - - // Take the difference between one array and a number of other arrays. - // Only the elements present in just the first array will remain. - _.difference = function(array) { - var rest = flatten(slice.call(arguments, 1), true, true, []); - return _.filter(array, function(value){ - return !_.contains(rest, value); - }); - }; - - // Zip together multiple lists into a single array -- elements that share - // an index go together. - _.zip = function(array) { - if (array == null) return []; - var length = _.max(arguments, 'length').length; - var results = Array(length); - for (var i = 0; i < length; i++) { - results[i] = _.pluck(arguments, i); - } - return results; - }; - - // Converts lists into objects. Pass either a single array of `[key, value]` - // pairs, or two parallel arrays of the same length -- one of keys, and one of - // the corresponding values. - _.object = function(list, values) { - if (list == null) return {}; - var result = {}; - for (var i = 0, length = list.length; i < length; i++) { - if (values) { - result[list[i]] = values[i]; - } else { - result[list[i][0]] = list[i][1]; - } - } - return result; - }; - - // Return the position of the first occurrence of an item in an array, - // or -1 if the item is not included in the array. - // If the array is large and already in sort order, pass `true` - // for **isSorted** to use binary search. - _.indexOf = function(array, item, isSorted) { - if (array == null) return -1; - var i = 0, length = array.length; - if (isSorted) { - if (typeof isSorted == 'number') { - i = isSorted < 0 ? Math.max(0, length + isSorted) : isSorted; - } else { - i = _.sortedIndex(array, item); - return array[i] === item ? i : -1; - } - } - for (; i < length; i++) if (array[i] === item) return i; - return -1; - }; - - _.lastIndexOf = function(array, item, from) { - if (array == null) return -1; - var idx = array.length; - if (typeof from == 'number') { - idx = from < 0 ? idx + from + 1 : Math.min(idx, from + 1); - } - while (--idx >= 0) if (array[idx] === item) return idx; - return -1; - }; - - // Generate an integer Array containing an arithmetic progression. A port of - // the native Python `range()` function. See - // [the Python documentation](http://docs.python.org/library/functions.html#range). - _.range = function(start, stop, step) { - if (arguments.length <= 1) { - stop = start || 0; - start = 0; - } - step = step || 1; - - var length = Math.max(Math.ceil((stop - start) / step), 0); - var range = Array(length); - - for (var idx = 0; idx < length; idx++, start += step) { - range[idx] = start; - } - - return range; - }; - - // Function (ahem) Functions - // ------------------ - - // Reusable constructor function for prototype setting. - var Ctor = function(){}; - - // Create a function bound to a given object (assigning `this`, and arguments, - // optionally). Delegates to **ECMAScript 5**'s native `Function.bind` if - // available. - _.bind = function(func, context) { - var args, bound; - if (nativeBind && func.bind === nativeBind) return nativeBind.apply(func, slice.call(arguments, 1)); - if (!_.isFunction(func)) throw new TypeError('Bind must be called on a function'); - args = slice.call(arguments, 2); - bound = function() { - if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments))); - Ctor.prototype = func.prototype; - var self = new Ctor; - Ctor.prototype = null; - var result = func.apply(self, args.concat(slice.call(arguments))); - if (_.isObject(result)) return result; - return self; - }; - return bound; - }; - - // Partially apply a function by creating a version that has had some of its - // arguments pre-filled, without changing its dynamic `this` context. _ acts - // as a placeholder, allowing any combination of arguments to be pre-filled. - _.partial = function(func) { - var boundArgs = slice.call(arguments, 1); - return function() { - var position = 0; - var args = boundArgs.slice(); - for (var i = 0, length = args.length; i < length; i++) { - if (args[i] === _) args[i] = arguments[position++]; - } - while (position < arguments.length) args.push(arguments[position++]); - return func.apply(this, args); - }; - }; - - // Bind a number of an object's methods to that object. Remaining arguments - // are the method names to be bound. Useful for ensuring that all callbacks - // defined on an object belong to it. - _.bindAll = function(obj) { - var i, length = arguments.length, key; - if (length <= 1) throw new Error('bindAll must be passed function names'); - for (i = 1; i < length; i++) { - key = arguments[i]; - obj[key] = _.bind(obj[key], obj); - } - return obj; - }; - - // Memoize an expensive function by storing its results. - _.memoize = function(func, hasher) { - var memoize = function(key) { - var cache = memoize.cache; - var address = hasher ? hasher.apply(this, arguments) : key; - if (!_.has(cache, address)) cache[address] = func.apply(this, arguments); - return cache[address]; - }; - memoize.cache = {}; - return memoize; - }; - - // Delays a function for the given number of milliseconds, and then calls - // it with the arguments supplied. - _.delay = function(func, wait) { - var args = slice.call(arguments, 2); - return setTimeout(function(){ - return func.apply(null, args); - }, wait); - }; - - // Defers a function, scheduling it to run after the current call stack has - // cleared. - _.defer = function(func) { - return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1))); - }; - - // Returns a function, that, when invoked, will only be triggered at most once - // during a given window of time. Normally, the throttled function will run - // as much as it can, without ever going more than once per `wait` duration; - // but if you'd like to disable the execution on the leading edge, pass - // `{leading: false}`. To disable execution on the trailing edge, ditto. - _.throttle = function(func, wait, options) { - var context, args, result; - var timeout = null; - var previous = 0; - if (!options) options = {}; - var later = function() { - previous = options.leading === false ? 0 : _.now(); - timeout = null; - result = func.apply(context, args); - if (!timeout) context = args = null; - }; - return function() { - var now = _.now(); - if (!previous && options.leading === false) previous = now; - var remaining = wait - (now - previous); - context = this; - args = arguments; - if (remaining <= 0 || remaining > wait) { - clearTimeout(timeout); - timeout = null; - previous = now; - result = func.apply(context, args); - if (!timeout) context = args = null; - } else if (!timeout && options.trailing !== false) { - timeout = setTimeout(later, remaining); - } - return result; - }; - }; - - // Returns a function, that, as long as it continues to be invoked, will not - // be triggered. The function will be called after it stops being called for - // N milliseconds. If `immediate` is passed, trigger the function on the - // leading edge, instead of the trailing. - _.debounce = function(func, wait, immediate) { - var timeout, args, context, timestamp, result; - - var later = function() { - var last = _.now() - timestamp; - - if (last < wait && last > 0) { - timeout = setTimeout(later, wait - last); - } else { - timeout = null; - if (!immediate) { - result = func.apply(context, args); - if (!timeout) context = args = null; - } - } - }; - - return function() { - context = this; - args = arguments; - timestamp = _.now(); - var callNow = immediate && !timeout; - if (!timeout) timeout = setTimeout(later, wait); - if (callNow) { - result = func.apply(context, args); - context = args = null; - } - - return result; - }; - }; - - // Returns the first function passed as an argument to the second, - // allowing you to adjust arguments, run code before and after, and - // conditionally execute the original function. - _.wrap = function(func, wrapper) { - return _.partial(wrapper, func); - }; - - // Returns a negated version of the passed-in predicate. - _.negate = function(predicate) { - return function() { - return !predicate.apply(this, arguments); - }; - }; - - // Returns a function that is the composition of a list of functions, each - // consuming the return value of the function that follows. - _.compose = function() { - var args = arguments; - var start = args.length - 1; - return function() { - var i = start; - var result = args[start].apply(this, arguments); - while (i--) result = args[i].call(this, result); - return result; - }; - }; - - // Returns a function that will only be executed after being called N times. - _.after = function(times, func) { - return function() { - if (--times < 1) { - return func.apply(this, arguments); - } - }; - }; - - // Returns a function that will only be executed before being called N times. - _.before = function(times, func) { - var memo; - return function() { - if (--times > 0) { - memo = func.apply(this, arguments); - } else { - func = null; - } - return memo; - }; - }; - - // Returns a function that will be executed at most one time, no matter how - // often you call it. Useful for lazy initialization. - _.once = _.partial(_.before, 2); - - // Object Functions - // ---------------- - - // Retrieve the names of an object's properties. - // Delegates to **ECMAScript 5**'s native `Object.keys` - _.keys = function(obj) { - if (!_.isObject(obj)) return []; - if (nativeKeys) return nativeKeys(obj); - var keys = []; - for (var key in obj) if (_.has(obj, key)) keys.push(key); - return keys; - }; - - // Retrieve the values of an object's properties. - _.values = function(obj) { - var keys = _.keys(obj); - var length = keys.length; - var values = Array(length); - for (var i = 0; i < length; i++) { - values[i] = obj[keys[i]]; - } - return values; - }; - - // Convert an object into a list of `[key, value]` pairs. - _.pairs = function(obj) { - var keys = _.keys(obj); - var length = keys.length; - var pairs = Array(length); - for (var i = 0; i < length; i++) { - pairs[i] = [keys[i], obj[keys[i]]]; - } - return pairs; - }; - - // Invert the keys and values of an object. The values must be serializable. - _.invert = function(obj) { - var result = {}; - var keys = _.keys(obj); - for (var i = 0, length = keys.length; i < length; i++) { - result[obj[keys[i]]] = keys[i]; - } - return result; - }; - - // Return a sorted list of the function names available on the object. - // Aliased as `methods` - _.functions = _.methods = function(obj) { - var names = []; - for (var key in obj) { - if (_.isFunction(obj[key])) names.push(key); - } - return names.sort(); - }; - - // Extend a given object with all the properties in passed-in object(s). - _.extend = function(obj) { - if (!_.isObject(obj)) return obj; - var source, prop; - for (var i = 1, length = arguments.length; i < length; i++) { - source = arguments[i]; - for (prop in source) { - if (hasOwnProperty.call(source, prop)) { - obj[prop] = source[prop]; - } - } - } - return obj; - }; - - // Return a copy of the object only containing the whitelisted properties. - _.pick = function(obj, iteratee, context) { - var result = {}, key; - if (obj == null) return result; - if (_.isFunction(iteratee)) { - iteratee = createCallback(iteratee, context); - for (key in obj) { - var value = obj[key]; - if (iteratee(value, key, obj)) result[key] = value; - } - } else { - var keys = concat.apply([], slice.call(arguments, 1)); - obj = new Object(obj); - for (var i = 0, length = keys.length; i < length; i++) { - key = keys[i]; - if (key in obj) result[key] = obj[key]; - } - } - return result; - }; - - // Return a copy of the object without the blacklisted properties. - _.omit = function(obj, iteratee, context) { - if (_.isFunction(iteratee)) { - iteratee = _.negate(iteratee); - } else { - var keys = _.map(concat.apply([], slice.call(arguments, 1)), String); - iteratee = function(value, key) { - return !_.contains(keys, key); - }; - } - return _.pick(obj, iteratee, context); - }; - - // Fill in a given object with default properties. - _.defaults = function(obj) { - if (!_.isObject(obj)) return obj; - for (var i = 1, length = arguments.length; i < length; i++) { - var source = arguments[i]; - for (var prop in source) { - if (obj[prop] === void 0) obj[prop] = source[prop]; - } - } - return obj; - }; - - // Create a (shallow-cloned) duplicate of an object. - _.clone = function(obj) { - if (!_.isObject(obj)) return obj; - return _.isArray(obj) ? obj.slice() : _.extend({}, obj); - }; - - // Invokes interceptor with the obj, and then returns obj. - // The primary purpose of this method is to "tap into" a method chain, in - // order to perform operations on intermediate results within the chain. - _.tap = function(obj, interceptor) { - interceptor(obj); - return obj; - }; - - // Internal recursive comparison function for `isEqual`. - var eq = function(a, b, aStack, bStack) { - // Identical objects are equal. `0 === -0`, but they aren't identical. - // See the [Harmony `egal` proposal](http://wiki.ecmascript.org/doku.php?id=harmony:egal). - if (a === b) return a !== 0 || 1 / a === 1 / b; - // A strict comparison is necessary because `null == undefined`. - if (a == null || b == null) return a === b; - // Unwrap any wrapped objects. - if (a instanceof _) a = a._wrapped; - if (b instanceof _) b = b._wrapped; - // Compare `[[Class]]` names. - var className = toString.call(a); - if (className !== toString.call(b)) return false; - switch (className) { - // Strings, numbers, regular expressions, dates, and booleans are compared by value. - case '[object RegExp]': - // RegExps are coerced to strings for comparison (Note: '' + /a/i === '/a/i') - case '[object String]': - // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is - // equivalent to `new String("5")`. - return '' + a === '' + b; - case '[object Number]': - // `NaN`s are equivalent, but non-reflexive. - // Object(NaN) is equivalent to NaN - if (+a !== +a) return +b !== +b; - // An `egal` comparison is performed for other numeric values. - return +a === 0 ? 1 / +a === 1 / b : +a === +b; - case '[object Date]': - case '[object Boolean]': - // Coerce dates and booleans to numeric primitive values. Dates are compared by their - // millisecond representations. Note that invalid dates with millisecond representations - // of `NaN` are not equivalent. - return +a === +b; - } - if (typeof a != 'object' || typeof b != 'object') return false; - // Assume equality for cyclic structures. The algorithm for detecting cyclic - // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`. - var length = aStack.length; - while (length--) { - // Linear search. Performance is inversely proportional to the number of - // unique nested structures. - if (aStack[length] === a) return bStack[length] === b; - } - // Objects with different constructors are not equivalent, but `Object`s - // from different frames are. - var aCtor = a.constructor, bCtor = b.constructor; - if ( - aCtor !== bCtor && - // Handle Object.create(x) cases - 'constructor' in a && 'constructor' in b && - !(_.isFunction(aCtor) && aCtor instanceof aCtor && - _.isFunction(bCtor) && bCtor instanceof bCtor) - ) { - return false; - } - // Add the first object to the stack of traversed objects. - aStack.push(a); - bStack.push(b); - var size, result; - // Recursively compare objects and arrays. - if (className === '[object Array]') { - // Compare array lengths to determine if a deep comparison is necessary. - size = a.length; - result = size === b.length; - if (result) { - // Deep compare the contents, ignoring non-numeric properties. - while (size--) { - if (!(result = eq(a[size], b[size], aStack, bStack))) break; - } - } - } else { - // Deep compare objects. - var keys = _.keys(a), key; - size = keys.length; - // Ensure that both objects contain the same number of properties before comparing deep equality. - result = _.keys(b).length === size; - if (result) { - while (size--) { - // Deep compare each member - key = keys[size]; - if (!(result = _.has(b, key) && eq(a[key], b[key], aStack, bStack))) break; - } - } - } - // Remove the first object from the stack of traversed objects. - aStack.pop(); - bStack.pop(); - return result; - }; - - // Perform a deep comparison to check if two objects are equal. - _.isEqual = function(a, b) { - return eq(a, b, [], []); - }; - - // Is a given array, string, or object empty? - // An "empty" object has no enumerable own-properties. - _.isEmpty = function(obj) { - if (obj == null) return true; - if (_.isArray(obj) || _.isString(obj) || _.isArguments(obj)) return obj.length === 0; - for (var key in obj) if (_.has(obj, key)) return false; - return true; - }; - - // Is a given value a DOM element? - _.isElement = function(obj) { - return !!(obj && obj.nodeType === 1); - }; - - // Is a given value an array? - // Delegates to ECMA5's native Array.isArray - _.isArray = nativeIsArray || function(obj) { - return toString.call(obj) === '[object Array]'; - }; - - // Is a given variable an object? - _.isObject = function(obj) { - var type = typeof obj; - return type === 'function' || type === 'object' && !!obj; - }; - - // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp. - _.each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp'], function(name) { - _['is' + name] = function(obj) { - return toString.call(obj) === '[object ' + name + ']'; - }; - }); - - // Define a fallback version of the method in browsers (ahem, IE), where - // there isn't any inspectable "Arguments" type. - if (!_.isArguments(arguments)) { - _.isArguments = function(obj) { - return _.has(obj, 'callee'); - }; - } - - // Optimize `isFunction` if appropriate. Work around an IE 11 bug. - if (typeof /./ !== 'function') { - _.isFunction = function(obj) { - return typeof obj == 'function' || false; - }; - } - - // Is a given object a finite number? - _.isFinite = function(obj) { - return isFinite(obj) && !isNaN(parseFloat(obj)); - }; - - // Is the given value `NaN`? (NaN is the only number which does not equal itself). - _.isNaN = function(obj) { - return _.isNumber(obj) && obj !== +obj; - }; - - // Is a given value a boolean? - _.isBoolean = function(obj) { - return obj === true || obj === false || toString.call(obj) === '[object Boolean]'; - }; - - // Is a given value equal to null? - _.isNull = function(obj) { - return obj === null; - }; - - // Is a given variable undefined? - _.isUndefined = function(obj) { - return obj === void 0; - }; - - // Shortcut function for checking if an object has a given property directly - // on itself (in other words, not on a prototype). - _.has = function(obj, key) { - return obj != null && hasOwnProperty.call(obj, key); - }; - - // Utility Functions - // ----------------- - - // Run Underscore.js in *noConflict* mode, returning the `_` variable to its - // previous owner. Returns a reference to the Underscore object. - _.noConflict = function() { - root._ = previousUnderscore; - return this; - }; - - // Keep the identity function around for default iteratees. - _.identity = function(value) { - return value; - }; - - // Predicate-generating functions. Often useful outside of Underscore. - _.constant = function(value) { - return function() { - return value; - }; - }; - - _.noop = function(){}; - - _.property = function(key) { - return function(obj) { - return obj[key]; - }; - }; - - // Returns a predicate for checking whether an object has a given set of `key:value` pairs. - _.matches = function(attrs) { - var pairs = _.pairs(attrs), length = pairs.length; - return function(obj) { - if (obj == null) return !length; - obj = new Object(obj); - for (var i = 0; i < length; i++) { - var pair = pairs[i], key = pair[0]; - if (pair[1] !== obj[key] || !(key in obj)) return false; - } - return true; - }; - }; - - // Run a function **n** times. - _.times = function(n, iteratee, context) { - var accum = Array(Math.max(0, n)); - iteratee = createCallback(iteratee, context, 1); - for (var i = 0; i < n; i++) accum[i] = iteratee(i); - return accum; - }; - - // Return a random integer between min and max (inclusive). - _.random = function(min, max) { - if (max == null) { - max = min; - min = 0; - } - return min + Math.floor(Math.random() * (max - min + 1)); - }; - - // A (possibly faster) way to get the current timestamp as an integer. - _.now = Date.now || function() { - return new Date().getTime(); - }; - - // List of HTML entities for escaping. - var escapeMap = { - '&': '&', - '<': '<', - '>': '>', - '"': '"', - "'": ''', - '`': '`' - }; - var unescapeMap = _.invert(escapeMap); - - // Functions for escaping and unescaping strings to/from HTML interpolation. - var createEscaper = function(map) { - var escaper = function(match) { - return map[match]; - }; - // Regexes for identifying a key that needs to be escaped - var source = '(?:' + _.keys(map).join('|') + ')'; - var testRegexp = RegExp(source); - var replaceRegexp = RegExp(source, 'g'); - return function(string) { - string = string == null ? '' : '' + string; - return testRegexp.test(string) ? string.replace(replaceRegexp, escaper) : string; - }; - }; - _.escape = createEscaper(escapeMap); - _.unescape = createEscaper(unescapeMap); - - // If the value of the named `property` is a function then invoke it with the - // `object` as context; otherwise, return it. - _.result = function(object, property) { - if (object == null) return void 0; - var value = object[property]; - return _.isFunction(value) ? object[property]() : value; - }; - - // Generate a unique integer id (unique within the entire client session). - // Useful for temporary DOM ids. - var idCounter = 0; - _.uniqueId = function(prefix) { - var id = ++idCounter + ''; - return prefix ? prefix + id : id; - }; - - // By default, Underscore uses ERB-style template delimiters, change the - // following template settings to use alternative delimiters. - _.templateSettings = { - evaluate : /<%([\s\S]+?)%>/g, - interpolate : /<%=([\s\S]+?)%>/g, - escape : /<%-([\s\S]+?)%>/g - }; - - // When customizing `templateSettings`, if you don't want to define an - // interpolation, evaluation or escaping regex, we need one that is - // guaranteed not to match. - var noMatch = /(.)^/; - - // Certain characters need to be escaped so that they can be put into a - // string literal. - var escapes = { - "'": "'", - '\\': '\\', - '\r': 'r', - '\n': 'n', - '\u2028': 'u2028', - '\u2029': 'u2029' - }; - - var escaper = /\\|'|\r|\n|\u2028|\u2029/g; - - var escapeChar = function(match) { - return '\\' + escapes[match]; - }; - - // JavaScript micro-templating, similar to John Resig's implementation. - // Underscore templating handles arbitrary delimiters, preserves whitespace, - // and correctly escapes quotes within interpolated code. - // NB: `oldSettings` only exists for backwards compatibility. - _.template = function(text, settings, oldSettings) { - if (!settings && oldSettings) settings = oldSettings; - settings = _.defaults({}, settings, _.templateSettings); - - // Combine delimiters into one regular expression via alternation. - var matcher = RegExp([ - (settings.escape || noMatch).source, - (settings.interpolate || noMatch).source, - (settings.evaluate || noMatch).source - ].join('|') + '|$', 'g'); - - // Compile the template source, escaping string literals appropriately. - var index = 0; - var source = "__p+='"; - text.replace(matcher, function(match, escape, interpolate, evaluate, offset) { - source += text.slice(index, offset).replace(escaper, escapeChar); - index = offset + match.length; - - if (escape) { - source += "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'"; - } else if (interpolate) { - source += "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'"; - } else if (evaluate) { - source += "';\n" + evaluate + "\n__p+='"; - } - - // Adobe VMs need the match returned to produce the correct offest. - return match; - }); - source += "';\n"; - - // If a variable is not specified, place data values in local scope. - if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n'; - - source = "var __t,__p='',__j=Array.prototype.join," + - "print=function(){__p+=__j.call(arguments,'');};\n" + - source + 'return __p;\n'; - - try { - var render = new Function(settings.variable || 'obj', '_', source); - } catch (e) { - e.source = source; - throw e; - } - - var template = function(data) { - return render.call(this, data, _); - }; - - // Provide the compiled source as a convenience for precompilation. - var argument = settings.variable || 'obj'; - template.source = 'function(' + argument + '){\n' + source + '}'; - - return template; - }; - - // Add a "chain" function. Start chaining a wrapped Underscore object. - _.chain = function(obj) { - var instance = _(obj); - instance._chain = true; - return instance; - }; - - // OOP - // --------------- - // If Underscore is called as a function, it returns a wrapped object that - // can be used OO-style. This wrapper holds altered versions of all the - // underscore functions. Wrapped objects may be chained. - - // Helper function to continue chaining intermediate results. - var result = function(obj) { - return this._chain ? _(obj).chain() : obj; - }; - - // Add your own custom functions to the Underscore object. - _.mixin = function(obj) { - _.each(_.functions(obj), function(name) { - var func = _[name] = obj[name]; - _.prototype[name] = function() { - var args = [this._wrapped]; - push.apply(args, arguments); - return result.call(this, func.apply(_, args)); - }; - }); - }; - - // Add all of the Underscore functions to the wrapper object. - _.mixin(_); - - // Add all mutator Array functions to the wrapper. - _.each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) { - var method = ArrayProto[name]; - _.prototype[name] = function() { - var obj = this._wrapped; - method.apply(obj, arguments); - if ((name === 'shift' || name === 'splice') && obj.length === 0) delete obj[0]; - return result.call(this, obj); - }; - }); - - // Add all accessor Array functions to the wrapper. - _.each(['concat', 'join', 'slice'], function(name) { - var method = ArrayProto[name]; - _.prototype[name] = function() { - return result.call(this, method.apply(this._wrapped, arguments)); - }; - }); - - // Extracts the result from a wrapped and chained object. - _.prototype.value = function() { - return this._wrapped; - }; - - // AMD registration happens at the end for compatibility with AMD loaders - // that may not enforce next-turn semantics on modules. Even though general - // practice for AMD registration is to be anonymous, underscore registers - // as a named module because, like jQuery, it is a base library that is - // popular enough to be bundled in a third party lib, but not be part of - // an AMD load request. Those cases could generate an error when an - // anonymous define() is called outside of a loader request. - if (typeof define === 'function' && define.amd) { - define('underscore', [], function() { - return _; - }); - } -}.call(this)); diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_anon_enum_inside_array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_anon_enum_inside_array.cwl deleted file mode 100644 index a7af048d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_anon_enum_inside_array.cwl +++ /dev/null @@ -1,25 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -inputs: - first: - type: - type: record - fields: - species: - - type: enum - symbols: [homo_sapiens, mus_musculus] - - "null" - second: - type: - - "null" - - type: enum - symbols: [homo_sapiens, mus_musculus] -baseCommand: echo -arguments: - - prefix: first - valueFrom: $(inputs.first.species) - - prefix: second - valueFrom: $(inputs.second) -outputs: - result: stdout - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_anon_enum_inside_array_inside_schemadef.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_anon_enum_inside_array_inside_schemadef.cwl deleted file mode 100644 index e753fd51..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_anon_enum_inside_array_inside_schemadef.cwl +++ /dev/null @@ -1,27 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -requirements: - SchemaDefRequirement: - types: - - name: vcf2maf_params - type: record - fields: - species: - - "null" - - type: enum - symbols: [homo_sapiens, mus_musculus] - ncbi_build: - - "null" - - type: enum - symbols: [GRCh37, GRCh38, GRCm38] -inputs: - first: vcf2maf_params -baseCommand: echo -arguments: - - prefix: species - valueFrom: $(inputs.first.species) - - prefix: ncbi_build - valueFrom: $(inputs.first.ncbi_build) -outputs: - result: stdout - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_any-type-compat.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_any-type-compat.cwl deleted file mode 100644 index b2ef5c11..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_any-type-compat.cwl +++ /dev/null @@ -1,22 +0,0 @@ -cwlVersion: v1.1 -class: Workflow - -steps: [] -inputs: - input1: - type: Any - input2: - type: Any[] - input3: - type: Any - -outputs: - - id: output1 - type: string[] - outputSource: input1 - - id: output2 - type: string[] - outputSource: input2 - - id: output3 - type: string - outputSource: input3 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_basename-fields-test.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_basename-fields-test.cwl deleted file mode 100644 index 811302a3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_basename-fields-test.cwl +++ /dev/null @@ -1,33 +0,0 @@ -cwlVersion: v1.1 -class: Workflow - -requirements: - - class: StepInputExpressionRequirement - -inputs: - tool: File - -outputs: - rootFile: - type: File - outputSource: root/out - extFile: - type: File - outputSource: ext/out - -steps: - root: - run: echo-file-tool.cwl - in: - tool: tool - in: - valueFrom: $(inputs.tool.nameroot) - out: [out] - ext: - run: echo-file-tool.cwl - in: - tool: tool - in: - valueFrom: $(inputs.tool.nameext) - out: [out] - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_binding-test.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_binding-test.cwl deleted file mode 100755 index 8d20fc43..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_binding-test.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 -hints: - - class: DockerRequirement - dockerPull: python:2-slim -inputs: - - id: reference - type: File - inputBinding: { position: 2 } - - - id: reads - type: - type: array - items: File - inputBinding: { prefix: "-YYY" } - inputBinding: { position: 3, prefix: "-XXX" } - - - id: "#args.py" - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - -outputs: - args: string[] - -baseCommand: python -arguments: ["bwa", "mem"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_bool-empty-inputbinding.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_bool-empty-inputbinding.cwl deleted file mode 100644 index e045bef6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_bool-empty-inputbinding.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -hints: - - class: DockerRequirement - dockerPull: python:2-slim -inputs: -- id: flag - type: boolean - inputBinding: {} -- id: "args.py" - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 -outputs: -- id: args - type: string[] -baseCommand: python -arguments: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_bwa-mem-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_bwa-mem-tool.cwl deleted file mode 100755 index 8b2b1a8c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_bwa-mem-tool.cwl +++ /dev/null @@ -1,61 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 - -class: CommandLineTool - -hints: - - class: ResourceRequirement - coresMin: 2 - - class: DockerRequirement - dockerPull: python:2-slim - -inputs: - - id: reference - type: File - inputBinding: { position: 2 } - - - id: reads - type: - type: array - items: File - inputBinding: { position: 3 } - - - id: minimum_seed_length - type: int - inputBinding: { position: 1, prefix: -m } - - - id: min_std_max_min - type: { type: array, items: int } - inputBinding: - position: 1 - prefix: -I - itemSeparator: "," - - - id: args.py - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - -outputs: - - id: sam - type: ["null", File] - outputBinding: { glob: output.sam } - - id: args - type: - type: array - items: string - -baseCommand: python - -arguments: - - bwa - - mem - - valueFrom: $(runtime.cores) - position: 1 - prefix: -t - -stdout: output.sam diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat-from-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat-from-dir.cwl deleted file mode 100644 index 7567e99d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat-from-dir.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 - -inputs: - dir1: Directory - -outputs: - output: - type: stdout - -baseCommand: [cat] - -stdin: $(inputs.dir1.listing[0].path) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat-tool.cwl deleted file mode 100644 index 1daa51c2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 - -inputs: - file1: File - -outputs: - output: - type: File - outputBinding: { glob: output } - -baseCommand: [cat] - -stdin: $(inputs.file1.path) -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat1-testcli.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat1-testcli.cwl deleted file mode 100755 index 22cd2d71..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat1-testcli.cwl +++ /dev/null @@ -1,41 +0,0 @@ -#!/usr/bin/env cwl-runner -{ - "class": "CommandLineTool", - "cwlVersion": "v1.1", - "doc": "Print the contents of a file to stdout using 'cat' running in a docker container.", - "hints": [ - { - "class": "DockerRequirement", - "dockerPull": "python:2-slim" - } - ], - "inputs": [ - { - "id": "file1", - "type": "File", - "inputBinding": {"position": 1} - }, - { - "id": "numbering", - "type": ["null", "boolean"], - "inputBinding": { - "position": 0, - "prefix": "-n" - } - }, - { - id: "args.py", - type: File, - default: { - class: File, - location: args.py - }, - inputBinding: { - position: -1 - } - } - ], - "outputs": [{"id": "args", "type": "string[]"}], - "baseCommand": "python", - "arguments": ["cat"] -} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-from-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-from-dir.cwl deleted file mode 100755 index 7d8a7793..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-from-dir.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -inputs: - dir1: - type: Directory - inputBinding: - valueFrom: $(self.listing[0].path) -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-nodocker.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-nodocker.cwl deleted file mode 100755 index 385057d9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-nodocker.cwl +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "Print the contents of a file to stdout using 'cat'." -inputs: - file1: - type: File - label: Input File - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-tool-docker.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-tool-docker.cwl deleted file mode 100755 index b7dfd06f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-tool-docker.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." -requirements: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - label: Input File - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-tool-mediumcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-tool-mediumcut.cwl deleted file mode 100755 index 95599a47..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-tool-mediumcut.cwl +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." -requirements: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - label: Input File - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: stdout -baseCommand: cat -stdout: cat-out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-tool-shortcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-tool-shortcut.cwl deleted file mode 100755 index 833879c6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-tool-shortcut.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." -requirements: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - label: Input File - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: stdout -baseCommand: cat diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-tool.cwl deleted file mode 100755 index 1db66a49..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat3-tool.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - label: Input File - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat4-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat4-tool.cwl deleted file mode 100755 index ef420ee8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat4-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "Print the contents of a file to stdout using 'cat' running in a docker container if docker is available." -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: File -outputs: - output_txt: - type: File - outputBinding: - glob: output.txt -baseCommand: cat -stdout: output.txt -stdin: $(inputs.file1.path) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat5-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat5-tool.cwl deleted file mode 100755 index b7240716..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_cat5-tool.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -$namespaces: - ex: http://example.com/ -cwlVersion: v1.1 -class: CommandLineTool -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." -hints: - DockerRequirement: - dockerPull: "debian:stretch-slim" - ex:BlibberBlubberFakeRequirement: - fakeField: fraggleFroogle -inputs: - file1: - type: File - label: "Input File" - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_conflict-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_conflict-wf.cwl deleted file mode 100644 index a78772a0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_conflict-wf.cwl +++ /dev/null @@ -1,72 +0,0 @@ -cwlVersion: v1.1 -$graph: -- id: echo - class: CommandLineTool - inputs: - text: - type: string - inputBinding: {} - - outputs: - fileout: - type: File - outputBinding: - glob: out.txt - - baseCommand: echo - stdout: out.txt - -- id: cat - class: CommandLineTool - inputs: - file1: - type: File - inputBinding: - position: 1 - file2: - type: File - inputBinding: - position: 2 - - outputs: - fileout: - type: File - outputBinding: - glob: out.txt - - baseCommand: cat - stdout: out.txt - -- class: Workflow - id: collision - - inputs: - input_1: string - input_2: string - - outputs: - fileout: - type: File - outputSource: cat_step/fileout - - steps: - echo_1: - run: "#echo" - in: - text: input_1 - out: [fileout] - - echo_2: - run: "#echo" - in: - text: input_2 - out: [fileout] - - cat_step: - run: "#cat" - in: - file1: - source: echo_1/fileout - file2: - source: echo_2/fileout - out: [fileout] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines1-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines1-wf-noET.cwl deleted file mode 100755 index 744cd7c0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines1-wf-noET.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: - type: File - -outputs: - wc_output: - type: File - outputSource: step1/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: file1 - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines1-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines1-wf.cwl deleted file mode 100755 index 0d428d06..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines1-wf.cwl +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: - type: File - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: file1 - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines10-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines10-wf.cwl deleted file mode 100755 index f84997cc..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines10-wf.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -inputs: - file1: File -outputs: - count_output: {type: int, outputSource: step0/count_output} -requirements: - SubworkflowFeatureRequirement: {} -steps: - step0: - in: {file1: file1} - out: [count_output] - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step2/output} - steps: - step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} - step2: {run: parseInt-tool.cwl, in: {file1: step1/output}, out: [output]} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-extra-step-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-extra-step-wf-noET.cwl deleted file mode 100755 index 3af2a41f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-extra-step-wf-noET.cwl +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: File? - -outputs: - wc_output: - type: File - outputSource: step1/output - -steps: - step0: - run: cat-tool.cwl - in: - file1: file1 - out: [ output ] - step1: - run: wc-tool.cwl - in: - file1: - source: step0/output - default: - class: File - location: whale.txt - out: [output] - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-extra-step-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-extra-step-wf.cwl deleted file mode 100755 index 8b39bd0d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-extra-step-wf.cwl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: File? - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step0: - run: cat-tool.cwl - in: - file1: file1 - out: [ output ] - step1: - run: wc-tool.cwl - in: - file1: - source: step0/output - default: - class: File - location: whale.txt - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-null-step-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-null-step-wf-noET.cwl deleted file mode 100755 index 4332d9e3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-null-step-wf-noET.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: [] - -outputs: - wc_output: - type: File - outputSource: step1/output - -steps: - step0: - run: null-expression3-tool.cwl - in: [] - out: [ output ] - - step1: - run: wc-tool.cwl - in: - file1: - source: step0/output - default: - class: File - location: whale.txt - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-null-step-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-null-step-wf.cwl deleted file mode 100755 index d76418e7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-null-step-wf.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: [] - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step0: - run: null-expression3-tool.cwl - in: [] - out: [ output ] - - step1: - run: wc-tool.cwl - in: - file1: - source: step0/output - default: - class: File - location: whale.txt - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-wf-noET.cwl deleted file mode 100755 index c5d1fdce..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-wf-noET.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: File? - -outputs: - wc_output: - type: File - outputSource: step1/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: - source: file1 - default: - class: File - location: whale.txt - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-wf.cwl deleted file mode 100755 index d5d4e8a5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines11-wf.cwl +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: File? - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: - source: file1 - default: - class: File - location: whale.txt - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines12-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines12-wf.cwl deleted file mode 100755 index 8ab8ac3d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines12-wf.cwl +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -requirements: - - class: MultipleInputFeatureRequirement - -inputs: - file1: - - type: array - items: File - file2: - - type: array - items: File - -outputs: - count_output: - type: int - outputSource: step1/output - -steps: - step1: - run: wc3-tool.cwl - in: - file1: - source: [file1, file2] - linkMerge: merge_flattened - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines13-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines13-wf.cwl deleted file mode 100644 index d90f1c41..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines13-wf.cwl +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: File[] - file2: File[] - -outputs: - count_output: - type: int - outputSource: step1/output - -steps: - step1: - run: wc3-tool.cwl - in: - file1: - source: [file1] - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines14-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines14-wf.cwl deleted file mode 100644 index d00bd370..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines14-wf.cwl +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: - type: File - file2: - type: File - -outputs: - count_output: - type: int[] - outputSource: step1/count_output - -requirements: - ScatterFeatureRequirement: {} - SubworkflowFeatureRequirement: {} - MultipleInputFeatureRequirement: {} - -steps: - step1: - in: - file1: [file1, file2] - out: [count_output] - scatter: file1 - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step2/output} - steps: - step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} - step2: {run: parseInt-tool.cwl, in: {file1: step1/output}, out: [output]} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines15-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines15-wf.cwl deleted file mode 100644 index f85b5d99..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines15-wf.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -inputs: - file1: File -outputs: - count_output: {type: int, outputSource: step1/count_output} -requirements: - SubworkflowFeatureRequirement: {} -steps: - step1: - in: {file1: file1} - out: [count_output] - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step1/count_output} - steps: - step1: - in: {file1: file1} - out: [count_output] - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step2/output} - steps: - step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} - step2: {run: parseInt-tool.cwl, in: {file1: step1/output}, out: [output]} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines16-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines16-wf.cwl deleted file mode 100644 index ce13b101..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines16-wf.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -inputs: - file1: File -outputs: - count_output: {type: int, outputSource: step1/count_output} -requirements: - SubworkflowFeatureRequirement: {} -steps: - step1: - in: {file1: file1} - out: [count_output] - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step2/count_output} - steps: - step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} - step2: - in: {file1: step1/output} - out: [count_output] - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step1/output} - steps: - step1: {run: parseInt-tool.cwl, in: {file1: file1}, out: [output]} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines17-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines17-wf.cwl deleted file mode 100644 index 40e74995..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines17-wf.cwl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -inputs: - file1: File -outputs: - count_output: {type: int, outputSource: step1/count_output} -requirements: - SubworkflowFeatureRequirement: {} -steps: - step1: - in: {file1: file1} - out: [count_output] - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step2/output} - steps: - step1: - in: {file1: file1} - out: [wc_output] - run: - class: Workflow - inputs: - file1: File - outputs: - wc_output: {type: File, outputSource: step1/output} - steps: - step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} - - step2: {run: parseInt-tool.cwl, in: {file1: step1/wc_output}, out: [output]} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines18-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines18-wf.cwl deleted file mode 100644 index adbebfab..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines18-wf.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: - type: File[] - -outputs: - count_output: - type: int[] - outputSource: step1/count_output - -requirements: - ScatterFeatureRequirement: {} - SubworkflowFeatureRequirement: {} - MultipleInputFeatureRequirement: {} - -steps: - step1: - in: {file1: file1} - out: [count_output] - scatter: file1 - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step2/output} - steps: - step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} - step2: {run: parseInt-tool.cwl, in: {file1: step1/output}, out: [output]} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines2-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines2-wf.cwl deleted file mode 100755 index cd9268e0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines2-wf.cwl +++ /dev/null @@ -1,50 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -requirements: - InlineJavascriptRequirement: {} - -inputs: - file1: - type: File - -outputs: - count_output: - type: int - outputSource: step2/parseInt_output - -steps: - step1: - in: - wc_file1: file1 - out: [wc_output] - run: - id: wc - class: CommandLineTool - inputs: - wc_file1: - type: File - inputBinding: {} - outputs: - wc_output: - type: File - outputBinding: - glob: output.txt - stdout: output.txt - baseCommand: wc - - step2: - in: - parseInt_file1: step1/wc_output - out: [parseInt_output] - run: - class: ExpressionTool - inputs: - parseInt_file1: - type: File - inputBinding: { loadContents: true } - outputs: - parseInt_output: - type: int - expression: > - ${return {'parseInt_output': parseInt(inputs.parseInt_file1.contents)};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines3-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines3-wf.cwl deleted file mode 100755 index 06394c54..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines3-wf.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: - type: File[] - -outputs: - count_output: - type: int[] - outputSource: step1/output - -requirements: - ScatterFeatureRequirement: {} - -steps: - step1: - run: wc2-tool.cwl - scatter: file1 - in: - file1: file1 - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines4-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines4-wf.cwl deleted file mode 100755 index e2750cf3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines4-wf.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: - type: File - file2: - type: File - -outputs: - count_output: - type: int[] - outputSource: step1/output - -requirements: - - class: ScatterFeatureRequirement - - class: MultipleInputFeatureRequirement - -steps: - step1: - run: wc2-tool.cwl - scatter: file1 - in: - file1: [file1, file2] - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines5-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines5-wf.cwl deleted file mode 100755 index a610095e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines5-wf.cwl +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: - type: File - default: {class: File, location: hello.txt} -outputs: - count_output: - type: int - outputSource: step1/output -steps: - step1: - run: wc2-tool.cwl - in: - file1: file1 - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines6-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines6-wf.cwl deleted file mode 100755 index 2d998f2b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines6-wf.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: File[] - file2: File[] - -outputs: - count_output: - type: int[] - outputSource: step1/output - -requirements: - - class: ScatterFeatureRequirement - - class: MultipleInputFeatureRequirement - -steps: - step1: - run: wc3-tool.cwl - scatter: file1 - in: - file1: - source: [file1, file2] - linkMerge: merge_nested - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines7-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines7-wf.cwl deleted file mode 100755 index 7677bc08..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines7-wf.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -requirements: - - class: MultipleInputFeatureRequirement - -inputs: - file1: - type: File[] - file2: - type: File[] - -outputs: - count_output: - type: int - outputSource: step1/output - -steps: - step1: - run: wc3-tool.cwl - in: - file1: - source: [file1, file2] - linkMerge: merge_flattened - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines8-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines8-wf-noET.cwl deleted file mode 100755 index e2f5a437..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines8-wf-noET.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: File - -outputs: - wc_output: - type: File - outputSource: step1/wc_output - -requirements: - - class: SubworkflowFeatureRequirement - -steps: - step1: - run: count-lines1-wf-noET.cwl - in: - file1: file1 - out: [wc_output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines8-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines8-wf.cwl deleted file mode 100755 index 188ab1c8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines8-wf.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - file1: File - -outputs: - count_output: - type: int - outputSource: step1/count_output - -requirements: - - class: SubworkflowFeatureRequirement - -steps: - step1: - run: count-lines1-wf.cwl - in: - file1: file1 - out: [count_output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines9-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines9-wf-noET.cwl deleted file mode 100755 index 42d2e866..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines9-wf-noET.cwl +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: [] - -outputs: - wc_output: - type: File - outputSource: step1/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: - default: - class: File - location: whale.txt - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines9-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines9-wf.cwl deleted file mode 100755 index ca110985..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_count-lines9-wf.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: [] - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: - default: - class: File - location: whale.txt - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_default_path.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_default_path.cwl deleted file mode 100644 index 8fb99285..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_default_path.cwl +++ /dev/null @@ -1,10 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -inputs: - - id: "file1" - type: File - default: - class: File - path: whale.txt -outputs: [] -arguments: [cat,$(inputs.file1.path)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir.cwl deleted file mode 100644 index 56f2ad2a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir.cwl +++ /dev/null @@ -1,17 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - - class: ShellCommandRequirement -inputs: - indir: Directory -outputs: - outlist: - type: File - outputBinding: - glob: output.txt -arguments: ["cd", "$(inputs.indir.path)", - {shellQuote: false, valueFrom: "&&"}, - "find", ".", - {shellQuote: false, valueFrom: "|"}, - "sort"] -stdout: output.txt \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir2.cwl deleted file mode 100644 index 05eb7465..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir2.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - ShellCommandRequirement: {} -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - indir: Directory -outputs: - outlist: - type: File - outputBinding: - glob: output.txt -arguments: ["cd", "$(inputs.indir.path)", - {shellQuote: false, valueFrom: "&&"}, - "find", ".", - {shellQuote: false, valueFrom: "|"}, - "sort"] -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir3.cwl deleted file mode 100644 index d02e6315..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir3.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -baseCommand: [tar, xvf] -inputs: - inf: - type: File - inputBinding: - position: 1 -outputs: - outdir: - type: Directory - outputBinding: - glob: . diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir4.cwl deleted file mode 100644 index 0b8d9ab4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir4.cwl +++ /dev/null @@ -1,17 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - - class: ShellCommandRequirement -inputs: - inf: File -outputs: - outlist: - type: File - outputBinding: - glob: output.txt -arguments: ["cd", "$(inputs.inf.dirname)/xtestdir", - {shellQuote: false, valueFrom: "&&"}, - "find", ".", - {shellQuote: false, valueFrom: "|"}, - "sort"] -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir5.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir5.cwl deleted file mode 100644 index f7bbd062..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir5.cwl +++ /dev/null @@ -1,19 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - - class: ShellCommandRequirement - - class: InitialWorkDirRequirement - listing: $(inputs.indir.listing) -inputs: - indir: - type: Directory - loadListing: shallow_listing -outputs: - outlist: - type: File - outputBinding: - glob: output.txt -arguments: ["find", "-L", ".", "!", "-path", "*.txt", - {shellQuote: false, valueFrom: "|"}, - "sort"] -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir6.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir6.cwl deleted file mode 100644 index 94c59b37..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir6.cwl +++ /dev/null @@ -1,21 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - - class: ShellCommandRequirement -inputs: - indir: - type: Directory - inputBinding: - prefix: cd - position: -1 -outputs: - outlist: - type: File - outputBinding: - glob: output.txt -arguments: [ - {shellQuote: false, valueFrom: "&&"}, - "find", ".", - {shellQuote: false, valueFrom: "|"}, - "sort"] -stdout: output.txt \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir7.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir7.cwl deleted file mode 100644 index 29cc188b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dir7.cwl +++ /dev/null @@ -1,12 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.1 -requirements: - InlineJavascriptRequirement: {} -inputs: - files: File[] -outputs: - dir: Directory -expression: | - ${ - return {"dir": {"class": "Directory", "basename": "a_directory", "listing": inputs.files}}; - } \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_docker-array-secondaryfiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_docker-array-secondaryfiles.cwl deleted file mode 100644 index aa2fa962..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_docker-array-secondaryfiles.cwl +++ /dev/null @@ -1,50 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 - -requirements: - - class: DockerRequirement - dockerPull: debian:stretch-slim - - class: InlineJavascriptRequirement - - class: ShellCommandRequirement - -class: CommandLineTool - -inputs: - fasta_path: - type: - type: array - items: File - secondaryFiles: - - pattern: .fai - required: true - - pattern: .crai - required: false - - .bai? - - "${ if (inputs.require_dat) {return '.dat'} else {return null} }" - - "${ return null; }" - - pattern: .dat2 - required: $(inputs.require_dat) - require_dat: boolean? - -outputs: - bai_list: - type: File - outputBinding: - glob: "fai.list" - secondaryFiles: - - .bai? - - pattern: "${ return null }" - -arguments: - - valueFrom: ${ - var fai_list = ""; - for (var i = 0; i < inputs.fasta_path.length; i ++) { - fai_list += " cat " + inputs.fasta_path[i].path +".fai" + " >> fai.list && " - } - return fai_list.slice(0,-3) - } - position: 1 - shellQuote: false - -baseCommand: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_docker-output-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_docker-output-dir.cwl deleted file mode 100644 index 5d91408f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_docker-output-dir.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - DockerRequirement: - dockerPull: debian:stretch-slim - dockerOutputDirectory: /other -inputs: [] -outputs: - thing: - type: File - outputBinding: - glob: thing -baseCommand: ["touch", "/other/thing"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_docker-run-cmd.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_docker-run-cmd.cwl deleted file mode 100644 index e56c6e20..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_docker-run-cmd.cwl +++ /dev/null @@ -1,12 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - DockerRequirement: - dockerPull: bash:4.4.12 -inputs: [] -outputs: - cow: - type: File - outputBinding: - glob: cow -baseCommand: ["-c", "echo 'moo' > cow"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-default.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-default.cwl deleted file mode 100644 index 431f43eb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-default.cwl +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 - -requirements: - ResourceRequirement: - coresMin: $(inputs.special_file.size) - coresMax: $(inputs.special_file.size) - -inputs: - special_file: - type: File - default: - class: File - location: special_file - -outputs: - output: - type: stdout - -baseCommand: echo - -stdout: cores.txt - -arguments: [ $(runtime.cores) ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-dir.cwl deleted file mode 100644 index ae1e08f5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-dir.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 - -requirements: - InlineJavascriptRequirement: {} - ResourceRequirement: - coresMin: $(inputs.dir.listing[0].size) - coresMax: $(inputs.dir.listing[0].size) - -inputs: - dir: Directory - -outputs: - output: - type: stdout - -baseCommand: echo - -stdout: cores.txt - -arguments: [ $(runtime.cores) ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-workflow-inputdefault.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-workflow-inputdefault.cwl deleted file mode 100644 index 53d8850a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-workflow-inputdefault.cwl +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - special_file: - type: File - default: - class: File - path: special_file - -outputs: - cores: - type: File - outputSource: report/output - -steps: - count: - in: - special_file: special_file - out: [output] - run: dynresreq.cwl - - report: - in: - file1: count/output - out: [output] - run: cat-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-workflow-stepdefault.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-workflow-stepdefault.cwl deleted file mode 100644 index 138fbb05..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-workflow-stepdefault.cwl +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - special_file: File? -outputs: - cores: - type: File - outputSource: report/output - -steps: - count: - in: - special_file: - source: special_file - default: - class: File - location: special_file - out: [output] - run: dynresreq.cwl - - report: - in: - file1: count/output - out: [output] - run: cat-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-workflow-tooldefault.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-workflow-tooldefault.cwl deleted file mode 100644 index 4a0d85e6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-workflow-tooldefault.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - special_file: File? -outputs: - cores: - type: File - outputSource: report/output - -steps: - count: - in: - special_file: special_file - out: [output] - run: dynresreq-default.cwl - - report: - in: - file1: count/output - out: [output] - run: cat-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-workflow.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-workflow.cwl deleted file mode 100644 index bf4e5820..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq-workflow.cwl +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - special_file: File - -outputs: - cores: - type: File - outputSource: report/output - -steps: - count: - in: - special_file: special_file - out: [output] - run: dynresreq.cwl - - report: - in: - file1: count/output - out: [output] - run: cat-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq.cwl deleted file mode 100644 index ef81e26a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_dynresreq.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 - -requirements: - ResourceRequirement: - coresMin: $(inputs.special_file.size) - coresMax: $(inputs.special_file.size) - -inputs: - special_file: File - -outputs: - output: - type: stdout - -baseCommand: echo - -stdout: cores.txt - -arguments: [ $(runtime.cores) ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-file-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-file-tool.cwl deleted file mode 100644 index e904749b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-file-tool.cwl +++ /dev/null @@ -1,13 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -baseCommand: [echo] -inputs: - in: - type: string - inputBinding: - position: 1 - name: string? -stdout: out.txt -outputs: - out: - type: stdout diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-position-expr.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-position-expr.cwl deleted file mode 100644 index 55d64ade..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-position-expr.cwl +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 -requirements: - InlineJavascriptRequirement: {} -inputs: - one: - type: int - inputBinding: - position: $(self) - two: - type: int - inputBinding: - valueFrom: sensation! - position: ${return self+1;} -arguments: - - position: ${return 2;} - valueFrom: singular - - position: ${return null;} - valueFrom: 🕺 -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -baseCommand: echo -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-tool-default.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-tool-default.cwl deleted file mode 100644 index 9ddc12a8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-tool-default.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 -inputs: - in: - type: string - default: tool_default - inputBinding: - position: 1 -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -baseCommand: [echo, -n] -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-tool-packed.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-tool-packed.cwl deleted file mode 100644 index 084b22f8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-tool-packed.cwl +++ /dev/null @@ -1,31 +0,0 @@ -cwlVersion: v1.1 -$graph: - - class: CommandLineTool - id: first - inputs: - in: - type: Any - outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) - baseCommand: [ echo, first ] - stdout: out.txt - - class: CommandLineTool - id: main - inputs: - in: - type: Any - inputBinding: {} - outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) - baseCommand: echo - stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-tool-packed2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-tool-packed2.cwl deleted file mode 100644 index fad63db7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-tool-packed2.cwl +++ /dev/null @@ -1,31 +0,0 @@ -cwlVersion: v1.1 -$graph: - - class: CommandLineTool - id: first - inputs: - in: - type: Any - outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) - baseCommand: [ echo, first ] - stdout: out.txt - - class: CommandLineTool - id: '#main' - inputs: - in: - type: Any - inputBinding: {} - outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) - baseCommand: echo - stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-tool.cwl deleted file mode 100644 index d5d5ddb6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 -inputs: - in: - type: Any - inputBinding: {} -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -baseCommand: echo -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-wf-default.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-wf-default.cwl deleted file mode 100644 index e7ce035f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_echo-wf-default.cwl +++ /dev/null @@ -1,19 +0,0 @@ - -class: Workflow -cwlVersion: v1.1 - -inputs: [] - -steps: - step1: - run: echo-tool-default.cwl - in: - in: - default: workflow_default - out: [out] - -outputs: - default_output: - type: string - outputSource: step1/out - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_empty-array-input.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_empty-array-input.cwl deleted file mode 100644 index c0bbde8b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_empty-array-input.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 -class: CommandLineTool - -hints: - - class: DockerRequirement - dockerPull: python:2-slim - -inputs: - - id: array - type: { type: array, items: int } - inputBinding: - position: 1 - prefix: -I - itemSeparator: "," - - - id: args.py - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - -outputs: - - id: args - type: - type: array - items: string - -baseCommand: python diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-tool1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-tool1.cwl deleted file mode 100644 index 5850fa57..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-tool1.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: - in: string -outputs: - out: - type: File - outputBinding: - glob: out - -requirements: - EnvVarRequirement: - envDef: - TEST_ENV: $(inputs.in) - -baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"] - -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-tool2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-tool2.cwl deleted file mode 100644 index 4281374e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-tool2.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: - in: string -outputs: - out: - type: File - outputBinding: - glob: out - -hints: - EnvVarRequirement: - envDef: - TEST_ENV: $(inputs.in) - -baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"] - -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-tool3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-tool3.cwl deleted file mode 100644 index 3f0d3173..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-tool3.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: - in: string -outputs: - out: - type: File - outputBinding: - glob: out - -baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"] - -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-tool4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-tool4.cwl deleted file mode 100644 index 671de445..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-tool4.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: - in: string -outputs: - out: - type: File - outputBinding: - glob: out - -requirements: - EnvVarRequirement: - envDef: - TEST_ENV: conflict_original - -baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"] - -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-wf1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-wf1.cwl deleted file mode 100644 index 27f5d3e3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-wf1.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - in: string - -outputs: - out: - type: File - outputSource: step1/out - -requirements: - EnvVarRequirement: - envDef: - TEST_ENV: override - -steps: - step1: - run: env-tool1.cwl - in: - in: in - out: [out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-wf2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-wf2.cwl deleted file mode 100644 index 3c13bf8e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-wf2.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - in: string - -outputs: - out: - type: File - outputSource: step1/out - -requirements: - EnvVarRequirement: - envDef: - TEST_ENV: override - -steps: - step1: - run: env-tool2.cwl - in: - in: in - out: [out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-wf3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-wf3.cwl deleted file mode 100644 index 7085bd2d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_env-wf3.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - in: string - -outputs: - out: - type: File - outputSource: step1/out - -steps: - step1: - run: env-tool2.cwl - requirements: - EnvVarRequirement: - envDef: - TEST_ENV: override - in: - in: in - out: [out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_envvar.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_envvar.cwl deleted file mode 100644 index 61d30e71..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_envvar.cwl +++ /dev/null @@ -1,11 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: [] -outputs: [] -requirements: - ShellCommandRequirement: {} -arguments: [ - echo, {valueFrom: '"HOME=$HOME"', shellQuote: false}, {valueFrom: '"TMPDIR=$TMPDIR"', shellQuote: false}, - {valueFrom: '&&', shellQuote: false}, - test, {valueFrom: '"$HOME"', shellQuote: false}, "=", $(runtime.outdir), - "-a", {valueFrom: '"$TMPDIR"', shellQuote: false}, "=", $(runtime.tmpdir)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_envvar2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_envvar2.cwl deleted file mode 100644 index a0229d38..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_envvar2.cwl +++ /dev/null @@ -1,14 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: [] -outputs: [] -requirements: - ShellCommandRequirement: {} -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -arguments: [ - echo, {valueFrom: '"HOME=$HOME"', shellQuote: false}, {valueFrom: '"TMPDIR=$TMPDIR"', shellQuote: false}, - {valueFrom: '&&', shellQuote: false}, - test, {valueFrom: '"$HOME"', shellQuote: false}, "=", $(runtime.outdir), - "-a", {valueFrom: '"$TMPDIR"', shellQuote: false}, "=", $(runtime.tmpdir)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_envvar3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_envvar3.cwl deleted file mode 100644 index 287ea350..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_envvar3.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -inputs: [] -outputs: - results: - type: File - outputBinding: { glob: results } -requirements: - ShellCommandRequirement: {} -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -arguments: - - shellQuote: false - valueFrom: | - echo HOME=$HOME TMPDIR=$TMPDIR > log - if [ "$HOME" = "$(runtime.outdir)" ] && [ "$TMPDIR" = "$(runtime.tmpdir)" ] - then - echo success > results - else - echo failure > results - fi diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_exit-success.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_exit-success.cwl deleted file mode 100644 index fdaab1ee..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_exit-success.cwl +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: CommandLineTool - -inputs: [] -baseCommand: "false" -outputs: [] - -successCodes: [ 1 ] -permanentFailCodes: [ 0 ] -temporaryFailCodes: [ 42 ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_exitcode.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_exitcode.cwl deleted file mode 100644 index 12f4bb21..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_exitcode.cwl +++ /dev/null @@ -1,12 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -requirements: - ShellCommandRequirement: {} -inputs: [] -outputs: - code: - type: int - outputBinding: - outputEval: $(runtime.exitCode) -successCodes: [7] -arguments: ["exit", "7"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_fail-unconnected.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_fail-unconnected.cwl deleted file mode 100644 index 456761dd..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_fail-unconnected.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: Workflow -cwlVersion: v1.1 -inputs: - inp1: - type: string - default: hello inp1 - inp2: - type: string - default: hello inp2 -outputs: - out: - type: string - outputSource: step1/out -steps: - step1: - in: - in: inp1 - in2: inp2 - out: [out] - run: fail-unspecified-input.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_fail-unspecified-input.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_fail-unspecified-input.cwl deleted file mode 100644 index 9b5d8f82..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_fail-unspecified-input.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: - in: string -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -stdout: out.txt -arguments: [echo, $(inputs.in), $(inputs.in2)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_file-literal-ex.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_file-literal-ex.cwl deleted file mode 100644 index 03dc92d3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_file-literal-ex.cwl +++ /dev/null @@ -1,11 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.1 -requirements: - InlineJavascriptRequirement: {} -inputs: [] -outputs: - lit: File -expression: | - ${ - return {"lit": {"class": "File", "basename": "a_file", "contents": "Hello file literal."}}; - } \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_formattest.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_formattest.cwl deleted file mode 100644 index 35c696ee..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_formattest.cwl +++ /dev/null @@ -1,20 +0,0 @@ -$namespaces: - edam: "http://edamontology.org/" -cwlVersion: v1.1 -class: CommandLineTool -doc: "Reverse each line using the `rev` command" -inputs: - input: - type: File - inputBinding: {} - format: edam:format_2330 - -outputs: - output: - type: File - outputBinding: - glob: output.txt - format: edam:format_2330 - -baseCommand: rev -stdout: output.txt \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_formattest2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_formattest2.cwl deleted file mode 100644 index 9d424d60..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_formattest2.cwl +++ /dev/null @@ -1,26 +0,0 @@ -$namespaces: - edam: http://edamontology.org/ -$schemas: - - EDAM.owl -class: CommandLineTool -cwlVersion: v1.1 -doc: "Reverse each line using the `rev` command" -hints: - DockerRequirement: - dockerPull: "debian:stretch-slim" - -inputs: - input: - type: File - inputBinding: {} - format: edam:format_2330 - -outputs: - output: - type: File - outputBinding: - glob: output.txt - format: $(inputs.input.format) - -baseCommand: rev -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_formattest3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_formattest3.cwl deleted file mode 100644 index 72d5b475..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_formattest3.cwl +++ /dev/null @@ -1,28 +0,0 @@ -$namespaces: - edam: http://edamontology.org/ - gx: http://galaxyproject.org/formats/ -$schemas: - - EDAM.owl - - gx_edam.ttl -class: CommandLineTool -cwlVersion: v1.1 -doc: "Reverse each line using the `rev` command" -hints: - DockerRequirement: - dockerPull: "debian:stretch-slim" - -inputs: - input: - type: File - inputBinding: {} - format: gx:fasta - -outputs: - output: - type: File - outputBinding: - glob: output.txt - format: $(inputs.input.format) - -baseCommand: rev -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_glob-expr-list.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_glob-expr-list.cwl deleted file mode 100644 index 9b8d7901..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_glob-expr-list.cwl +++ /dev/null @@ -1,16 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 - -inputs: - ids: - type: string[] - inputBinding: - position: 1 - -outputs: - files: - type: File[] - outputBinding: - glob: $(inputs.ids) - -baseCommand: touch diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_glob-path-error.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_glob-path-error.cwl deleted file mode 100644 index 9881b25f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_glob-path-error.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 - -requirements: - - class: DockerRequirement - dockerPull: debian:stretch-slim - -class: CommandLineTool - -inputs: [] - -outputs: - - id: OUTPUT - type: File - outputBinding: - glob: /etc/passwd - -baseCommand: [echo] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_glob_directory.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_glob_directory.cwl deleted file mode 100644 index 5ac0de66..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_glob_directory.cwl +++ /dev/null @@ -1,10 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: CommandLineTool - -inputs: [] -baseCommand: [mkdir, a_dir, b_dir, c_dir] -outputs: - directories: - type: Directory[] - outputBinding: { glob: '[a,b,c]_dir' } diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_glob_test.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_glob_test.cwl deleted file mode 100644 index 414fe5c6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_glob_test.cwl +++ /dev/null @@ -1,10 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: CommandLineTool - -inputs: [] -baseCommand: [touch, z, y, x, w, c, b, a] -outputs: - letters: - type: File[] - outputBinding: { glob: '*' } diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_import_schema-def.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_import_schema-def.cwl deleted file mode 100644 index c74d6bb6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_import_schema-def.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 - -class: Workflow - -requirements: - SchemaDefRequirement: - types: - - $import: capture_kit.yml - -inputs: - bam: string - capture_kit: capture_kit.yml#capture_kit - -outputs: - output_bam: - type: File - outputSource: touch_bam/empty_file - -steps: - touch_bam: - run: touch.cwl - in: - name: bam - out: [ empty_file ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_import_schema-def_packed.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_import_schema-def_packed.cwl deleted file mode 100644 index 1fd4cca4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_import_schema-def_packed.cwl +++ /dev/null @@ -1,89 +0,0 @@ -{ - "cwlVersion": "v1.1", - "$graph": [ - { - "inputs": [ - { - "type": "string", - "id": "#main/bam" - }, - { - "type": "#capture_kit.yml/capture_kit", - "id": "#main/capture_kit" - } - ], - "requirements": [ - { - "class": "SchemaDefRequirement", - "types": [ - { - "fields": [ - { - "type": "string", - "name": "#capture_kit.yml/capture_kit/bait" - } - ], - "type": "record", - "name": "#capture_kit.yml/capture_kit" - } - ] - } - ], - "outputs": [ - { - "outputSource": "#main/touch_bam/empty_file", - "type": "File", - "id": "#main/output_bam" - } - ], - "class": "Workflow", - "steps": [ - { - "out": [ - "#main/touch_bam/empty_file" - ], - "run": "#touch.cwl", - "id": "#main/touch_bam", - "in": [ - { - "source": "#main/bam", - "id": "#main/touch_bam/name" - } - ] - } - ], - "id": "#main" - }, - { - "inputs": [ - { - "inputBinding": { - "position": 0 - }, - "type": "string", - "id": "#touch.cwl/name" - } - ], - "outputs": [ - { - "outputBinding": { - "glob": "$(inputs.name)" - }, - "type": "File", - "id": "#touch.cwl/empty_file" - } - ], - "baseCommand": [ - "touch" - ], - "class": "CommandLineTool", - "id": "#touch.cwl", - "hints": [ - { - "dockerPull": "debian:stretch-slim", - "class": "DockerRequirement" - } - ] - } - ] -} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_imported-hint.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_imported-hint.cwl deleted file mode 100755 index 06b50252..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_imported-hint.cwl +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: CommandLineTool -inputs: [] -outputs: - out: stdout - -hints: -- $import: envvar.yml - -baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"] - -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_initialwork-path.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_initialwork-path.cwl deleted file mode 100644 index d8b3c524..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_initialwork-path.cwl +++ /dev/null @@ -1,15 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.file1) - entryname: bob.txt - ShellCommandRequirement: {} -inputs: - file1: File -outputs: [] -arguments: - - shellQuote: false - valueFrom: | - test "$(inputs.file1.path)" = "$(runtime.outdir)/bob.txt" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_initialworkdir-glob-fullpath.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_initialworkdir-glob-fullpath.cwl deleted file mode 100644 index e76fa3b8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_initialworkdir-glob-fullpath.cwl +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 - -requirements: - - class: InitialWorkDirRequirement - listing: - - $(inputs.INPUT) - -class: CommandLineTool - -inputs: - - id: INPUT - type: File - -outputs: - - id: OUTPUT - type: File - outputBinding: - glob: $(runtime.outdir)/$(inputs.INPUT.basename) - secondaryFiles: - - .fai - -arguments: - - valueFrom: $(inputs.INPUT.basename).fai - position: 0 - -baseCommand: [touch] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_initialworkdirrequirement-docker-out.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_initialworkdirrequirement-docker-out.cwl deleted file mode 100644 index 69c53e65..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_initialworkdirrequirement-docker-out.cwl +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 - -requirements: - - class: DockerRequirement - dockerPull: debian:stretch-slim - - class: InitialWorkDirRequirement - listing: - - $(inputs.INPUT) - -class: CommandLineTool - -inputs: - - id: INPUT - type: File - -outputs: - - id: OUTPUT - type: File - outputBinding: - glob: $(inputs.INPUT.basename) - secondaryFiles: - - .fai - -arguments: - - valueFrom: $(inputs.INPUT.basename).fai - position: 0 - -baseCommand: [touch] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_inline-js.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_inline-js.cwl deleted file mode 100755 index 6e19b3cb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_inline-js.cwl +++ /dev/null @@ -1,45 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool - -requirements: - - class: InlineJavascriptRequirement -hints: - - class: DockerRequirement - dockerPull: python:2-slim - -inputs: - - id: args.py - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - -outputs: - - id: args - type: - type: array - items: string - -baseCommand: python - -arguments: - - prefix: -A - valueFrom: $(1+1) - - prefix: -B - valueFrom: $("/foo/bar/baz".split('/').slice(-1)[0]) - - prefix: -C - valueFrom: | - ${ - var r = []; - for (var i = 10; i >= 1; i--) { - r.push(i); - } - return r; - } - # Test errors similar to https://github.com/common-workflow-language/cwltool/issues/648 are fixed - - prefix: -D - valueFrom: $(true) - - prefix: -E - valueFrom: $(false) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_inp_update_wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_inp_update_wf.cwl deleted file mode 100644 index a7d18bc6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_inp_update_wf.cwl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -inputs: [] -outputs: - a: - type: int - outputSource: step3/output - b: - type: int - outputSource: step4/output -steps: - step1: - in: - in: {default: "3"} - out: [out] - run: echo-file-tool.cwl - step2: - in: - r: step1/out - out: [out] - run: updateval_inplace.cwl - step3: - in: - file1: step1/out - wait: step2/out - out: [output] - run: parseInt-tool.cwl - step4: - in: - file1: step2/out - out: [output] - run: parseInt-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_inpdir_update_wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_inpdir_update_wf.cwl deleted file mode 100644 index 4d6fee43..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_inpdir_update_wf.cwl +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -inputs: [] -requirements: - InlineJavascriptRequirement: {} -outputs: - a: - type: File[] - outputSource: step3/d1out - b: - type: File[] - outputSource: step3/d2out -steps: - step1: - in: - dirname: {default: step1dir} - out: [out] - run: mkdir.cwl - step2: - in: - r: step1/out - out: [out] - run: updatedir_inplace.cwl - step3: - in: - d1: step1/out - d2: step2/out - out: [d1out, d2out] - run: - class: ExpressionTool - inputs: - d1: - type: Directory - loadListing: shallow_listing - d2: - type: Directory - loadListing: shallow_listing - outputs: - d1out: File[] - d2out: File[] - expression: "$({d1out: inputs.d1.listing, d2out: inputs.d2.listing})" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-any-1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-any-1.cwl deleted file mode 100644 index 1a21f0aa..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-any-1.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -requirements: - - class: InlineJavascriptRequirement - -inputs: - - id: bar - type: Any - -outputs: - - id: t1 - type: Any - outputBinding: - outputEval: $(inputs.bar.class || inputs.bar) - -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-any-wf-1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-any-wf-1.cwl deleted file mode 100644 index a7081a90..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-any-wf-1.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - bar: - type: Any - -outputs: - t1: - type: Any - outputSource: step1/t1 - -steps: - step1: - in: - bar: bar - out: [t1] - run: io-any-1.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-file-default-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-file-default-wf.cwl deleted file mode 100644 index 5182b0cd..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-file-default-wf.cwl +++ /dev/null @@ -1,34 +0,0 @@ -cwlVersion: v1.1 -class: Workflow - -inputs: - file1: - type: File - default: - class: File - path: whale.txt - -outputs: - o: - type: File - outputSource: step1/o - -steps: - step1: - in: - catfile1: file1 - out: [o] - run: - class: CommandLineTool - - inputs: - catfile1: - type: File - - outputs: - o: - type: File - outputBinding: { glob: output } - - arguments: [cat, $(inputs.catfile1.path)] - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-file-or-files.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-file-or-files.cwl deleted file mode 100644 index 082c875f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-file-or-files.cwl +++ /dev/null @@ -1,43 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 - -requirements: - - class: InlineJavascriptRequirement - -class: CommandLineTool - -inputs: - - id: input - type: - - "null" - - File - - type: array - items: File - -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} - -arguments: - - valueFrom: | - ${ - var cmd = []; - if (inputs.input === null) { - cmd.push('echo'); - cmd.push('no_inputs'); - } else { - cmd.push('cat'); - if (Array.isArray(inputs.input)) { - for (var i = 0; i < inputs.input.length; i++) { - cmd.push(inputs.input[i].path); - } - } else { - cmd.push(inputs.input.path); - } - } - return cmd; - } -baseCommand: [] -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-int-default-tool-and-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-int-default-tool-and-wf.cwl deleted file mode 100644 index 280bb1f3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-int-default-tool-and-wf.cwl +++ /dev/null @@ -1,49 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - i: - type: int - default: 4 - -outputs: - o: - type: int - outputSource: step2/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int - outputs: - o: - type: int - expression: > - ${return {'o': (inputs.i || 2)};} - step2: - in: - i: step1/o - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int - i2: - type: int - default: 5 - outputs: - o: - type: int - expression: > - ${return {'o': inputs.i * 2 + inputs.i2};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-int-default-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-int-default-wf.cwl deleted file mode 100644 index 591e2840..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-int-default-wf.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - i: - type: int - default: 4 - -outputs: - o: - type: int - outputSource: step1/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int - outputs: - o: - type: int - expression: > - ${return {'o': (inputs.i || 2) * 2};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-int-optional-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-int-optional-wf.cwl deleted file mode 100644 index 53492471..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-int-optional-wf.cwl +++ /dev/null @@ -1,31 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - i: - type: int? - -outputs: - o: - type: int - outputSource: step1/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int? - outputs: - o: - type: int - expression: > - ${return {'o': (inputs.i || 2) * 2};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-int-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-int-wf.cwl deleted file mode 100644 index 49b10a88..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-int-wf.cwl +++ /dev/null @@ -1,31 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - i: - type: int - -outputs: - o: - type: int - outputSource: step1/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int - outputs: - o: - type: int - expression: > - ${return {'o': inputs.i * 2};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-union-input-default-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-union-input-default-wf.cwl deleted file mode 100644 index 79781059..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_io-union-input-default-wf.cwl +++ /dev/null @@ -1,38 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - bar: - type: - - File - - 'null' - - string - default: the default value - -outputs: - o: - type: string - outputSource: step1/o - -steps: - step1: - in: - i: bar - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: - - File - - 'null' - - string - outputs: - o: - type: string - expression: > - ${return {'o': (inputs.i.class || inputs.i)};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_iwdr-entry.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_iwdr-entry.cwl deleted file mode 100644 index b32b153f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_iwdr-entry.cwl +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 -baseCommand: ["cat", "example.conf"] - -requirements: - InitialWorkDirRequirement: - listing: - - entryname: example.conf - entry: | - CONFIGVAR=$(inputs.message) - -inputs: - message: string -outputs: - out: - type: File - outputBinding: - glob: example.conf diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_iwdr_with_nested_dirs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_iwdr_with_nested_dirs.cwl deleted file mode 100644 index 241fdf1f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_iwdr_with_nested_dirs.cwl +++ /dev/null @@ -1,41 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: Workflow - -inputs: [] -outputs: - ya_empty: - type: File - outputSource: second/ya - -steps: - first: - run: - class: CommandLineTool - baseCommand: [ mkdir, -p, deeply/nested/dir/structure ] - inputs: [] - outputs: - deep_dir: - type: Directory - outputBinding: { glob: deeply } - in: {} - out: [ deep_dir ] - - second: - run: - class: CommandLineTool - baseCommand: [ touch, deeply/nested/dir/structure/ya ] - requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.dir) - writable: true - inputs: - dir: Directory - outputs: - ya: - type: File - outputBinding: { glob: deeply/nested/dir/structure/ya } - - in: { dir: first/deep_dir } - out: [ ya ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_js-expr-req-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_js-expr-req-wf.cwl deleted file mode 100644 index 578d34ac..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_js-expr-req-wf.cwl +++ /dev/null @@ -1,30 +0,0 @@ -cwlVersion: v1.1 -$graph: - - id: tool - class: CommandLineTool - requirements: - InlineJavascriptRequirement: - expressionLib: - - "function foo() { return 2; }" - inputs: [] - outputs: - out: stdout - arguments: [echo, $(foo())] - stdout: whatever.txt - - - id: wf - class: Workflow - requirements: - InlineJavascriptRequirement: - expressionLib: - - "function bar() { return 1; }" - inputs: [] - outputs: - out: - type: File - outputSource: tool/out - steps: - tool: - run: "#tool" - in: {} - out: [out] \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_linkfile.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_linkfile.cwl deleted file mode 100644 index d86447a4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_linkfile.cwl +++ /dev/null @@ -1,22 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool - -requirements: - InitialWorkDirRequirement: - listing: - - $(inputs.src) - -inputs: - src: - type: File - inputBinding: - position: 1 - valueFrom: $(self.nameroot).class - -baseCommand: touch - -outputs: - classfile: - type: File - outputBinding: - glob: "*.class" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_deep1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_deep1.cwl deleted file mode 100755 index 09af9320..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_deep1.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -requirements: - LoadListingRequirement: - loadListing: deep_listing - InlineJavascriptRequirement: {} -inputs: - d: Directory -outputs: - out: - type: boolean - outputBinding: - outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing.length === 1)' -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_deep2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_deep2.cwl deleted file mode 100755 index 0559bb8c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_deep2.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -requirements: - InlineJavascriptRequirement: {} -inputs: - d: - type: Directory - loadListing: deep_listing -outputs: - out: - type: boolean - outputBinding: - outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing.length === 1)' -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_none1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_none1.cwl deleted file mode 100755 index 58b13ffb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_none1.cwl +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -requirements: - InlineJavascriptRequirement: {} -inputs: - d: Directory -outputs: - out: - type: boolean - outputBinding: - outputEval: $(inputs.d.listing === undefined) -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_none2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_none2.cwl deleted file mode 100755 index 10ff864b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_none2.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -requirements: - LoadListingRequirement: - loadListing: no_listing - InlineJavascriptRequirement: {} -inputs: - d: Directory -outputs: - out: - type: boolean - outputBinding: - outputEval: $(inputs.d.listing === undefined) -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_none3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_none3.cwl deleted file mode 100755 index 30da2a05..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_none3.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -requirements: - InlineJavascriptRequirement: {} -inputs: - d: - type: Directory - loadListing: no_listing -outputs: - out: - type: boolean - outputBinding: - outputEval: $(inputs.d.listing === undefined) -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_shallow1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_shallow1.cwl deleted file mode 100755 index 9489e2c1..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_shallow1.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -requirements: - LoadListingRequirement: - loadListing: shallow_listing - InlineJavascriptRequirement: {} -inputs: - d: Directory -outputs: - out: - type: boolean - outputBinding: - outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing === undefined)' -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_shallow2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_shallow2.cwl deleted file mode 100755 index 7e808bf3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_listing_shallow2.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -requirements: - InlineJavascriptRequirement: {} -inputs: - d: - type: Directory - loadListing: shallow_listing -outputs: - out: - type: boolean - outputBinding: - outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing === undefined)' -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_metadata.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_metadata.cwl deleted file mode 100644 index 843e1a3d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_metadata.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner -$namespaces: - dct: http://purl.org/dc/terms/ - foaf: http://xmlns.com/foaf/0.1/ -$schemas: - - foaf.rdf - - dcterms.rdf - -cwlVersion: v1.1 -class: CommandLineTool -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." - -dct:creator: - id: "http://orcid.org/0000-0003-3566-7705" - class: foaf:Person - foaf:name: Peter Amstutz - foaf:mbox: "mailto:peter.amstutz@curoverse.com" - -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - inputBinding: {position: 1} - numbering: - type: boolean? - inputBinding: - position: 0 - prefix: -n -outputs: [] -baseCommand: cat diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_mkdir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_mkdir.cwl deleted file mode 100644 index a6dc4b9e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_mkdir.cwl +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -inputs: - dirname: string -outputs: - out: - type: Directory - outputBinding: - glob: $(inputs.dirname) -arguments: [mkdir, $(inputs.dirname)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_nameroot.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_nameroot.cwl deleted file mode 100644 index 5cd6deae..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_nameroot.cwl +++ /dev/null @@ -1,9 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -inputs: - file1: File -outputs: - b: stdout -stdout: $(inputs.file1.nameroot).xtx -baseCommand: [] -arguments: [echo, $(inputs.file1.basename), $(inputs.file1.nameroot), $(inputs.file1.nameext)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_nested-array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_nested-array.cwl deleted file mode 100644 index 7ea576ca..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_nested-array.cwl +++ /dev/null @@ -1,15 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -baseCommand: echo -inputs: - letters: - type: - type: array - items: - type: array - items: string - inputBinding: - position: 1 -stdout: echo.txt -outputs: - echo: stdout \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_networkaccess.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_networkaccess.cwl deleted file mode 100644 index 6d3a219f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_networkaccess.cwl +++ /dev/null @@ -1,15 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - DockerRequirement: - dockerPull: python:3 - NetworkAccess: - networkAccess: true -inputs: [] -outputs: [] -baseCommand: python -arguments: - - "-c" - - valueFrom: | - import urllib.request - assert(urllib.request.urlopen("http://commonwl.org").code == 200) \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_networkaccess2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_networkaccess2.cwl deleted file mode 100644 index 077d0b49..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_networkaccess2.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - DockerRequirement: - dockerPull: python:3 -inputs: [] -outputs: [] -baseCommand: python -arguments: - - "-c" - - valueFrom: | - import urllib.request - assert(urllib.request.urlopen("http://commonwl.org").code == 200) \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_no-inputs-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_no-inputs-tool.cwl deleted file mode 100644 index 36e4fdfe..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_no-inputs-tool.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "CommandLineTool without inputs." -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: [] -outputs: - output: - type: File - outputBinding: { glob: output } -baseCommand: [echo, cwl] -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_no-inputs-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_no-inputs-wf.cwl deleted file mode 100644 index 3cb0568f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_no-inputs-wf.cwl +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -doc: "Workflow without inputs." -inputs: [] -outputs: - output: - type: File - outputSource: step0/output -steps: - step0: - in: [] - out: [output] - run: - class: CommandLineTool - cwlVersion: v1.1 - doc: "CommandLineTool without inputs." - hints: - DockerRequirement: - dockerPull: debian:stretch-slim - inputs: [] - outputs: - output: - type: File - outputBinding: { glob: output } - baseCommand: [echo, cwl] - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_no-outputs-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_no-outputs-tool.cwl deleted file mode 100644 index 3be04ed1..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_no-outputs-tool.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "CommandLineTool without outputs." -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - label: Input File - inputBinding: {position: 1} -outputs: [] -baseCommand: echo diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_no-outputs-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_no-outputs-wf.cwl deleted file mode 100644 index ff91d9f8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_no-outputs-wf.cwl +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -doc: "Workflow without outputs." -inputs: - file1: File -outputs: [] -steps: - step0: - in: {file1: file1} - out: [] - run: - class: CommandLineTool - cwlVersion: v1.1 - doc: "CommandLineTool without outputs." - hints: - DockerRequirement: - dockerPull: debian:stretch-slim - inputs: - file1: - type: File - label: Input File - inputBinding: {position: 1} - outputs: [] - baseCommand: echo \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_null-defined.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_null-defined.cwl deleted file mode 100644 index 3cd2e6ef..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_null-defined.cwl +++ /dev/null @@ -1,15 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -requirements: - InlineJavascriptRequirement: {} -inputs: - file1: File? -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -stdout: out.txt -arguments: [echo, '$(inputs.file1 === null ? "t" : "f")'] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_null-expression1-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_null-expression1-tool.cwl deleted file mode 100644 index e179a0d5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_null-expression1-tool.cwl +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: ExpressionTool -requirements: - - class: InlineJavascriptRequirement -cwlVersion: v1.1 - -inputs: - i1: - type: Any - default: "the-default" - -outputs: - output: int - -expression: "$({'output': (inputs.i1 == 'the-default' ? 1 : 2)})" \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_null-expression2-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_null-expression2-tool.cwl deleted file mode 100644 index 7f574907..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_null-expression2-tool.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: ExpressionTool -requirements: - - class: InlineJavascriptRequirement -cwlVersion: v1.1 - -inputs: - i1: Any - -outputs: - output: int - -expression: "$({'output': (inputs.i1 == 'the-default' ? 1 : 2)})" \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_null-expression3-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_null-expression3-tool.cwl deleted file mode 100644 index 0f11e82d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_null-expression3-tool.cwl +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: ExpressionTool -requirements: { InlineJavascriptRequirement: {} } -cwlVersion: v1.1 - -inputs: [] - -outputs: - output: Any - -expression: "$({'output': null })" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_optional-numerical-output-0.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_optional-numerical-output-0.cwl deleted file mode 100644 index d74c1e7e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_optional-numerical-output-0.cwl +++ /dev/null @@ -1,16 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -baseCommand: - - echo - - "0" -stdout: a.txt -requirements: -- class: InlineJavascriptRequirement -inputs: [] -outputs: - out: - type: float? - outputBinding: - glob: "a.txt" - loadContents: true - outputEval: "${\n return parseFloat(self[0].contents);\n}" \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_optional-output.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_optional-output.cwl deleted file mode 100644 index f676c858..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_optional-output.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: "v1.1" -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - label: Input File - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: File - outputBinding: - glob: output.txt - secondaryFiles: - - .idx - optional_file: - type: File? - outputBinding: - glob: bumble.txt -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_output-arrays-file-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_output-arrays-file-wf.cwl deleted file mode 100644 index 927e1eb0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_output-arrays-file-wf.cwl +++ /dev/null @@ -1,53 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - i: File - -outputs: - o: - type: File[] - outputSource: step2/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: File - inputBinding: { loadContents: true } - - outputs: - o: - type: string[] - expression: > - ${return {'o': inputs.i.contents.split(" ")};} - step2: - in: - i: - source: step1/o - out: [o] - run: - class: CommandLineTool - - inputs: - i: - type: string[] - inputBinding: - position: 1 - - outputs: - o: - type: File[] - outputBinding: - glob: $(inputs.i) - - baseCommand: touch diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_output-arrays-int-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_output-arrays-int-wf.cwl deleted file mode 100644 index 682e66e8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_output-arrays-int-wf.cwl +++ /dev/null @@ -1,60 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -requirements: - InlineJavascriptRequirement: {} - -inputs: - i: int - -outputs: - o: - type: int - outputSource: step3/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int - outputs: - o: - type: int[] - expression: > - ${return {'o': Array.apply(null, {length: inputs.i}).map(Number.call, Number)};} - step2: - in: - i: - source: step1/o - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int[] - outputs: - o: - type: int[] - expression: > - ${return {'o': inputs.i.map(function(x) { return (x + 1) * 2; })};} - step3: - in: - i: - source: step2/o - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int[] - outputs: - o: - type: int - expression: > - ${return {'o': inputs.i.reduce(function(a, b) { return a + b; })};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_output-arrays-int.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_output-arrays-int.cwl deleted file mode 100644 index 884f982f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_output-arrays-int.cwl +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 -class: ExpressionTool - -requirements: - InlineJavascriptRequirement: {} - -inputs: - i: - type: int - -outputs: - o: - type: int[] - -expression: > - ${return {'o': Array.apply(null, {length: inputs.i}).map(Number.call, Number)};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_params.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_params.cwl deleted file mode 100644 index 8a3fac9a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_params.cwl +++ /dev/null @@ -1,16 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: - bar: - type: Any - default: { - "baz": "zab1", - "b az": 2, - "b'az": true, - 'b"az': null, - "buz": ['a', 'b', 'c'] - } - -outputs: {"$import": params_inc.yml} - -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_params2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_params2.cwl deleted file mode 100644 index ac50a805..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_params2.cwl +++ /dev/null @@ -1,19 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - - class: InlineJavascriptRequirement # needed by params_inc.yml - -inputs: - bar: - type: Any - default: { - "baz": "zab1", - "b az": 2, - "b'az": true, - 'b"az': null, - "buz": ['a', 'b', 'c'] - } - -outputs: {"$import": params_inc.yml} - -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_parseInt-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_parseInt-tool.cwl deleted file mode 100755 index b199821c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_parseInt-tool.cwl +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: ExpressionTool -requirements: - - class: InlineJavascriptRequirement -cwlVersion: v1.1 - -inputs: - file1: - type: File - inputBinding: { loadContents: true } - -outputs: - output: int - -expression: "$({'output': parseInt(inputs.file1.contents)})" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_pass-unconnected.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_pass-unconnected.cwl deleted file mode 100644 index 9e407f6e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_pass-unconnected.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: Workflow -cwlVersion: v1.1 -inputs: - inp1: - type: string - default: hello inp1 - inp2: - type: string - default: hello inp2 -outputs: - out: - type: string - outputSource: step1/out -steps: - step1: - in: - in: inp1 - in2: inp2 - out: [out] - run: echo-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-in-format.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-in-format.cwl deleted file mode 100644 index 2863acbd..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-in-format.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: - regular_input: - type: File - format: http://example.com/format1 - record_input: - type: - type: record - fields: - f1: - type: File - format: http://example.com/format1 - f2: - type: - type: array - items: File - format: http://example.com/format2 -outputs: [] -arguments: ['true'] \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-in-secondaryFiles-missing-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-in-secondaryFiles-missing-wf.cwl deleted file mode 100644 index ed28c989..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-in-secondaryFiles-missing-wf.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: Workflow -cwlVersion: v1.1 -inputs: - record_input: - type: - type: record - fields: - f1: - type: File - f2: - type: - type: array - items: File -outputs: [] -steps: - step1: - in: - record_input: record_input - out: [] - run: record-in-secondaryFiles.cwl \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-in-secondaryFiles-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-in-secondaryFiles-wf.cwl deleted file mode 100644 index 16ceafd8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-in-secondaryFiles-wf.cwl +++ /dev/null @@ -1,22 +0,0 @@ -class: Workflow -cwlVersion: v1.1 -inputs: - record_input: - type: - type: record - fields: - f1: - type: File - secondaryFiles: .s2 - f2: - type: - type: array - items: File - secondaryFiles: .s3 -outputs: [] -steps: - step1: - in: - record_input: record_input - out: [] - run: record-in-secondaryFiles.cwl \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-in-secondaryFiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-in-secondaryFiles.cwl deleted file mode 100644 index f52010b3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-in-secondaryFiles.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: - record_input: - type: - type: record - fields: - f1: - type: File - secondaryFiles: .s2 - f2: - type: - type: array - items: File - secondaryFiles: .s3 -outputs: [] -baseCommand: test -arguments: [-f, $(inputs.record_input.f1.path).s2, - '-a', '-f', '$(inputs.record_input.f2[0].path).s3', - '-a', '-f', '$(inputs.record_input.f2[1].path).s3'] \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-out-format.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-out-format.cwl deleted file mode 100644 index fe1f7f6a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-out-format.cwl +++ /dev/null @@ -1,25 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: - record_input: - type: - type: record - fields: - f1: File - f2: File[] -outputs: - f1out: - type: File - format: http://example.com/format1 - outputBinding: - outputEval: $(inputs.record_input.f1) - record_output: - type: - type: record - fields: - f2out: - type: File - format: http://example.com/format2 - outputBinding: - outputEval: $(inputs.record_input.f2[0]) -arguments: ['true'] \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-out-secondaryFiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-out-secondaryFiles.cwl deleted file mode 100644 index 6c84cc0d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-out-secondaryFiles.cwl +++ /dev/null @@ -1,23 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: [] -outputs: - record_output: - type: - type: record - fields: - f1: - type: File - secondaryFiles: .s2 - outputBinding: - glob: A - f2: - type: - type: array - items: File - secondaryFiles: .s3 - outputBinding: - glob: [B, C] - -baseCommand: touch -arguments: [A, A.s2, B, B.s3, C, C.s3] \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-output-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-output-wf.cwl deleted file mode 100644 index ebc72186..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-output-wf.cwl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -inputs: - irec: - type: - name: irec - type: record - fields: - - name: ifoo - type: File - - name: ibar - type: File - -outputs: - orec: - type: - name: orec - type: record - fields: - - name: ofoo - type: File - - name: obar - type: File - outputSource: step1/orec - -steps: - step1: - run: record-output.cwl - in: - irec: irec - out: [orec] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-output.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-output.cwl deleted file mode 100644 index e1ab1a8f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-output.cwl +++ /dev/null @@ -1,38 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - - class: ShellCommandRequirement -inputs: - irec: - type: - name: irec - type: record - fields: - - name: ifoo - type: File - inputBinding: - position: 2 - - name: ibar - type: File - inputBinding: - position: 6 -outputs: - orec: - type: - name: orec - type: record - fields: - - name: ofoo - type: File - outputBinding: - glob: foo - - name: obar - type: File - outputBinding: - glob: bar -arguments: - - {valueFrom: "cat", position: 1} - - {valueFrom: "> foo", position: 3, shellQuote: false} - - {valueFrom: "&&", position: 4, shellQuote: false} - - {valueFrom: "cat", position: 5} - - {valueFrom: "> bar", position: 7, shellQuote: false} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-sd-secondaryFiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-sd-secondaryFiles.cwl deleted file mode 100644 index 2568752f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_record-sd-secondaryFiles.cwl +++ /dev/null @@ -1,26 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - SchemaDefRequirement: - types: - - name: RecordTestType - type: record - doc: Type test record - fields: - f1: - type: File - secondaryFiles: .s2 - f2: - type: - type: array - items: File - secondaryFiles: .s3 -inputs: - record_input: - type: RecordTestType - -outputs: [] -baseCommand: test -arguments: [-f, $(inputs.record_input.f1.path).s2, - '-a', '-f', '$(inputs.record_input.f2[0].path).s3', - '-a', '-f', '$(inputs.record_input.f2[1].path).s3'] \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_recursive-input-directory.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_recursive-input-directory.cwl deleted file mode 100644 index 3b99d3f4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_recursive-input-directory.cwl +++ /dev/null @@ -1,33 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.input_dir) - entryname: work_dir - writable: true - ShellCommandRequirement: {} -stdout: output.txt -arguments: - - shellQuote: false - valueFrom: | - touch work_dir/e; - if [ ! -w work_dir ]; then echo work_dir not writable; fi; - if [ -L work_dir ]; then echo work_dir is a symlink; fi; - if [ ! -w work_dir/a ]; then echo work_dir/a not writable; fi; - if [ -L work_dir/a ]; then echo work_dir/a is a symlink; fi; - if [ ! -w work_dir/c ]; then echo work_dir/c not writable; fi; - if [ -L work_dir/c ]; then echo work_dir/c is a symlink; fi; - if [ ! -w work_dir/c/d ]; then echo work_dir/c/d not writable; fi; - if [ -L work_dir/c/d ]; then echo work_dir/c/d is a symlink; fi; - if [ ! -w work_dir/e ]; then echo work_dir/e not writable; fi; - if [ -L work_dir/e ]; then echo work_dir/e is a symlink ; fi; -inputs: - input_dir: Directory -outputs: - output_dir: - type: Directory - outputBinding: - glob: work_dir - test_result: - type: stdout diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_rename.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_rename.cwl deleted file mode 100644 index 88b3a43d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_rename.cwl +++ /dev/null @@ -1,16 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -baseCommand: "true" -requirements: - InitialWorkDirRequirement: - listing: - - entryname: $(inputs.newname) - entry: $(inputs.srcfile) -inputs: - srcfile: File - newname: string -outputs: - outfile: - type: File - outputBinding: - glob: $(inputs.newname) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_revsort-packed.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_revsort-packed.cwl deleted file mode 100644 index 828ec91a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_revsort-packed.cwl +++ /dev/null @@ -1,125 +0,0 @@ -{ - "cwlVersion": "v1.1", - "$graph": [ - { - "class": "Workflow", - "doc": "Reverse the lines in a document, then sort those lines.", - "hints": [ - { - "class": "DockerRequirement", - "dockerPull": "debian:stretch-slim" - } - ], - "inputs": [ - { - "type": "File", - "doc": "The input file to be processed.", - "id": "#main/input" - }, - { - "type": "boolean", - "default": true, - "doc": "If true, reverse (decending) sort", - "id": "#main/reverse_sort" - } - ], - "outputs": [ - { - "type": "File", - "outputSource": "#main/sorted/output", - "doc": "The output with the lines reversed and sorted.", - "id": "#main/output" - } - ], - "steps": [ - { - "in": [ - { - "source": "#main/input", - "id": "#main/rev/input" - } - ], - "out": [ - "#main/rev/output" - ], - "run": "#revtool.cwl", - "id": "#main/rev" - }, - { - "in": [ - { - "source": "#main/rev/output", - "id": "#main/sorted/input" - }, - { - "source": "#main/reverse_sort", - "id": "#main/sorted/reverse" - } - ], - "out": [ - "#main/sorted/output" - ], - "run": "#sorttool.cwl", - "id": "#main/sorted" - } - ], - "id": "#main" - }, - { - "class": "CommandLineTool", - "doc": "Reverse each line using the `rev` command", - "inputs": [ - { - "type": "File", - "inputBinding": {}, - "id": "#revtool.cwl/input" - } - ], - "outputs": [ - { - "type": "File", - "outputBinding": { - "glob": "output.txt" - }, - "id": "#revtool.cwl/output" - } - ], - "baseCommand": "rev", - "stdout": "output.txt", - "id": "#revtool.cwl" - }, - { - "class": "CommandLineTool", - "doc": "Sort lines using the `sort` command", - "inputs": [ - { - "id": "#sorttool.cwl/reverse", - "type": "boolean", - "inputBinding": { - "position": 1, - "prefix": "-r" - } - }, - { - "id": "#sorttool.cwl/input", - "type": "File", - "inputBinding": { - "position": 2 - } - } - ], - "outputs": [ - { - "id": "#sorttool.cwl/output", - "type": "File", - "outputBinding": { - "glob": "output.txt" - } - } - ], - "baseCommand": "sort", - "stdout": "output.txt", - "id": "#sorttool.cwl" - } - ] -} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_revsort.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_revsort.cwl deleted file mode 100644 index 10ea95ef..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_revsort.cwl +++ /dev/null @@ -1,65 +0,0 @@ -# -# This is a two-step workflow which uses "revtool" and "sorttool" defined above. -# -class: Workflow -doc: "Reverse the lines in a document, then sort those lines." -cwlVersion: v1.1 - -# Requirements & hints specify prerequisites and extensions to the workflow. -# In this example, DockerRequirement specifies a default Docker container -# in which the command line tools will execute. -hints: - - class: DockerRequirement - dockerPull: debian:stretch-slim - - -# The inputs array defines the structure of the input object that describes -# the inputs to the workflow. -# -# The "reverse_sort" input parameter demonstrates the "default" field. If the -# field "reverse_sort" is not provided in the input object, the default value will -# be used. -inputs: - input: - type: File - doc: "The input file to be processed." - reverse_sort: - type: boolean - default: true - doc: "If true, reverse (decending) sort" - -# The "outputs" array defines the structure of the output object that describes -# the outputs of the workflow. -# -# Each output field must be connected to the output of one of the workflow -# steps using the "connect" field. Here, the parameter "#output" of the -# workflow comes from the "#sorted" output of the "sort" step. -outputs: - output: - type: File - outputSource: sorted/output - doc: "The output with the lines reversed and sorted." - -# The "steps" array lists the executable steps that make up the workflow. -# The tool to execute each step is listed in the "run" field. -# -# In the first step, the "inputs" field of the step connects the upstream -# parameter "#input" of the workflow to the input parameter of the tool -# "revtool.cwl#input" -# -# In the second step, the "inputs" field of the step connects the output -# parameter "#reversed" from the first step to the input parameter of the -# tool "sorttool.cwl#input". -steps: - rev: - in: - input: input - out: [output] - run: revtool.cwl - - sorted: - in: - input: rev/output - reverse: reverse_sort - out: [output] - run: sorttool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_revtool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_revtool.cwl deleted file mode 100644 index acc2376a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_revtool.cwl +++ /dev/null @@ -1,37 +0,0 @@ -# -# Simplest example command line program wrapper for the Unix tool "rev". -# -class: CommandLineTool -cwlVersion: v1.1 -doc: "Reverse each line using the `rev` command" - -# The "inputs" array defines the structure of the input object that describes -# the inputs to the underlying program. Here, there is one input field -# defined that will be called "input" and will contain a "File" object. -# -# The input binding indicates that the input value should be turned into a -# command line argument. In this example inputBinding is an empty object, -# which indicates that the file name should be added to the command line at -# a default location. -inputs: - input: - type: File - inputBinding: {} - -# The "outputs" array defines the structure of the output object that -# describes the outputs of the underlying program. Here, there is one -# output field defined that will be called "output", must be a "File" type, -# and after the program executes, the output value will be the file -# output.txt in the designated output directory. -outputs: - output: - type: File - outputBinding: - glob: output.txt - -# The actual program to execute. -baseCommand: rev - -# Specify that the standard output stream must be redirected to a file called -# output.txt in the designated output directory. -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_runtime-paths-distinct.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_runtime-paths-distinct.cwl deleted file mode 100644 index cb34f39e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_runtime-paths-distinct.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - ShellCommandRequirement: {} -inputs: {} -outputs: - foo: File -arguments: - - shellQuote: false - valueFrom: | - echo "cow" > "$(runtime.outdir)/foo" && - echo "moo" > "$(runtime.tmpdir)/foo" && - echo '{"foo": {"path": "$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valueFrom-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valueFrom-tool.cwl deleted file mode 100644 index 1a85a586..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valueFrom-tool.cwl +++ /dev/null @@ -1,15 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -inputs: - scattered_message: - type: string - inputBinding: - position: 2 - message: - type: string - inputBinding: - position: 1 -outputs: - out_message: - type: stdout -baseCommand: echo diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-inputs-wf1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-inputs-wf1.cwl deleted file mode 100644 index 8e865e36..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-inputs-wf1.cwl +++ /dev/null @@ -1,59 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: Workflow -inputs: - inp: - type: - type: array - items: - type: record - name: instr - fields: - - name: instr - type: string -outputs: - out: - type: - type: array - items: string - outputSource: step1/echo_out - -requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - -steps: - step1: - in: - echo_unused: inp - echo_in: - valueFrom: $(inputs.echo_unused.instr) - first: - source: inp - valueFrom: "$(self[0].instr)" - out: [echo_out] - scatter: echo_unused - run: - class: CommandLineTool - inputs: - first: - type: string - inputBinding: - position: 1 - echo_in: - type: string - inputBinding: - position: 2 - echo_unused: Any - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: - - "-n" - - "foo" - stdout: "step1_out" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf1.cwl deleted file mode 100644 index 14ee6572..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf1.cwl +++ /dev/null @@ -1,58 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: Workflow -inputs: - inp: - type: - type: array - items: - type: record - name: instr - fields: - - name: instr - type: string -outputs: - out: - type: - type: array - items: string - outputSource: step1/echo_out - -requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - -steps: - step1: - in: - echo_in: - source: inp - valueFrom: $(self.instr) - first: - source: inp - valueFrom: "$(self[0].instr)" - out: [echo_out] - scatter: echo_in - run: - class: CommandLineTool - inputs: - first: - type: string - inputBinding: - position: 1 - echo_in: - type: string - inputBinding: - position: 2 - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: - - "-n" - - "foo" - stdout: "step1_out" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf2.cwl deleted file mode 100644 index 96afdbc2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf2.cwl +++ /dev/null @@ -1,73 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: Workflow - -inputs: - inp1: - type: - type: array - items: - type: record - name: instr - fields: - - name: instr - type: string - inp2: - type: - type: array - items: string -outputs: - out: - outputSource: step1/echo_out - type: - type: array - items: - type: array - items: string - -requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - -steps: - step1: - in: - echo_in1: - source: inp1 - valueFrom: $(self.instr) - echo_in2: inp2 - first: - source: inp1 - valueFrom: "$(self[0].instr)" - out: [echo_out] - - scatter: [echo_in1, echo_in2] - scatterMethod: nested_crossproduct - run: - class: CommandLineTool - id: step1command - inputs: - first: - type: string - inputBinding: - position: 1 - echo_in1: - type: string - inputBinding: - position: 2 - echo_in2: - type: string - inputBinding: - position: 3 - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: - - "-n" - - "foo" - stdout: step1_out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf3.cwl deleted file mode 100644 index 2b8f7894..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf3.cwl +++ /dev/null @@ -1,69 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 -$graph: - -- id: echo - class: CommandLineTool - inputs: - first: - type: string - inputBinding: - position: 1 - echo_in1: - type: string - inputBinding: - position: 2 - echo_in2: - type: string - inputBinding: - position: 3 - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: ["-n", "foo"] - stdout: step1_out - -- id: main - class: Workflow - inputs: - inp1: - type: - type: array - items: - type: record - name: instr - fields: - - name: instr - type: string - inp2: - type: { type: array, items: string } - requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - steps: - step1: - scatter: [echo_in1, echo_in2] - scatterMethod: flat_crossproduct - in: - echo_in1: - source: inp1 - valueFrom: $(self.instr) - echo_in2: inp2 - first: - source: inp1 - valueFrom: "$(self[0].instr)" - out: [echo_out] - run: "#echo" - - outputs: - out: - outputSource: step1/echo_out - type: - type: array - items: string diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf4.cwl deleted file mode 100644 index 2fb9fce7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf4.cwl +++ /dev/null @@ -1,67 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -$graph: -- id: echo - class: CommandLineTool - inputs: - first: - type: string - inputBinding: - position: 1 - echo_in1: - type: string - inputBinding: - position: 2 - echo_in2: - type: string - inputBinding: - position: 3 - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: ["-n", "foo"] - stdout: step1_out - -- id: main - class: Workflow - inputs: - inp1: - type: - type: array - items: - type: record - name: instr - fields: - - name: instr - type: string - inp2: - type: { type: array, items: string } - requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - steps: - step1: - scatter: [echo_in1, echo_in2] - scatterMethod: dotproduct - in: - echo_in1: - source: inp1 - valueFrom: $(self.instr) - echo_in2: inp2 - first: - source: inp1 - valueFrom: "$(self[0].instr)" - out: [echo_out] - run: "#echo" - - outputs: - out: - outputSource: step1/echo_out - type: - type: array - items: string diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf5.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf5.cwl deleted file mode 100644 index 2db8cc9b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf5.cwl +++ /dev/null @@ -1,58 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: Workflow -inputs: - inp: - type: - type: array - items: - type: record - name: instr - fields: - - name: instr - type: string -outputs: - out: - type: - type: array - items: string - outputSource: step1/echo_out - -requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - -steps: - step1: - in: - echo_in: - source: inp - valueFrom: $(self.instr) - first: - source: inp - valueFrom: $(inputs.echo_in.instr) - out: [echo_out] - scatter: echo_in - run: - class: CommandLineTool - inputs: - first: - type: string - inputBinding: - position: 1 - echo_in: - type: string - inputBinding: - position: 2 - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: - - "-n" - - "foo" - stdout: "step1_out" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf6.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf6.cwl deleted file mode 100644 index 3ada7e73..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-valuefrom-wf6.cwl +++ /dev/null @@ -1,21 +0,0 @@ -cwlVersion: v1.1 -class: Workflow -requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement -inputs: - scattered_messages: string[] -outputs: - out_message: - type: File[] - outputSource: step1/out_message -steps: - step1: - run: scatter-valueFrom-tool.cwl - scatter: [scattered_message] - scatterMethod: dotproduct - in: - scattered_message: scattered_messages - message: - valueFrom: "Hello" - out: [out_message] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-wf1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-wf1.cwl deleted file mode 100644 index 7111f805..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-wf1.cwl +++ /dev/null @@ -1,37 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: Workflow -inputs: - inp: string[] -outputs: - out: - type: string[] - outputSource: step1/echo_out - -requirements: - - class: ScatterFeatureRequirement - -steps: - step1: - in: - echo_in: inp - out: [echo_out] - scatter: echo_in - run: - class: CommandLineTool - inputs: - echo_in: - type: string - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: - - "-n" - - "foo" - stdout: "step1_out" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-wf2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-wf2.cwl deleted file mode 100644 index 954d57ba..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-wf2.cwl +++ /dev/null @@ -1,51 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: Workflow - -inputs: - inp1: string[] - inp2: string[] - -outputs: - out: - outputSource: step1/echo_out - type: - type: array - items: - type: array - items: string - -requirements: - - class: ScatterFeatureRequirement - -steps: - step1: - in: - echo_in1: inp1 - echo_in2: inp2 - out: [echo_out] - - scatter: [echo_in1, echo_in2] - scatterMethod: nested_crossproduct - run: - class: CommandLineTool - id: step1command - inputs: - echo_in1: - type: string - inputBinding: {} - echo_in2: - type: string - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: - - "-n" - - "foo" - stdout: step1_out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-wf3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-wf3.cwl deleted file mode 100644 index c738481a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-wf3.cwl +++ /dev/null @@ -1,48 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 -$graph: - -- id: echo - class: CommandLineTool - inputs: - echo_in1: - type: string - inputBinding: {} - echo_in2: - type: string - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: ["-n", "foo"] - stdout: step1_out - -- id: main - class: Workflow - inputs: - inp1: string[] - inp2: string[] - requirements: - - class: ScatterFeatureRequirement - steps: - step1: - scatter: [echo_in1, echo_in2] - scatterMethod: flat_crossproduct - in: - echo_in1: inp1 - echo_in2: inp2 - out: [echo_out] - run: "#echo" - - outputs: - out: - outputSource: step1/echo_out - type: - type: array - items: string diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-wf4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-wf4.cwl deleted file mode 100644 index ee96ccf8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_scatter-wf4.cwl +++ /dev/null @@ -1,46 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -$graph: -- id: echo - class: CommandLineTool - inputs: - echo_in1: - type: string - inputBinding: {} - echo_in2: - type: string - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: ["-n", "foo"] - stdout: step1_out - -- id: main - class: Workflow - inputs: - inp1: string[] - inp2: string[] - requirements: - - class: ScatterFeatureRequirement - steps: - step1: - scatter: [echo_in1, echo_in2] - scatterMethod: dotproduct - in: - echo_in1: inp1 - echo_in2: inp2 - out: [echo_out] - run: "#echo" - - outputs: - - id: out - outputSource: step1/echo_out - type: - type: array - items: string diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_schemadef-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_schemadef-tool.cwl deleted file mode 100644 index 04b71510..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_schemadef-tool.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 - -requirements: - - $import: schemadef-type.yml - -inputs: - - id: hello - type: "schemadef-type.yml#HelloType" - inputBinding: - valueFrom: $(self.a)/$(self.b) - -outputs: - - id: output - type: File - outputBinding: - glob: output.txt - -stdout: output.txt -baseCommand: echo diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_schemadef-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_schemadef-wf.cwl deleted file mode 100644 index 24a18f00..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_schemadef-wf.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 -class: Workflow - -requirements: - - $import: schemadef-type.yml - -inputs: - hello: "schemadef-type.yml#HelloType" - -outputs: - output: - type: File - outputSource: step1/output - -steps: - step1: - in: - hello: hello - out: [output] - run: schemadef-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_search.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_search.cwl deleted file mode 100644 index df07982c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_search.cwl +++ /dev/null @@ -1,110 +0,0 @@ -cwlVersion: v1.1 -$graph: -- id: index - class: CommandLineTool - baseCommand: python - arguments: - - valueFrom: input.txt - position: 1 - requirements: - - class: InitialWorkDirRequirement - listing: - - entryname: input.txt - entry: $(inputs.file) - - class: InlineJavascriptRequirement - hints: - - class: DockerRequirement - dockerPull: python:2-slim - - inputs: - file: File - secondfile: File - index.py: - type: File - default: - class: File - location: index.py - inputBinding: - position: 0 - outputs: - result: - type: File - outputBinding: - glob: input.txt - secondaryFiles: - - ".idx1" - - "^.idx2" - - '$(self.basename).idx3' - - '${ return self.basename+".idx4"; }' - - '$({"path": self.path+".idx5", "class": "File"})' - - '$(self.nameroot).idx6$(self.nameext)' - - '${ return [self.basename+".idx7", inputs.secondfile]; }' - - "_idx8" - -- id: search - class: CommandLineTool - baseCommand: python - requirements: - - class: InlineJavascriptRequirement - hints: - - class: DockerRequirement - dockerPull: python:2-slim - inputs: - file: - type: File - inputBinding: - position: 1 - secondaryFiles: - - ".idx1" - - "^.idx2" - - '$(self.basename).idx3' - - '${ return self.basename+".idx4"; }' - - '$(self.nameroot).idx6$(self.nameext)' - - '${ return [self.basename+".idx7"]; }' - - "_idx8" - search.py: - type: File - default: - class: File - location: search.py - inputBinding: - position: 0 - term: - type: string - inputBinding: - position: 2 - outputs: - result: - type: File - outputBinding: - glob: result.txt - stdout: result.txt - -- id: main - class: Workflow - inputs: - infile: File - secondfile: File - term: string - outputs: - outfile: - type: File - outputSource: search/result - indexedfile: - type: File - outputSource: index/result - - steps: - index: - run: "#index" - in: - file: infile - secondfile: secondfile - out: [result] - - search: - run: "#search" - in: - file: index/result - term: term - out: [result] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_shellchar.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_shellchar.cwl deleted file mode 100644 index 444586d8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_shellchar.cwl +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: | - Ensure that arguments containing shell directives are not interpreted and - that `shellQuote: false` has no effect when ShellCommandRequirement is not in - effect. -inputs: [] -outputs: - stdout_file: stdout - stderr_file: stderr -baseCommand: echo -arguments: [{valueFrom: "foo 1>&2", shellQuote: false}] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_shellchar2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_shellchar2.cwl deleted file mode 100644 index d946f301..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_shellchar2.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: | - Ensure that `shellQuote: true` is the default behavior when - ShellCommandRequirement is in effect. -requirements: - ShellCommandRequirement: {} -inputs: [] -outputs: - stdout_file: stdout - stderr_file: stderr -baseCommand: echo -arguments: ["foo 1>&2"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_size-expression-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_size-expression-tool.cwl deleted file mode 100644 index fe6c4f32..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_size-expression-tool.cwl +++ /dev/null @@ -1,43 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 - -requirements: - - class: InlineJavascriptRequirement - -class: CommandLineTool - -inputs: - - id: input - type: - type: array - items: File - -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} - -arguments: - - valueFrom: | - ${ - var cmd = ["echo"]; - if (inputs.input.length == 0) { - cmd.push('no_inputs'); - } - else { - for (var i = 0; i < inputs.input.length; i++) { - var filesize = inputs.input[i].size; - if (filesize == 0) { - cmd.push("empty_file"); - } else if (filesize <= 16) { - cmd.push("small_file"); - } else { - cmd.push("big_file") - } - } - } - return cmd; - } -baseCommand: [] -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_sorttool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_sorttool.cwl deleted file mode 100644 index 93fd1c7c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_sorttool.cwl +++ /dev/null @@ -1,35 +0,0 @@ -# Example command line program wrapper for the Unix tool "sort" -# demonstrating command line flags. -class: CommandLineTool -doc: "Sort lines using the `sort` command" -cwlVersion: v1.1 - -# This example is similar to the previous one, with an additional input -# parameter called "reverse". It is a boolean parameter, which is -# intepreted as a command line flag. The value of "prefix" is used for -# flag to put on the command line if "reverse" is true, if "reverse" is -# false, no flag is added. -# -# This example also introduced the "position" field. This indicates the -# sorting order of items on the command line. Lower numbers are placed -# before higher numbers. Here, the "-r" (same as "--reverse") flag (if -# present) will be added to the command line before the input file path. -inputs: - - id: reverse - type: boolean - inputBinding: - position: 1 - prefix: "-r" - - id: input - type: File - inputBinding: - position: 2 - -outputs: - - id: output - type: File - outputBinding: - glob: output.txt - -baseCommand: sort -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage-array-dirs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage-array-dirs.cwl deleted file mode 100644 index ea2a33d0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage-array-dirs.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 -id: stage_array_dirs -baseCommand: - - ls -inputs: - - id: input_list - type: Directory[] -outputs: - - id: output - type: File[] - outputBinding: - glob: - - testdir/a - - rec/B -label: stage-array-dirs.cwl -requirements: - - class: InitialWorkDirRequirement - listing: - - $(inputs.input_list) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage-array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage-array.cwl deleted file mode 100644 index 6d1493b8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage-array.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 -id: stage_array -arguments: - - {shellQuote: false, valueFrom: "ls | grep -v lsout"} -inputs: - - id: input_file - type: File - - id: optional_file - type: File? - - id: input_list - type: 'File[]' - secondaryFiles: - - ^.tar -stdout: lsout -outputs: - - id: output - type: File? - outputBinding: - glob: lsout -label: stage-array.cwl -requirements: - - class: InitialWorkDirRequirement - listing: - - $(inputs.input_file) - - $(inputs.optional_file) - - $(inputs.input_list) - - entryname: a - entry: b - - class: ShellCommandRequirement diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage-unprovided-file.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage-unprovided-file.cwl deleted file mode 100644 index da89063e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage-unprovided-file.cwl +++ /dev/null @@ -1,24 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -hints: - - class: DockerRequirement - dockerPull: python:2-slim -inputs: - - id: infile - type: File? - inputBinding: - prefix: -cfg - valueFrom: $(self.basename) - - id: "args.py" - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - -baseCommand: python - -outputs: -- id: args - type: string[] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage_file_array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage_file_array.cwl deleted file mode 100644 index 3f666430..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage_file_array.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 -id: stage_file_array -label: Stage File Array -arguments: [ls] -inputs: - - id: input_list - type: 'File[]' - secondaryFiles: - - .sec -outputs: - - id: output - type: File[] - outputBinding: - glob: input_dir/* -requirements: - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: - - entryname: input_dir - entry: "${ return {class: 'Directory', listing: inputs.input_list} }" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage_file_array_basename.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage_file_array_basename.cwl deleted file mode 100644 index 601c0933..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage_file_array_basename.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 -id: stage_file_array_basename -label: Stage File Array (with Directory Basename) -arguments: [ls] -inputs: - - id: input_list - type: 'File[]' - secondaryFiles: - - .sec -outputs: - - id: output - type: File[] - outputBinding: - glob: input_dir/* -requirements: - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: - - entry: "${ return {class: 'Directory', basename: 'input_dir', listing: inputs.input_list} }" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage_file_array_basename_and_entryname.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage_file_array_basename_and_entryname.cwl deleted file mode 100644 index 241c2057..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stage_file_array_basename_and_entryname.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 -id: stage_file_array_basename_and_entryname -label: Stage File Array (with Directory Basename AND entryname) -arguments: [ls] -inputs: - - id: input_list - type: 'File[]' - secondaryFiles: - - .sec -outputs: - - id: output - type: File[] - outputBinding: - glob: input_dir/* -requirements: - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: - - entryname: input_dir - entry: "${ return {class: 'Directory', basename: 'not_input_dir', listing: inputs.input_list} }" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stagefile.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stagefile.cwl deleted file mode 100644 index 70b9760c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stagefile.cwl +++ /dev/null @@ -1,26 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -hints: - - class: DockerRequirement - dockerPull: python:2-slim -requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.infile) - entryname: bob.txt - writable: true -inputs: - infile: File -outputs: - outfile: - type: File - outputBinding: - glob: bob.txt -baseCommand: "python" -arguments: - - "-c" - - | - f = open("bob.txt", "r+") - f.seek(8) - f.write("Bob. ") - f.close() diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stderr-mediumcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stderr-mediumcut.cwl deleted file mode 100644 index eb2cc9a4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stderr-mediumcut.cwl +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "Test of capturing stderr output in a docker container." -requirements: - ShellCommandRequirement: {} -inputs: [] -outputs: - output_file: - type: stderr -arguments: - - { valueFrom: "echo foo 1>&2", shellQuote: False } -stderr: std.err diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stderr-shortcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stderr-shortcut.cwl deleted file mode 100644 index 25577fee..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stderr-shortcut.cwl +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "Test of capturing stderr output." -requirements: - ShellCommandRequirement: {} -inputs: [] -outputs: - output_file: - type: stderr -arguments: - - { valueFrom: "echo foo 1>&2", shellQuote: False } diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stderr.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stderr.cwl deleted file mode 100644 index e2dbf0df..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_stderr.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "Test of capturing stderr output." -requirements: - ShellCommandRequirement: {} -inputs: [] -outputs: - output_file: - type: File - outputBinding: {glob: error.txt} -arguments: - - { valueFrom: "echo foo 1>&2", shellQuote: False } -stderr: error.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom-wf.cwl deleted file mode 100644 index 46d494be..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom-wf.cwl +++ /dev/null @@ -1,34 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -requirements: - - class: StepInputExpressionRequirement - -inputs: - in: - type: - name: in - type: record - fields: - - name: file1 - type: File - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: - source: in - valueFrom: $(self.file1) - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom2-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom2-wf.cwl deleted file mode 100644 index 5c28b025..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom2-wf.cwl +++ /dev/null @@ -1,41 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -requirements: - - class: StepInputExpressionRequirement - - class: InlineJavascriptRequirement - - class: MultipleInputFeatureRequirement - -inputs: - a: int - b: int - -outputs: - val: - type: string - outputSource: step1/echo_out - -steps: - step1: - run: - id: echo - class: CommandLineTool - inputs: - c: - type: int - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - stdout: step1_out - - in: - c: - source: [a, b] - valueFrom: "$(self[0] + self[1])" - out: [echo_out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom3-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom3-wf.cwl deleted file mode 100644 index 496e2378..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom3-wf.cwl +++ /dev/null @@ -1,41 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -requirements: - - class: StepInputExpressionRequirement - - class: InlineJavascriptRequirement - -inputs: - a: int - b: int - -outputs: - val: - type: string - outputSource: step1/echo_out - -steps: - step1: - run: - id: echo - class: CommandLineTool - inputs: - c: - type: int - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - stdout: step1_out - - in: - a: a - b: b - c: - valueFrom: "$(inputs.a + inputs.b)" - out: [echo_out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom4-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom4-wf.cwl deleted file mode 100644 index 8a8e04a9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom4-wf.cwl +++ /dev/null @@ -1,36 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -requirements: - StepInputExpressionRequirement: {} - -inputs: [] - -outputs: - val: - type: string - outputSource: step1/echo_out - -steps: - step1: - run: - id: echo - class: CommandLineTool - inputs: - a: - type: string - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: step1_out - loadContents: true - outputEval: $(self[0].contents) - baseCommand: echo - stdout: step1_out - - in: - a: - valueFrom: moocow - out: [echo_out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom5-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom5-wf.cwl deleted file mode 100644 index a68eb933..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_step-valuefrom5-wf.cwl +++ /dev/null @@ -1,74 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 -requirements: - StepInputExpressionRequirement: {} - -inputs: - file1: File - -outputs: - val1: - type: string - outputSource: step1/echo_out - val2: - type: string - outputSource: step2/echo_out - -steps: - step1: - run: - class: CommandLineTool - - inputs: - name: - type: string - inputBinding: {} - - outputs: - echo_out: - type: string - outputBinding: - glob: step1_out - loadContents: true - outputEval: $(self[0].contents) - echo_out_file: - type: File - outputBinding: - glob: step1_out - - baseCommand: echo - stdout: step1_out - - in: - name: - source: file1 - valueFrom: $(self.basename) - out: [echo_out, echo_out_file] - - - step2: - run: - class: CommandLineTool - - inputs: - name: - type: string - inputBinding: {} - - outputs: - echo_out: - type: string - outputBinding: - glob: step1_out - loadContents: true - outputEval: $(self[0].contents) - - baseCommand: echo - stdout: step1_out - - in: - name: - source: step1/echo_out_file - valueFrom: $(self.basename) - out: [echo_out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_steplevel-resreq.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_steplevel-resreq.cwl deleted file mode 100644 index f453082f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_steplevel-resreq.cwl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -requirements: - ResourceRequirement: - coresMin: 4 - coresMax: 4 - -inputs: [] - -steps: - step1: - requirements: - ResourceRequirement: - coresMin: 1 - coresMax: 1 - run: - class: CommandLineTool - inputs: [] - outputs: - output: - type: stdout - baseCommand: echo - stdout: cores.txt - arguments: [ $(runtime.cores) ] - in: [] - out: [output] - -outputs: - out: - type: File - outputSource: step1/output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_sum-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_sum-wf-noET.cwl deleted file mode 100644 index 7886aed1..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_sum-wf-noET.cwl +++ /dev/null @@ -1,50 +0,0 @@ -cwlVersion: v1.1 -class: Workflow - -requirements: - - class: StepInputExpressionRequirement - - class: MultipleInputFeatureRequirement - - class: InlineJavascriptRequirement - -inputs: - int_1: - type: - - int - - string - int_2: - type: - - int - - string - -outputs: - result: - type: File - outputSource: sum/result - -steps: - sum: - in: - data: - source: [int_1, int_2] - valueFrom: | - ${ - var sum = 0; - for (var i = 0; i < self.length; i++){ - sum += self[i]; - }; - return sum; - } - out: - - result - run: - class: CommandLineTool - inputs: - data: - type: int - inputBinding: {} - baseCommand: echo - stdout: result.txt - outputs: - result: - type: stdout - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_sum-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_sum-wf.cwl deleted file mode 100644 index 72145f4d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_sum-wf.cwl +++ /dev/null @@ -1,49 +0,0 @@ -cwlVersion: v1.1 -class: Workflow - -requirements: - - class: StepInputExpressionRequirement - - class: MultipleInputFeatureRequirement - - class: InlineJavascriptRequirement - -inputs: - int_1: - type: - - int - - string - int_2: - type: - - int - - string - -outputs: - result: - type: int - outputSource: sum/result - -steps: - sum: - in: - data: - source: [int_1, int_2] - valueFrom: | - ${ - var sum = 0; - for (var i = 0; i < self.length; i++){ - sum += self[i]; - }; - return sum; - } - out: - - result - run: - class: ExpressionTool - inputs: - data: - type: int - outputs: - result: int - expression: | - ${ - return {"result": inputs.data}; - } diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_symlink-illegal.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_symlink-illegal.cwl deleted file mode 100644 index 359249df..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_symlink-illegal.cwl +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "Create a file under /tmp, symlink it to working directory and glob symlink. The executor should NOT resolve this symlink" -hints: - DockerRequirement: - dockerPull: alpine -inputs: [] -outputs: - output_file: - type: File - outputBinding: {glob: symlink.txt} - -requirements: - - class: ShellCommandRequirement - -arguments: - - echo - - "Who's gonna drive you home" - - {valueFrom: "> /tmp/original.txt", shellQuote: false} - - {valueFrom: " && ", shellQuote: false} - - ln - - -s - - /tmp/original.txt - - symlink.txt \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_symlink-legal.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_symlink-legal.cwl deleted file mode 100644 index 2df53bfb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_symlink-legal.cwl +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -doc: "Create a file under adir/, symlink it to working directory (./) and glob symlink. The executor should resolve this symlink" -hints: - DockerRequirement: - dockerPull: alpine -inputs: [] -outputs: - output_file: - type: File - outputBinding: {glob: symlink.txt} - -requirements: - - class: ShellCommandRequirement - -arguments: - - mkdir - - adir - - {valueFrom: " && ", shellQuote: false} - - echo - - "Who's gonna drive you home" - - {valueFrom: "> adir/original.txt", shellQuote: false} - - {valueFrom: " && ", shellQuote: false} - - ln - - -s - - adir/original.txt - - symlink.txt \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_template-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_template-tool.cwl deleted file mode 100755 index e6231843..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_template-tool.cwl +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: CommandLineTool -requirements: - - class: InlineJavascriptRequirement - expressionLib: - - { $include: underscore.js } - - "var t = function(s) { return _.template(s, {variable: 'data'})({'inputs': inputs}); };" - - class: InitialWorkDirRequirement - listing: - - entryname: foo.txt - entry: $(t("The file is <%= data.inputs.file1.path.split('/').slice(-1)[0] %>\n")) -hints: - DockerRequirement: - dockerPull: "debian:stretch-slim" -inputs: - - id: file1 - type: File -outputs: - - id: foo - type: File - outputBinding: - glob: foo.txt -baseCommand: [cat, foo.txt] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_test-cwl-out.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_test-cwl-out.cwl deleted file mode 100644 index f614f92d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_test-cwl-out.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - - class: ShellCommandRequirement -hints: - DockerRequirement: - dockerPull: "debian:stretch-slim" - -inputs: [] - -outputs: - - id: foo - type: File - -arguments: - - valueFrom: > - echo foo > foo && echo '{"foo": {"path": "$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json - shellQuote: false diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_test-cwl-out2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_test-cwl-out2.cwl deleted file mode 100644 index ec041322..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_test-cwl-out2.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -requirements: - - class: ShellCommandRequirement -hints: - DockerRequirement: - dockerPull: "debian:stretch-slim" - -inputs: [] - -outputs: - - id: foo - type: File - -arguments: - - valueFrom: > - echo foo > foo && echo '{"foo": {"location": "file://$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json - shellQuote: false diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit.cwl deleted file mode 100644 index 35d96796..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit.cwl +++ /dev/null @@ -1,10 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: [] -outputs: [] -requirements: - ToolTimeLimit: - timelimit: 3 - WorkReuse: - enableReuse: false -baseCommand: [sleep, "15"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit2-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit2-wf.cwl deleted file mode 100644 index 58211697..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit2-wf.cwl +++ /dev/null @@ -1,49 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -requirements: - ToolTimeLimit: - timelimit: 5 - InlineJavascriptRequirement: {} - -inputs: - i: - type: string? - -outputs: - o: - type: string? - outputSource: step2/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: CommandLineTool - baseCommand: ["sleep", "3"] - inputs: - i: - type: string? - outputs: - o: - type: string? - outputBinding: - outputEval: $("time passed") - step2: - in: - i: step1/o - out: [o] - run: - class: CommandLineTool - baseCommand: ["sleep", "3"] - inputs: - i: - type: string? - outputs: - o: - type: string? - outputBinding: - outputEval: $("time passed") diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit2.cwl deleted file mode 100644 index 973c6ce9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit2.cwl +++ /dev/null @@ -1,8 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: [] -outputs: [] -requirements: - ToolTimeLimit: - timelimit: -1 -baseCommand: [sleep, "15"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit3-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit3-wf.cwl deleted file mode 100644 index 2f656971..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit3-wf.cwl +++ /dev/null @@ -1,36 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.1 - -requirements: - ToolTimeLimit: - timelimit: 0 - WorkReuse: - enableReuse: false - InlineJavascriptRequirement: {} - -inputs: - i: - type: int? - -outputs: - o: - type: string? - outputSource: step1/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: CommandLineTool - baseCommand: ["sleep", "10"] - inputs: - i: - type: int? - outputs: - o: - type: string? - outputBinding: - outputEval: $("time passed") diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit3.cwl deleted file mode 100644 index 5efd0a52..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit3.cwl +++ /dev/null @@ -1,10 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: [] -outputs: [] -requirements: - ToolTimeLimit: - timelimit: 0 - WorkReuse: - enableReuse: false -baseCommand: [sleep, "15"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit4.cwl deleted file mode 100644 index 187f5a87..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit4.cwl +++ /dev/null @@ -1,11 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 -inputs: [] -outputs: [] -requirements: - InlineJavascriptRequirement: {} - ToolTimeLimit: - timelimit: $(1+2) - WorkReuse: - enableReuse: false -baseCommand: [sleep, "15"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit5.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit5.cwl deleted file mode 100644 index 866b6539..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_timelimit5.cwl +++ /dev/null @@ -1,22 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.1 -inputs: [] -outputs: - status: string -requirements: - ToolTimeLimit: - timelimit: 3 - InlineJavascriptRequirement: {} -expression: | - ${ - function sleep(milliseconds) { - var start = new Date().getTime(); - for (var i = 0; i < 1e7; i++) { - if ((new Date().getTime() - start) > milliseconds){ - break; - } - } - }; - sleep(5000); - return {"status": "Done"} - } \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_tmap-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_tmap-tool.cwl deleted file mode 100755 index b8fbc028..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_tmap-tool.cwl +++ /dev/null @@ -1,257 +0,0 @@ -#!/usr/bin/env cwl-runner -{ - "cwlVersion": "v1.1", - - "class": "CommandLineTool", - "hints": [ - { - "class": "DockerRequirement", - "dockerPull": "python:2-slim" - } - ], - "inputs": [ - { - "id": "reads", - "type": "File" - }, - { - "id": "stages", - "inputBinding": { - "position": 1 - }, - "type": { - "type": "array", - "items": "#Stage" - } - }, - { - id: "#args.py", - type: File, - default: { - class: File, - location: args.py - }, - inputBinding: { - position: -1 - } - } - ], - "outputs": [ - { - "id": "sam", - "outputBinding": { - "glob": "output.sam" - }, - "type": ["null", "File"] - }, - {"id": "args", "type": "string[]"} - ], - "requirements": [ - {"class": "SchemaDefRequirement", - "types": [ - { - "fields": [ - { - "inputBinding": { - "position": 0 - }, - "name": "algo", - "type": { - "type": "enum", - "name": "JustMap1", - "symbols": ["map1"] - } - }, - { - "name": "maxSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--max-seq-length", - "position": 2 - } - }, - { - "name": "minSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--min-seq-length", - "position": 2 - } - }, - { - "inputBinding": { - "position": 2, - "prefix": "--seed-length" - }, - "name": "seedLength", - "type": ["null", "int"] - } - ], - "name": "Map1", - "type": "record" - }, - { - "fields": [ - { - "inputBinding": { - "position": 0 - }, - "name": "algo", - "type": { - "type": "enum", - "name": "JustMap2", - "symbols": ["map2"] - } - }, - { - "name": "maxSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--max-seq-length", - "position": 2 - } - }, - { - "name": "minSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--min-seq-length", - "position": 2 - } - }, - { - "inputBinding": { - "position": 2, - "prefix": "--max-seed-hits" - }, - "name": "maxSeedHits", - "type": ["null", "int"] - } - ], - "name": "Map2", - "type": "record" - }, - { - "fields": [ - { - "inputBinding": { - "position": 0 - }, - "name": "algo", - "type": { - "type": "enum", - "name": "JustMap3", - "symbols": ["map3"] - } - }, - { - "name": "maxSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--max-seq-length", - "position": 2 - } - }, - { - "name": "minSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--min-seq-length", - "position": 2 - } - }, - { - "inputBinding": { - "position": 2, - "prefix": "--fwd-search" - }, - "name": "fwdSearch", - "type": ["null", "boolean"] - } - ], - "name": "Map3", - "type": "record" - }, - { - "fields": [ - { - "inputBinding": { - "position": 0 - }, - "name": "algo", - "type": { - "type": "enum", - "name": "JustMap4", - "symbols": ["map4"] - } - }, - { - "name": "maxSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--max-seq-length", - "position": 2 - } - }, - { - "name": "minSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--min-seq-length", - "position": 2 - } - }, - { - "inputBinding": { - "position": 2, - "prefix": "--seed-step" - }, - "name": "seedStep", - "type": ["null", "int"] - } - ], - "name": "Map4", - "type": "record" - }, - { - "type": "record", - "name": "Stage", - "fields": [ - { - "inputBinding": { - "position": 0, - "prefix": "stage", - "separate": false - }, - "name": "stageId", - "type": ["null", "int"] - }, - { - "inputBinding": { - "position": 1, - "prefix": "-n" - }, - "name": "stageOption1", - "type": ["null", "boolean"] - }, - { - "inputBinding": { - "position": 2 - }, - "name": "algos", - "type": { - "type": "array", - "items": [ - "#Map1", - "#Map2", - "#Map3", - "#Map4" - ] - } - } - ] - } - ]}], - "baseCommand": "python", - "arguments": ["tmap", "mapall"] -} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_touch.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_touch.cwl deleted file mode 100644 index bd01fa2e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_touch.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.1 -class: CommandLineTool - -hints: - DockerRequirement: - dockerPull: debian:stretch-slim - -inputs: - name: - type: string - inputBinding: - position: 0 - -outputs: - empty_file: - type: File - outputBinding: - glob: $(inputs.name) - -baseCommand: [touch] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_updatedir_inplace.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_updatedir_inplace.cwl deleted file mode 100755 index 178d4a56..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_updatedir_inplace.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.r) - entryname: inp - writable: true - InplaceUpdateRequirement: - inplaceUpdate: true -inputs: - r: Directory -outputs: - out: - type: Directory - outputBinding: - glob: inp -arguments: [touch, inp/blurb] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_updateval_inplace.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_updateval_inplace.cwl deleted file mode 100755 index b94e4bea..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_updateval_inplace.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.r) - writable: true - InplaceUpdateRequirement: - inplaceUpdate: true -hints: - DockerRequirement: - dockerPull: "python:2.7.15-alpine3.7" -inputs: - r: File - script: - type: File - default: - class: File - location: updateval.py -outputs: - out: - type: File - outputBinding: - glob: $(inputs.r.basename) -arguments: [python, $(inputs.script), $(inputs.r.basename)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_valueFrom-constant.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_valueFrom-constant.cwl deleted file mode 100644 index 15c7342f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_valueFrom-constant.cwl +++ /dev/null @@ -1,28 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.1 - -hints: - - class: DockerRequirement - dockerPull: python:2-slim - -inputs: - - id: array_input - type: - - type: array - items: File - inputBinding: - valueFrom: replacementValue - - - id: args.py - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - -outputs: - - id: args - type: string[] - -baseCommand: python diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_vf-concat.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_vf-concat.cwl deleted file mode 100644 index 777bcf01..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_vf-concat.cwl +++ /dev/null @@ -1,19 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -requirements: - - class: InlineJavascriptRequirement - -baseCommand: echo -inputs: - file1: - type: File? - inputBinding: - valueFrom: $("a ")$("string") -outputs: - out: - type: string - outputBinding: - glob: output.txt - loadContents: true - outputEval: $(self[0].contents) -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc-tool-shortcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc-tool-shortcut.cwl deleted file mode 100755 index 53f543fe..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc-tool-shortcut.cwl +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 - -requirements: - - class: DockerRequirement - dockerPull: debian:stretch-slim - -inputs: - file1: stdin - -outputs: - output: - type: File - outputBinding: { glob: output } - -baseCommand: [wc] - -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc-tool.cwl deleted file mode 100755 index 42977e4d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 - -inputs: - file1: File - -outputs: - output: - type: File - outputBinding: { glob: output } - -baseCommand: [wc, -l] - -stdin: $(inputs.file1.path) -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc2-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc2-tool.cwl deleted file mode 100755 index 26b45ab6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc2-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -requirements: - - class: InlineJavascriptRequirement - -inputs: - - { id: file1, type: File, inputBinding: {} } -outputs: - - id: output - type: int - outputBinding: - glob: output.txt - loadContents: true - outputEval: "$(parseInt(self[0].contents))" -stdout: output.txt -baseCommand: wc diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc3-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc3-tool.cwl deleted file mode 100644 index d357ab29..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc3-tool.cwl +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - file1: - type: File[] - inputBinding: {} -outputs: - output: - type: int - outputBinding: - glob: output.txt - loadContents: true - outputEval: | - ${ - var s = self[0].contents.split(/\r?\n/); - return parseInt(s[s.length-2]); - } -stdout: output.txt -baseCommand: wc diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc4-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc4-tool.cwl deleted file mode 100644 index 9586e76b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wc4-tool.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.1 -requirements: - - class: InlineJavascriptRequirement - -inputs: - file1: - type: File - inputBinding: {} -outputs: - - id: output - type: int - outputBinding: - glob: output.txt - loadContents: true - outputEval: | - ${ - var s = self[0].contents.split(/\r?\n/); - return parseInt(s[s.length-2]); - } -stdout: output.txt -baseCommand: wc diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wf-loadContents.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wf-loadContents.cwl deleted file mode 100644 index cabf65e6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wf-loadContents.cwl +++ /dev/null @@ -1,30 +0,0 @@ -cwlVersion: v1.1 -class: Workflow -requirements: - StepInputExpressionRequirement: {} - InlineJavascriptRequirement: {} -inputs: - my_file: - type: File - inputBinding: - loadContents: true - -steps: - one: - run: - class: ExpressionTool - requirements: { InlineJavascriptRequirement: {} } - inputs: { my_number: int } - outputs: { my_int: int } - expression: | - ${ return { "my_int": inputs.my_number }; } - in: - my_number: - source: my_file - valueFrom: $(parseInt(self.contents)) - out: [ my_int ] - -outputs: - my_int: - type: int - outputSource: one/my_int \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wf-loadContents2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wf-loadContents2.cwl deleted file mode 100644 index 2cd55f3c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wf-loadContents2.cwl +++ /dev/null @@ -1,29 +0,0 @@ -cwlVersion: v1.1 -class: Workflow -requirements: - StepInputExpressionRequirement: {} - InlineJavascriptRequirement: {} -inputs: - my_file: - type: File - loadContents: true - -steps: - one: - run: - class: ExpressionTool - requirements: { InlineJavascriptRequirement: {} } - inputs: { my_number: int } - outputs: { my_int: int } - expression: | - ${ return { "my_int": inputs.my_number }; } - in: - my_number: - source: my_file - valueFrom: $(parseInt(self.contents)) - out: [ my_int ] - -outputs: - my_int: - type: int - outputSource: one/my_int \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wf-loadContents3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wf-loadContents3.cwl deleted file mode 100644 index 89b29dab..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wf-loadContents3.cwl +++ /dev/null @@ -1,28 +0,0 @@ -cwlVersion: v1.1 -class: Workflow -requirements: - StepInputExpressionRequirement: {} - InlineJavascriptRequirement: {} -inputs: - my_file: File - -steps: - one: - run: - class: ExpressionTool - requirements: { InlineJavascriptRequirement: {} } - inputs: - my_number: - type: File - loadContents: true - outputs: { my_int: int } - expression: | - ${ return { "my_int": parseInt(inputs.my_number.contents) }; } - in: - my_number: my_file - out: [ my_int ] - -outputs: - my_int: - type: int - outputSource: one/my_int \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wf-loadContents4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wf-loadContents4.cwl deleted file mode 100644 index 8b0d338f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_wf-loadContents4.cwl +++ /dev/null @@ -1,28 +0,0 @@ -cwlVersion: v1.1 -class: Workflow -requirements: - StepInputExpressionRequirement: {} - InlineJavascriptRequirement: {} -inputs: - my_file: File - -steps: - one: - run: - class: ExpressionTool - requirements: { InlineJavascriptRequirement: {} } - inputs: { my_number: int } - outputs: { my_int: int } - expression: | - ${ return { "my_int": inputs.my_number }; } - in: - my_number: - source: my_file - loadContents: true - valueFrom: $(parseInt(self.contents)) - out: [ my_int ] - -outputs: - my_int: - type: int - outputSource: one/my_int \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_writable-dir-docker.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_writable-dir-docker.cwl deleted file mode 100644 index 517d05f7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_writable-dir-docker.cwl +++ /dev/null @@ -1,23 +0,0 @@ -cwlVersion: v1.1 - -class: CommandLineTool - -requirements: - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: - - entryname: emptyWritableDir - entry: "$({class: 'Directory', listing: []})" - writable: true - -hints: - - class: DockerRequirement - dockerPull: alpine - -inputs: [] -outputs: - out: - type: Directory - outputBinding: - glob: emptyWritableDir -arguments: [touch, emptyWritableDir/blurg] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_writable-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_writable-dir.cwl deleted file mode 100644 index a3164b23..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_1/utils/valid_writable-dir.cwl +++ /dev/null @@ -1,16 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: emptyWritableDir - writable: true - entry: "$({class: 'Directory', listing: []})" -inputs: [] -outputs: - out: - type: Directory - outputBinding: - glob: emptyWritableDir -arguments: [touch, emptyWritableDir/blurg] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/525.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/525.cwl deleted file mode 100644 index 10e8da9c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/525.cwl +++ /dev/null @@ -1,118 +0,0 @@ -{ - "cwlVersion": "v1.2", - "$graph": [ - { - "id": "main", - "class": "Workflow", - "inputs": [ - { - "id": "command", - "type": "string" - }, - { - "id": "wf_file_input", - "type": "File", - "secondaryFiles": [ - { - "pattern": ".also", - "required": true - } - ] - }, - { - "id": "wf_file_input_array", - "type": { - "type": "array", - "items": "File" - }, - "secondaryFiles": [ - { - "pattern": ".also", - "required": true - } - ] - } - ], - "outputs": [ - { - "id": "the_answer", - "type": "string", - "outputSource": "run_tool/the_answer" - } - ], - "steps": [ - { - "id": "run_tool", - "run": "#cwl_secondary_files_workflow_tool", - "in": { - "command": "command", - "f": "wf_file_input", - "fs": "wf_file_input_array" - }, - "out": [ - { - "id": "the_answer" - } - ] - } - ] - }, - { - "id": "cwl_secondary_files_workflow_tool", - "class": "CommandLineTool", - "requirements": [ - { - "class": "InlineJavascriptRequirement" - } - ], - "hints": { - "DockerRequirement": { - "dockerPull": "debian:stretch-slim" - }, - "NetworkAccess": { - "networkAccess": true - }, - "LoadListingRequirement": { - "loadListing": "deep_listing" - } - }, - "inputs": [ - { - "id": "command", - "type": "string" - }, - { - "id": "f", - "type": "File", - "inputBinding": { - "position": 2 - } - }, - { - "id": "fs", - "type": { - "type": "array", - "items": "File", - "inputBinding": { - "position": 3 - } - } - } - ], - "outputs": { - "the_answer": { - "type": "string", - "outputBinding": { - "outputEval": "${ return \"\\$(\" + 42 + \")\"; }" - } - } - }, - "baseCommand": [], - "arguments": [ - "bash", - "-c", - "$(inputs.command)" - ] - } - ] -} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/EDAM.owl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/EDAM.owl deleted file mode 100644 index 092fccda..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/EDAM.owl +++ /dev/null @@ -1,51294 +0,0 @@ - - - - - - - - - - - - - -]> - - - - - EDAM_topic http://edamontology.org/topic_ "EDAM topics" - EDAM_operation http://edamontology.org/operation_ "EDAM operations" - 09:07:2015 - 3625 - formats "EDAM data formats" - EDAM - An ontology of bioinformatics topics, operations, types of data including identifiers, and data formats - identifiers "EDAM types of identifiers" - data "EDAM types of data" - relations "EDAM relations" - edam "EDAM" - EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. - operations "EDAM operations" - EDAM http://edamontology.org/ "EDAM relations and concept properties" - application/rdf+xml - EDAM_data http://edamontology.org/data_ "EDAM types of data" - concept_properties "EDAM concept properties" - Jon Ison - Matúš Kalaš - Jon Ison, Matus Kalas, Hervé Ménager - EDAM_format http://edamontology.org/format_ "EDAM data formats" - topics "EDAM topics" - 1.11 - Hervé Ménager - EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. - - - - - - - - - - - - - - - Created in - Version in which a concept was created. - true - concept_properties - - - - - - - - Documentation - Specification - 'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format. - true - concept_properties - - - - - - - - Example - 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. - true - concept_properties - - - - - - - - - - - - - - Obsolete since - true - concept_properties - Version in which a concept was made obsolete. - - - - - - - - Regular expression - 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. - concept_properties - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - has format - "http://purl.obolibrary.org/obo/OBI_0000298" - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. - false - OBO_REL:is_a - relations - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" - false - false - edam - 'A has_format B' defines for the subject A, that it has the object B as its data format. - false - - - - - - - - - - has function - http://wsio.org/has_function - false - OBO_REL:is_a - OBO_REL:bearer_of - edam - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. - false - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" - true - 'A has_function B' defines for the subject A, that it has the object B as its function. - "http://purl.obolibrary.org/obo/OBI_0000306" - relations - false - - - - true - In very unusual cases. - - - - - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. - OBO_REL:bearer_of - - - - - - - - - - has identifier - false - false - relations - OBO_REL:is_a - edam - 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. - false - false - - - - - - - - - - has input - OBO_REL:has_participant - "http://purl.obolibrary.org/obo/OBI_0000293" - false - http://wsio.org/has_input - Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. - relations - OBO_REL:is_a - false - 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument. - false - true - edam - - - - - OBO_REL:has_participant - 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. - - - - - true - In very unusual cases. - - - - - - - - - - has output - http://wsio.org/has_output - Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. - edam - "http://purl.obolibrary.org/obo/OBI_0000299" - OBO_REL:is_a - relations - OBO_REL:has_participant - true - 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. - false - false - false - - - - - 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. - OBO_REL:has_participant - - - - - In very unusual cases. - true - - - - - - - - - - has topic - relations - true - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. - false - 'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B). - edam - OBO_REL:is_a - http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic - false - "http://purl.obolibrary.org/obo/IAO_0000136" - false - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality - "http://purl.obolibrary.org/obo/OBI_0000298" - - - - - - - - - - - - In very unusual cases. - true - - - - - - - - - - is format of - false - OBO_REL:is_a - false - false - false - 'A is_format_of B' defines for the subject A, that it is a data format of the object B. - edam - relations - Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. - OBO_REL:quality_of - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in - - - - - - OBO_REL:quality_of - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. - - - - - - - - - - is function of - Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used. - OBO_REL:inheres_in - true - OBO_REL:is_a - false - 'A is_function_of B' defines for the subject A, that it is a function of the object B. - OBO_REL:function_of - edam - http://wsio.org/is_function_of - relations - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in - false - false - - - - - OBO_REL:inheres_in - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. - - - - - true - In very unusual cases. - - - - - OBO_REL:function_of - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. - - - - - - - - - - is identifier of - false - false - edam - false - relations - Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined. - 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B. - OBO_REL:is_a - false - - - - - - - - - - - is input of - false - http://wsio.org/is_input_of - relations - true - false - OBO_REL:participates_in - OBO_REL:is_a - "http://purl.obolibrary.org/obo/OBI_0000295" - edam - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'. - false - 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. - - - - - - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. - OBO_REL:participates_in - - - - - In very unusual cases. - true - - - - - - - - - - is output of - OBO_REL:is_a - false - false - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. - edam - false - 'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B. - OBO_REL:participates_in - http://wsio.org/is_output_of - true - relations - "http://purl.obolibrary.org/obo/OBI_0000312" - - - - - - In very unusual cases. - true - - - - - OBO_REL:participates_in - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. - - - - - - - - - - is topic of - 'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B). - relations - OBO_REL:quality_of - false - true - false - Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in - false - OBO_REL:is_a - edam - - - - - - - - - - - - - OBO_REL:quality_of - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. - - - - - In very unusual cases. - true - - - - - - - - - - - - - - - - Resource type - - beta12orEarlier - beta12orEarlier - A type of computational resource used in bioinformatics. - true - - - - - - - - - Data - - - - - Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output. - http://www.onto-med.de/ontologies/gfo.owl#Perpetuant - http://semanticscience.org/resource/SIO_000088 - http://semanticscience.org/resource/SIO_000069 - "http://purl.obolibrary.org/obo/IAO_0000030" - "http://purl.obolibrary.org/obo/IAO_0000027" - Data set - Data record - beta12orEarlier - http://wsio.org/data_002 - http://purl.org/biotop/biotop.owl#DigitalEntity - http://www.ifomis.org/bfo/1.1/snap#Continuant - Datum - - - - - Data set - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - - - - - Datum - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - - - - - Data record - EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). - - - - - - - - - - Tool - - beta12orEarlier - A bioinformatics package or tool, e.g. a standalone application or web service. - beta12orEarlier - true - - - - - - - - - Database - - A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - Ontology - - - - - - - - beta12orEarlier - Ontologies - An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. - - - - - - - - - - Directory metadata - - 1.5 - A directory on disk from which files are read. - beta12orEarlier - true - - - - - - - - - - MeSH vocabulary - - beta12orEarlier - true - Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. - beta12orEarlier - - - - - - - - - - HGNC vocabulary - - beta12orEarlier - beta12orEarlier - Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee. - true - - - - - - - - - - UMLS vocabulary - - Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System). - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Identifier - - - - - - - - - - http://semanticscience.org/resource/SIO_000115 - beta12orEarlier - ID - "http://purl.org/dc/elements/1.1/identifier" - http://wsio.org/data_005 - A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things). - - - - - - - Almost exact but limited to identifying resources. - - - - - - - - - - - Database entry - - beta12orEarlier - beta12orEarlier - An entry (retrievable via URL) from a biological database. - true - - - - - - - - - - Molecular mass - - Mass of a molecule. - beta12orEarlier - - - - - - - - - - Molecular charge - - Net charge of a molecule. - beta12orEarlier - PDBML:pdbx_formal_charge - - - - - - - - - - Chemical formula - - Chemical structure specification - A specification of a chemical structure. - beta12orEarlier - - - - - - - - - - QSAR descriptor - - A QSAR quantitative descriptor (name-value pair) of chemical structure. - QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties. - beta12orEarlier - - - - - - - - - - Raw sequence - - beta12orEarlier - A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters. - Non-sequence characters may be used for example for gaps and translation stop. - - - - - - - - - - Sequence record - - http://purl.bioontology.org/ontology/MSH/D058977 - beta12orEarlier - A molecular sequence and associated metadata. - SO:2000061 - - - - - - - - - - Sequence set - - A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method. - This concept may be used for arbitrary sequence sets and associated data arising from processing. - beta12orEarlier - SO:0001260 - - - - - - - - - - Sequence mask character - - true - beta12orEarlier - 1.5 - A character used to replace (mask) other characters in a molecular sequence. - - - - - - - - - - Sequence mask type - - A label (text token) describing the type of sequence masking to perform. - Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits. - beta12orEarlier - 1.5 - true - - - - - - - - - - DNA sense specification - - DNA strand specification - beta12orEarlier - Strand - The strand of a DNA sequence (forward or reverse). - The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. - - - - - - - - - - Sequence length specification - - true - A specification of sequence length(s). - beta12orEarlier - 1.5 - - - - - - - - - - Sequence metadata - - beta12orEarlier - Basic or general information concerning molecular sequences. - This is used for such things as a report including the sequence identifier, type and length. - 1.5 - true - - - - - - - - - - Sequence feature source - - This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). - How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived. - beta12orEarlier - - - - - - - - - - Sequence search results - - beta12orEarlier - Database hits (sequence) - - Sequence database hits - Sequence search hits - The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc. - A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits. - Sequence database search results - - - - - - - - - - Sequence signature matches - - Sequence motif matches - Protein secondary database search results - beta12orEarlier - Report on the location of matches in one or more sequences to profiles, motifs (conserved or functional patterns) or other signatures. - Sequence profile matches - This ncluding reports of hits from a search of a protein secondary or domain database. - Search results (protein secondary database) - - - - - - - - - - Sequence signature model - - Data files used by motif or profile methods. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Sequence signature data - - - - - - - - beta12orEarlier - This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on. - Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element. - - - - - - - - - - Sequence alignment (words) - - 1.5 - beta12orEarlier - true - Sequence word alignment - Alignment of exact matches between subsequences (words) within two or more molecular sequences. - - - - - - - - - - Dotplot - - A dotplot of sequence similarities identified from word-matching or character comparison. - beta12orEarlier - - - - - - - - - - Sequence alignment - - - - - - - - http://en.wikipedia.org/wiki/Sequence_alignment - http://purl.bioontology.org/ontology/MSH/D016415 - http://semanticscience.org/resource/SIO_010066 - beta12orEarlier - Alignment of multiple molecular sequences. - - - - - - - - - - Sequence alignment parameter - - Some simple value controlling a sequence alignment (or similar 'match') operation. - true - 1.5 - beta12orEarlier - - - - - - - - - - Sequence similarity score - - A value representing molecular sequence similarity. - beta12orEarlier - - - - - - - - - - Sequence alignment metadata - - Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score. - beta12orEarlier - true - 1.5 - - - - - - - - - - Sequence alignment report - - Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score. - An informative report of molecular sequence alignment-derived data or metadata. - beta12orEarlier - - - - - - - - - - Sequence profile alignment - - beta12orEarlier - A profile-profile alignment (each profile typically representing a sequence alignment). - - - - - - - - - - Sequence-profile alignment - - beta12orEarlier - Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment). - Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores. - - - - - - - - - - Sequence distance matrix - - beta12orEarlier - Moby:phylogenetic_distance_matrix - A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation. - Phylogenetic distance matrix - Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. - - - - - - - - - - Phylogenetic character data - - Basic character data from which a phylogenetic tree may be generated. - As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments - http://www.evolutionaryontology.org/cdao.owl#Character - beta12orEarlier - - - - - - - - - - Phylogenetic tree - - - - - - - - Phylogeny - Moby:Tree - http://www.evolutionaryontology.org/cdao.owl#Tree - A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. - http://purl.bioontology.org/ontology/MSH/D010802 - Moby:phylogenetic_tree - The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length. - beta12orEarlier - Moby:myTree - - - - - - - - - - Comparison matrix - - beta12orEarlier - The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats). - Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison. - Substitution matrix - - - - - - - - - - Protein topology - - beta12orEarlier - beta12orEarlier - Predicted or actual protein topology represented as a string of protein secondary structure elements. - true - The location and size of the secondary structure elements and intervening loop regions is usually indicated. - - - - - - - - - - Protein features report (secondary structure) - - beta12orEarlier - 1.8 - true - Secondary structure (predicted or real) of a protein. - - - - - - - - - - Protein features report (super-secondary) - - 1.8 - Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. - true - beta12orEarlier - Super-secondary structure of protein sequence(s). - - - - - - - - - - Secondary structure alignment (protein) - - - Alignment of the (1D representations of) secondary structure of two or more proteins. - beta12orEarlier - - - - - - - - - - Secondary structure alignment metadata (protein) - - An informative report on protein secondary structure alignment-derived data or metadata. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - RNA secondary structure - - - - - - - - An informative report of secondary structure (predicted or real) of an RNA molecule. - This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. - Moby:RNAStructML - Secondary structure (RNA) - beta12orEarlier - - - - - - - - - - Secondary structure alignment (RNA) - - Moby:RNAStructAlignmentML - Alignment of the (1D representations of) secondary structure of two or more RNA molecules. - beta12orEarlier - - - - - - - - - - Secondary structure alignment metadata (RNA) - - true - beta12orEarlier - An informative report of RNA secondary structure alignment-derived data or metadata. - beta12orEarlier - - - - - - - - - - Structure - - - - - - - - beta12orEarlier - Coordinate model - Structure data - The coordinate data may be predicted or real. - http://purl.bioontology.org/ontology/MSH/D015394 - 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure. - - - - - - - - - - Tertiary structure record - - true - beta12orEarlier - beta12orEarlier - An entry from a molecular tertiary (3D) structure database. - - - - - - - - - - Structure database search results - - 1.8 - Results (hits) from searching a database of tertiary structure. - beta12orEarlier - true - - - - - - - - - - Structure alignment - - - - - - - - Alignment (superimposition) of molecular tertiary (3D) structures. - A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition. - beta12orEarlier - - - - - - - - - - Structure alignment report - - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. - An informative report of molecular tertiary structure alignment-derived data. - - - - - - - - - - Structure similarity score - - beta12orEarlier - A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison. - - - - - - - - - - Structural profile - - - - - - - - beta12orEarlier - 3D profile - Some type of structural (3D) profile or template (representing a structure or structure alignment). - Structural (3D) profile - - - - - - - - - - Structural (3D) profile alignment - - beta12orEarlier - Structural profile alignment - A 3D profile-3D profile alignment (each profile representing structures or a structure alignment). - - - - - - - - - - Sequence-3D profile alignment - - Sequence-structural profile alignment - 1.5 - An alignment of a sequence to a 3D profile (representing structures or a structure alignment). - beta12orEarlier - true - - - - - - - - - - Protein sequence-structure scoring matrix - - beta12orEarlier - Matrix of values used for scoring sequence-structure compatibility. - - - - - - - - - - Sequence-structure alignment - - beta12orEarlier - An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)). - - - - - - - - - - Amino acid annotation - - An informative report about a specific amino acid. - 1.4 - true - beta12orEarlier - - - - - - - - - - Peptide annotation - - 1.4 - true - An informative report about a specific peptide. - beta12orEarlier - - - - - - - - - - Protein report - - Gene product annotation - beta12orEarlier - An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data. - - - - - - - - - - Protein property - - Protein physicochemical property - A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model. - beta12orEarlier - Protein sequence statistics - Protein properties - The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. - - - - - - - - - - Protein structural motifs and surfaces - - true - 1.8 - 3D structural motifs in a protein. - beta12orEarlier - Protein 3D motifs - - - - - - - - - Protein domain classification - - true - Data concerning the classification of the sequences and/or structures of protein structural domain(s). - 1.5 - beta12orEarlier - - - - - - - - - - Protein features report (domains) - - true - structural domains or 3D folds in a protein or polypeptide chain. - 1.8 - beta12orEarlier - - - - - - - - - - Protein architecture report - - 1.4 - An informative report on architecture (spatial arrangement of secondary structure) of a protein structure. - Protein property (architecture) - Protein structure report (architecture) - beta12orEarlier - true - - - - - - - - - - Protein folding report - - beta12orEarlier - A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc. - true - 1.8 - - - - - - - - - - Protein features (mutation) - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Data on the effect of (typically point) mutation on protein folding, stability, structure and function. - true - beta12orEarlier - Protein property (mutation) - Protein structure report (mutation) - beta13 - Protein report (mutation) - - - - - - - - - - Protein interaction raw data - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. - beta12orEarlier - - - - - - - - - - Protein interaction report - - - - - - - - beta12orEarlier - Protein report (interaction) - Protein interaction record - An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with some other molecule(s), which might be another protein, nucleic acid or some other ligand. - - - - - - - - - - Protein family report - - - - - - - - beta12orEarlier - An informative report on a specific protein family or other classification or group of protein sequences or structures. - Protein family annotation - Protein classification data - - - - - - - - - - Vmax - - beta12orEarlier - The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large. - - - - - - - - - - Km - - Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction. - beta12orEarlier - - - - - - - - - - Nucleotide base annotation - - beta12orEarlier - true - An informative report about a specific nucleotide base. - 1.4 - - - - - - - - - - Nucleic acid property - - A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule. - The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. - Nucleic acid physicochemical property - beta12orEarlier - - - - - - - - - - Codon usage data - - - - - - - - beta12orEarlier - Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences. - This is a broad data type and is used a placeholder for other, more specific types. - - - - - - - - - - Gene report - - Gene structure (repot) - A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. - Gene and transcript structure (report) - Gene features report - Nucleic acid features (gene and transcript structure) - Moby:gene - This includes any report on a particular locus or gene. This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s). - Gene annotation - beta12orEarlier - Moby_namespace:Human_Readable_Description - Gene function (report) - Moby:GeneInfo - - - - - - - - - - Gene classification - - beta12orEarlier - true - A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. - beta12orEarlier - - - - - - - - - - DNA variation - - stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. - true - 1.8 - beta12orEarlier - - - - - - - - - - Chromosome report - - - - - - - - beta12orEarlier - An informative report on a specific chromosome. - This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. - - - - - - - - - - Genotype/phenotype report - - An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes. - Genotype/phenotype annotation - beta12orEarlier - - - - - - - - - - Nucleic acid features report (primers) - - true - 1.8 - beta12orEarlier - PCR primers and hybridization oligos in a nucleic acid sequence. - - - - - - - - - - PCR experiment report - - true - beta12orEarlier - PCR experiments, e.g. quantitative real-time PCR. - 1.8 - - - - - - - - - - Sequence trace - - - Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores. - This is the raw data produced by a DNA sequencing machine. - beta12orEarlier - - - - - - - - - - Sequence assembly - - beta12orEarlier - An assembly of fragments of a (typically genomic) DNA sequence. - http://en.wikipedia.org/wiki/Sequence_assembly - SO:0001248 - Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included. - SO:0000353 - - - - - SO:0001248 - Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. - - - - - - - - - - Radiation Hybrid (RH) scores - - beta12orEarlier - Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. - Radiation hybrid scores (RH) scores for one or more markers. - - - - - - - - - - Genetic linkage report - - beta12orEarlier - Gene annotation (linkage) - Linkage disequilibrium (report) - An informative report on the linkage of alleles. - This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). - - - - - - - - - - Gene expression profile - - Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments. - beta12orEarlier - Gene expression pattern - - - - - - - - - - Microarray experiment report - - true - microarray experiments including conditions, protocol, sample:data relationships etc. - 1.8 - beta12orEarlier - - - - - - - - - - Oligonucleotide probe data - - beta12orEarlier - beta13 - true - Data on oligonucleotide probes (typically for use with DNA microarrays). - - - - - - - - - - SAGE experimental data - - beta12orEarlier - true - Output from a serial analysis of gene expression (SAGE) experiment. - Serial analysis of gene expression (SAGE) experimental data - beta12orEarlier - - - - - - - - - - MPSS experimental data - - beta12orEarlier - Massively parallel signature sequencing (MPSS) data. - beta12orEarlier - Massively parallel signature sequencing (MPSS) experimental data - true - - - - - - - - - - SBS experimental data - - beta12orEarlier - beta12orEarlier - true - Sequencing by synthesis (SBS) experimental data - Sequencing by synthesis (SBS) data. - - - - - - - - - - Sequence tag profile (with gene assignment) - - beta12orEarlier - Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers. - - - - - - - - - - Protein X-ray crystallographic data - - X-ray crystallography data. - beta12orEarlier - - - - - - - - - - Protein NMR data - - Protein nuclear magnetic resonance (NMR) raw data. - beta12orEarlier - - - - - - - - - - Protein circular dichroism (CD) spectroscopic data - - beta12orEarlier - Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data. - - - - - - - - - - Electron microscopy volume map - - - - - - - - beta12orEarlier - Volume map data from electron microscopy. - EM volume map - - - - - - - - - - Electron microscopy model - - - - - - - - beta12orEarlier - Annotation on a structural 3D model (volume map) from electron microscopy. - This might include the location in the model of the known features of a particular macromolecule. - - - - - - - - - - 2D PAGE image - - - - - - - - beta12orEarlier - Two-dimensional gel electrophoresis image - - - - - - - - - - Mass spectrometry spectra - - - - - - - - beta12orEarlier - Spectra from mass spectrometry. - - - - - - - - - - Peptide mass fingerprint - - - - - - - - - Peak list - Protein fingerprint - A set of peptide masses (peptide mass fingerprint) from mass spectrometry. - beta12orEarlier - - - - - - - - - - Peptide identification - - - - - - - - Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database. - beta12orEarlier - - - - - - - - - - Pathway or network annotation - - beta12orEarlier - true - An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway. - beta12orEarlier - - - - - - - - - - Biological pathway map - - beta12orEarlier - true - A map (typically a diagram) of a biological pathway. - beta12orEarlier - - - - - - - - - - Data resource definition - - beta12orEarlier - true - 1.5 - A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper. - - - - - - - - - - Workflow metadata - - Basic information, annotation or documentation concerning a workflow (but not the workflow itself). - beta12orEarlier - - - - - - - - - - Mathematical model - - - - - - - - Biological model - beta12orEarlier - A biological model represented in mathematical terms. - - - - - - - - - - Statistical estimate score - - beta12orEarlier - A value representing estimated statistical significance of some observed data; typically sequence database hits. - - - - - - - - - - EMBOSS database resource definition - - beta12orEarlier - Resource definition for an EMBOSS database. - true - 1.5 - - - - - - - - - - Version information - - "http://purl.obolibrary.org/obo/IAO_0000129" - 1.5 - Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. - http://www.ebi.ac.uk/swo/maturity/SWO_9000061 - beta12orEarlier - Information on a version of software or data, for example name, version number and release date. - http://semanticscience.org/resource/SIO_000653 - true - http://usefulinc.com/ns/doap#Version - - - - - - - - - - Database cross-mapping - - beta12orEarlier - A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases. - The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc. - - - - - - - - - - Data index - - - - - - - - An index of data of biological relevance. - beta12orEarlier - - - - - - - - - - Data index report - - - - - - - - A report of an analysis of an index of biological data. - Database index annotation - beta12orEarlier - - - - - - - - - - Database metadata - - Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc. - beta12orEarlier - - - - - - - - - - Tool metadata - - beta12orEarlier - Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation. - - - - - - - - - - Job metadata - - beta12orEarlier - true - 1.5 - Moby:PDGJOB - Textual metadata on a submitted or completed job. - - - - - - - - - - User metadata - - beta12orEarlier - Textual metadata on a software author or end-user, for example a person or other software. - - - - - - - - - - Small molecule report - - - - - - - - Small molecule annotation - Small molecule report - Chemical structure report - An informative report on a specific chemical compound. - beta12orEarlier - Chemical compound annotation - - - - - - - - - - Cell line report - - Organism strain data - Cell line annotation - Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on. - beta12orEarlier - - - - - - - - - - Scent annotation - - beta12orEarlier - An informative report about a specific scent. - 1.4 - true - - - - - - - - - - Ontology term - - Ontology class name - beta12orEarlier - A term (name) from an ontology. - Ontology terms - - - - - - - - - - Ontology concept data - - beta12orEarlier - Ontology class metadata - Ontology term metadata - Data concerning or derived from a concept from a biological ontology. - - - - - - - - - - Keyword - - Phrases - Keyword(s) or phrase(s) used (typically) for text-searching purposes. - Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. - Moby:QueryString - beta12orEarlier - Moby:BooleanQueryString - Moby:Wildcard_Query - Moby:Global_Keyword - Terms - Text - - - - - - - - - - Citation - - Bibliographic data that uniquely identifies a scientific article, book or other published material. - A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available. - Moby:GCP_SimpleCitation - Reference - Bibliographic reference - Moby:Publication - beta12orEarlier - - - - - - - - - - Article - - - - - - - - A document of scientific text, typically a full text article from a scientific journal. - beta12orEarlier - - - - - - - - - - Text mining report - - An abstract of the results of text mining. - beta12orEarlier - Text mining output - A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. - - - - - - - - - - Entity identifier - - beta12orEarlier - true - beta12orEarlier - An identifier of a biological entity or phenomenon. - - - - - - - - - - Data resource identifier - - true - An identifier of a data resource. - beta12orEarlier - beta12orEarlier - - - - - - - - - - Identifier (typed) - - beta12orEarlier - This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. - An identifier that identifies a particular type of data. - - - - - - - - - - - Tool identifier - - An identifier of a bioinformatics tool, e.g. an application or web service. - beta12orEarlier - - - - - - - - - - - Discrete entity identifier - - beta12orEarlier - true - beta12orEarlier - Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence). - - - - - - - - - - Entity feature identifier - - true - beta12orEarlier - Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing). - beta12orEarlier - - - - - - - - - - Entity collection identifier - - beta12orEarlier - true - beta12orEarlier - Name or other identifier of a collection of discrete biological entities. - - - - - - - - - - Phenomenon identifier - - beta12orEarlier - true - beta12orEarlier - Name or other identifier of a physical, observable biological occurrence or event. - - - - - - - - - - Molecule identifier - - Name or other identifier of a molecule. - beta12orEarlier - - - - - - - - - - - Atom ID - - Atom identifier - Identifier (e.g. character symbol) of a specific atom. - beta12orEarlier - - - - - - - - - - - Molecule name - - - Name of a specific molecule. - beta12orEarlier - - - - - - - - - - - Molecule type - - For example, 'Protein', 'DNA', 'RNA' etc. - true - 1.5 - beta12orEarlier - A label (text token) describing the type a molecule. - Protein|DNA|RNA - - - - - - - - - - Chemical identifier - - true - beta12orEarlier - beta12orEarlier - Unique identifier of a chemical compound. - - - - - - - - - - Chromosome name - - - - - - - - - beta12orEarlier - Name of a chromosome. - - - - - - - - - - - Peptide identifier - - Identifier of a peptide chain. - beta12orEarlier - - - - - - - - - - - Protein identifier - - - - - - - - beta12orEarlier - Identifier of a protein. - - - - - - - - - - - Compound name - - - Chemical name - Unique name of a chemical compound. - beta12orEarlier - - - - - - - - - - - Chemical registry number - - beta12orEarlier - Unique registry number of a chemical compound. - - - - - - - - - - - Ligand identifier - - true - beta12orEarlier - Code word for a ligand, for example from a PDB file. - beta12orEarlier - - - - - - - - - - Drug identifier - - - - - - - - beta12orEarlier - Identifier of a drug. - - - - - - - - - - - Amino acid identifier - - - - - - - - Identifier of an amino acid. - beta12orEarlier - Residue identifier - - - - - - - - - - - Nucleotide identifier - - beta12orEarlier - Name or other identifier of a nucleotide. - - - - - - - - - - - Monosaccharide identifier - - beta12orEarlier - Identifier of a monosaccharide. - - - - - - - - - - - Chemical name (ChEBI) - - ChEBI chemical name - Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound. - beta12orEarlier - This is the recommended chemical name for use for example in database annotation. - - - - - - - - - - - Chemical name (IUPAC) - - IUPAC recommended name of a chemical compound. - IUPAC chemical name - beta12orEarlier - - - - - - - - - - - Chemical name (INN) - - INN chemical name - beta12orEarlier - International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO). - - - - - - - - - - - Chemical name (brand) - - Brand name of a chemical compound. - Brand chemical name - beta12orEarlier - - - - - - - - - - - Chemical name (synonymous) - - beta12orEarlier - Synonymous chemical name - Synonymous name of a chemical compound. - - - - - - - - - - - Chemical registry number (CAS) - - CAS chemical registry number - CAS registry number of a chemical compound. - beta12orEarlier - - - - - - - - - - - Chemical registry number (Beilstein) - - Beilstein chemical registry number - beta12orEarlier - Beilstein registry number of a chemical compound. - - - - - - - - - - - Chemical registry number (Gmelin) - - Gmelin chemical registry number - beta12orEarlier - Gmelin registry number of a chemical compound. - - - - - - - - - - - HET group name - - 3-letter code word for a ligand (HET group) from a PDB file, for example ATP. - Short ligand name - Component identifier code - beta12orEarlier - - - - - - - - - - - Amino acid name - - String of one or more ASCII characters representing an amino acid. - beta12orEarlier - - - - - - - - - - - Nucleotide code - - - beta12orEarlier - String of one or more ASCII characters representing a nucleotide. - - - - - - - - - - - Polypeptide chain ID - - - - - - - - beta12orEarlier - WHATIF: chain - Chain identifier - Identifier of a polypeptide chain from a protein. - PDBML:pdbx_PDB_strand_id - Protein chain identifier - PDB strand id - PDB chain identifier - This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA - Polypeptide chain identifier - - - - - - - - - - - Protein name - - - Name of a protein. - beta12orEarlier - - - - - - - - - - - Enzyme identifier - - beta12orEarlier - Name or other identifier of an enzyme or record from a database of enzymes. - - - - - - - - - - - EC number - - [0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+ - EC code - Moby:EC_Number - An Enzyme Commission (EC) number of an enzyme. - EC - Moby:Annotated_EC_Number - beta12orEarlier - Enzyme Commission number - - - - - - - - - - - Enzyme name - - - Name of an enzyme. - beta12orEarlier - - - - - - - - - - - Restriction enzyme name - - Name of a restriction enzyme. - beta12orEarlier - - - - - - - - - - - Sequence position specification - - 1.5 - A specification (partial or complete) of one or more positions or regions of a molecular sequence or map. - beta12orEarlier - true - - - - - - - - - - Sequence feature ID - - - A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file. - beta12orEarlier - - - - - - - - - - - Sequence position - - WHATIF: number - WHATIF: PDBx_atom_site - beta12orEarlier - PDBML:_atom_site.id - SO:0000735 - A position of one or more points (base or residue) in a sequence, or part of such a specification. - - - - - - - - - - Sequence range - - beta12orEarlier - Specification of range(s) of sequence positions. - - - - - - - - - - Nucleic acid feature identifier - - beta12orEarlier - beta12orEarlier - Name or other identifier of an nucleic acid feature. - true - - - - - - - - - - Protein feature identifier - - Name or other identifier of a protein feature. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - Sequence feature key - - Sequence feature method - The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key. - Sequence feature type - beta12orEarlier - A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. - - - - - - - - - - Sequence feature qualifier - - beta12orEarlier - Typically one of the EMBL or Swiss-Prot feature qualifiers. - Feature qualifiers hold information about a feature beyond that provided by the feature key and location. - - - - - - - - - - Sequence feature label - - Sequence feature name - Typically an EMBL or Swiss-Prot feature label. - A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. - beta12orEarlier - - - - - - - - - - EMBOSS Uniform Feature Object - - - beta12orEarlier - UFO - The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications. - - - - - - - - - - Codon name - - beta12orEarlier - beta12orEarlier - String of one or more ASCII characters representing a codon. - true - - - - - - - - - - Gene identifier - - - - - - - - Moby:GeneAccessionList - An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database. - beta12orEarlier - - - - - - - - - - - Gene symbol - - Moby_namespace:Global_GeneSymbol - beta12orEarlier - Moby_namespace:Global_GeneCommonName - The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name. - - - - - - - - - - - Gene ID (NCBI) - - - NCBI geneid - Gene identifier (NCBI) - http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene - Entrez gene ID - Gene identifier (Entrez) - http://www.geneontology.org/doc/GO.xrf_abbs:LocusID - An NCBI unique identifier of a gene. - NCBI gene ID - beta12orEarlier - - - - - - - - - - - Gene identifier (NCBI RefSeq) - - beta12orEarlier - true - beta12orEarlier - An NCBI RefSeq unique identifier of a gene. - - - - - - - - - - Gene identifier (NCBI UniGene) - - beta12orEarlier - An NCBI UniGene unique identifier of a gene. - beta12orEarlier - true - - - - - - - - - - Gene identifier (Entrez) - - An Entrez unique identifier of a gene. - beta12orEarlier - true - [0-9]+ - beta12orEarlier - - - - - - - - - - Gene ID (CGD) - - CGD ID - Identifier of a gene or feature from the CGD database. - beta12orEarlier - - - - - - - - - - - Gene ID (DictyBase) - - beta12orEarlier - Identifier of a gene from DictyBase. - - - - - - - - - - - Ensembl gene ID - - - beta12orEarlier - Gene ID (Ensembl) - Unique identifier for a gene (or other feature) from the Ensembl database. - - - - - - - - - - - Gene ID (SGD) - - - Identifier of an entry from the SGD database. - S[0-9]+ - SGD identifier - beta12orEarlier - - - - - - - - - - - Gene ID (GeneDB) - - Moby_namespace:GeneDB - GeneDB identifier - beta12orEarlier - [a-zA-Z_0-9\.-]* - Identifier of a gene from the GeneDB database. - - - - - - - - - - - TIGR identifier - - - beta12orEarlier - Identifier of an entry from the TIGR database. - - - - - - - - - - - TAIR accession (gene) - - - Gene:[0-9]{7} - beta12orEarlier - Identifier of an gene from the TAIR database. - - - - - - - - - - - Protein domain ID - - - - - - - - - beta12orEarlier - Identifier of a protein structural domain. - This is typically a character or string concatenated with a PDB identifier and a chain identifier. - - - - - - - - - - - SCOP domain identifier - - Identifier of a protein domain (or other node) from the SCOP database. - beta12orEarlier - - - - - - - - - - - CATH domain ID - - 1nr3A00 - beta12orEarlier - CATH domain identifier - Identifier of a protein domain from CATH. - - - - - - - - - - - SCOP concise classification string (sccs) - - A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification. - beta12orEarlier - An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs. - - - - - - - - - - - SCOP sunid - - Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229. - beta12orEarlier - A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level. - sunid - SCOP unique identifier - 33229 - - - - - - - - - - - CATH node ID - - 3.30.1190.10.1.1.1.1.1 - CATH code - A code number identifying a node from the CATH database. - CATH node identifier - beta12orEarlier - - - - - - - - - - - Kingdom name - - The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes). - beta12orEarlier - - - - - - - - - - - Species name - - The name of a species (typically a taxonomic group) of organism. - Organism species - beta12orEarlier - - - - - - - - - - - Strain name - - - beta12orEarlier - The name of a strain of an organism variant, typically a plant, virus or bacterium. - - - - - - - - - - - URI - - A string of characters that name or otherwise identify a resource on the Internet. - URIs - beta12orEarlier - - - - - - - - - - Database ID - - - - - - - - An identifier of a biological or bioinformatics database. - Database identifier - beta12orEarlier - - - - - - - - - - - Directory name - - beta12orEarlier - The name of a directory. - - - - - - - - - - - File name - - The name (or part of a name) of a file (of any type). - beta12orEarlier - - - - - - - - - - - Ontology name - - - - - - - - - beta12orEarlier - Name of an ontology of biological or bioinformatics concepts and relations. - - - - - - - - - - - URL - - A Uniform Resource Locator (URL). - Moby:URL - Moby:Link - beta12orEarlier - - - - - - - - - - URN - - beta12orEarlier - A Uniform Resource Name (URN). - - - - - - - - - - LSID - - beta12orEarlier - LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>] - Life Science Identifier - A Life Science Identifier (LSID) - a unique identifier of some data. - - - - - - - - - - Database name - - - The name of a biological or bioinformatics database. - beta12orEarlier - - - - - - - - - - - Sequence database name - - The name of a molecular sequence database. - true - beta13 - beta12orEarlier - - - - - - - - - - Enumerated file name - - beta12orEarlier - The name of a file (of any type) with restricted possible values. - - - - - - - - - - - File name extension - - The extension of a file name. - A file extension is the characters appearing after the final '.' in the file name. - beta12orEarlier - - - - - - - - - - - File base name - - beta12orEarlier - The base name of a file. - A file base name is the file name stripped of its directory specification and extension. - - - - - - - - - - - QSAR descriptor name - - - - - - - - - beta12orEarlier - Name of a QSAR descriptor. - - - - - - - - - - - Database entry identifier - - true - This concept is required for completeness. It should never have child concepts. - beta12orEarlier - An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type. - beta12orEarlier - - - - - - - - - - Sequence identifier - - - - - - - - An identifier of molecular sequence(s) or entries from a molecular sequence database. - beta12orEarlier - - - - - - - - - - - Sequence set ID - - - - - - - - - An identifier of a set of molecular sequence(s). - beta12orEarlier - - - - - - - - - - - Sequence signature identifier - - beta12orEarlier - beta12orEarlier - true - Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns. - - - - - - - - - - - Sequence alignment ID - - - - - - - - - Identifier of a molecular sequence alignment, for example a record from an alignment database. - beta12orEarlier - - - - - - - - - - - Phylogenetic distance matrix identifier - - beta12orEarlier - Identifier of a phylogenetic distance matrix. - true - beta12orEarlier - - - - - - - - - - Phylogenetic tree ID - - - - - - - - - beta12orEarlier - Identifier of a phylogenetic tree for example from a phylogenetic tree database. - - - - - - - - - - - Comparison matrix identifier - - - - - - - - An identifier of a comparison matrix. - Substitution matrix identifier - beta12orEarlier - - - - - - - - - - - Structure ID - - - beta12orEarlier - A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database. - - - - - - - - - - - Structural (3D) profile ID - - - - - - - - - Structural profile identifier - Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment). - beta12orEarlier - - - - - - - - - - - Structure alignment ID - - - - - - - - - beta12orEarlier - Identifier of an entry from a database of tertiary structure alignments. - - - - - - - - - - - Amino acid index ID - - - - - - - - - Identifier of an index of amino acid physicochemical and biochemical property data. - beta12orEarlier - - - - - - - - - - - Protein interaction ID - - - - - - - - - beta12orEarlier - Molecular interaction ID - Identifier of a report of protein interactions from a protein interaction database (typically). - - - - - - - - - - - Protein family identifier - - - - - - - - Protein secondary database record identifier - Identifier of a protein family. - beta12orEarlier - - - - - - - - - - - Codon usage table name - - - - - - - - - - - - - - - Unique name of a codon usage table. - beta12orEarlier - - - - - - - - - - - Transcription factor identifier - - - Identifier of a transcription factor (or a TF binding site). - beta12orEarlier - - - - - - - - - - - Experiment annotation ID - - - - - - - - beta12orEarlier - Identifier of an entry from a database of microarray data. - - - - - - - - - - - Electron microscopy model ID - - - - - - - - - Identifier of an entry from a database of electron microscopy data. - beta12orEarlier - - - - - - - - - - - Gene expression report ID - - - - - - - - - Accession of a report of gene expression (e.g. a gene expression profile) from a database. - beta12orEarlier - Gene expression profile identifier - - - - - - - - - - - Genotype and phenotype annotation ID - - - - - - - - - Identifier of an entry from a database of genotypes and phenotypes. - beta12orEarlier - - - - - - - - - - - Pathway or network identifier - - - - - - - - Identifier of an entry from a database of biological pathways or networks. - beta12orEarlier - - - - - - - - - - - Workflow ID - - - beta12orEarlier - Identifier of a biological or biomedical workflow, typically from a database of workflows. - - - - - - - - - - - Data resource definition ID - - beta12orEarlier - Identifier of a data type definition from some provider. - Data resource definition identifier - - - - - - - - - - - Biological model ID - - - - - - - - Biological model identifier - beta12orEarlier - Identifier of a mathematical model, typically an entry from a database. - - - - - - - - - - - Compound identifier - - - - - - - - beta12orEarlier - Chemical compound identifier - Identifier of an entry from a database of chemicals. - Small molecule identifier - - - - - - - - - - - Ontology concept ID - - - A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. - beta12orEarlier - Ontology concept ID - - - - - - - - - - - Article ID - - - - - - - - - beta12orEarlier - Unique identifier of a scientific article. - Article identifier - - - - - - - - - - - FlyBase ID - - - Identifier of an object from the FlyBase database. - FB[a-zA-Z_0-9]{2}[0-9]{7} - beta12orEarlier - - - - - - - - - - - WormBase name - - - Name of an object from the WormBase database, usually a human-readable name. - beta12orEarlier - - - - - - - - - - - WormBase class - - beta12orEarlier - Class of an object from the WormBase database. - A WormBase class describes the type of object such as 'sequence' or 'protein'. - - - - - - - - - - - Sequence accession - - - beta12orEarlier - A persistent, unique identifier of a molecular sequence database entry. - Sequence accession number - - - - - - - - - - - Sequence type - - 1.5 - Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). - A label (text token) describing a type of molecular sequence. - true - beta12orEarlier - - - - - - - - - - EMBOSS Uniform Sequence Address - - - EMBOSS USA - beta12orEarlier - The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications. - - - - - - - - - - - Sequence accession (protein) - - - - - - - - Accession number of a protein sequence database entry. - Protein sequence accession number - beta12orEarlier - - - - - - - - - - - Sequence accession (nucleic acid) - - - - - - - - Accession number of a nucleotide sequence database entry. - beta12orEarlier - Nucleotide sequence accession number - - - - - - - - - - - RefSeq accession - - Accession number of a RefSeq database entry. - beta12orEarlier - RefSeq ID - (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+ - - - - - - - - - - - UniProt accession (extended) - - true - Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. - [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+ - beta12orEarlier - Q7M1G0|P43353-2|P01012.107 - 1.0 - - - - - - - - - - PIR identifier - - - - - - - - An identifier of PIR sequence database entry. - beta12orEarlier - PIR ID - PIR accession number - - - - - - - - - - - TREMBL accession - - beta12orEarlier - Identifier of a TREMBL sequence database entry. - true - 1.2 - - - - - - - - - - Gramene primary identifier - - beta12orEarlier - Gramene primary ID - Primary identifier of a Gramene database entry. - - - - - - - - - - - EMBL/GenBank/DDBJ ID - - Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases. - beta12orEarlier - - - - - - - - - - - Sequence cluster ID (UniGene) - - UniGene identifier - UniGene cluster id - UniGene ID - UniGene cluster ID - beta12orEarlier - A unique identifier of an entry (gene cluster) from the NCBI UniGene database. - - - - - - - - - - - dbEST accession - - - dbEST ID - Identifier of a dbEST database entry. - beta12orEarlier - - - - - - - - - - - dbSNP ID - - beta12orEarlier - dbSNP identifier - Identifier of a dbSNP database entry. - - - - - - - - - - - EMBOSS sequence type - - beta12orEarlier - true - See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. - beta12orEarlier - The EMBOSS type of a molecular sequence. - - - - - - - - - - EMBOSS listfile - - 1.5 - List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile). - true - beta12orEarlier - - - - - - - - - - Sequence cluster ID - - - - - - - - An identifier of a cluster of molecular sequence(s). - beta12orEarlier - - - - - - - - - - - Sequence cluster ID (COG) - - COG ID - beta12orEarlier - Unique identifier of an entry from the COG database. - - - - - - - - - - - Sequence motif identifier - - - - - - - - Identifier of a sequence motif, for example an entry from a motif database. - beta12orEarlier - - - - - - - - - - - Sequence profile ID - - - - - - - - - Identifier of a sequence profile. - beta12orEarlier - A sequence profile typically represents a sequence alignment. - - - - - - - - - - - ELM ID - - Identifier of an entry from the ELMdb database of protein functional sites. - beta12orEarlier - - - - - - - - - - - Prosite accession number - - beta12orEarlier - Accession number of an entry from the Prosite database. - PS[0-9]{5} - Prosite ID - - - - - - - - - - - HMMER hidden Markov model ID - - - - - - - - Unique identifier or name of a HMMER hidden Markov model. - beta12orEarlier - - - - - - - - - - - JASPAR profile ID - - beta12orEarlier - Unique identifier or name of a profile from the JASPAR database. - - - - - - - - - - - Sequence alignment type - - beta12orEarlier - 1.5 - true - Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. - A label (text token) describing the type of a sequence alignment. - - - - - - - - - - BLAST sequence alignment type - - true - beta12orEarlier - beta12orEarlier - The type of a BLAST sequence alignment. - - - - - - - - - - Phylogenetic tree type - - For example 'nj', 'upgmp' etc. - beta12orEarlier - true - A label (text token) describing the type of a phylogenetic tree. - 1.5 - nj|upgmp - - - - - - - - - - TreeBASE study accession number - - Accession number of an entry from the TreeBASE database. - beta12orEarlier - - - - - - - - - - - TreeFam accession number - - beta12orEarlier - Accession number of an entry from the TreeFam database. - - - - - - - - - - - Comparison matrix type - - 1.5 - true - beta12orEarlier - blosum|pam|gonnet|id - A label (text token) describing the type of a comparison matrix. - Substitution matrix type - For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. - - - - - - - - - - Comparison matrix name - - - - - - - - - beta12orEarlier - Substitution matrix name - See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. - Unique name or identifier of a comparison matrix. - - - - - - - - - - - PDB ID - - An identifier of an entry from the PDB database. - [a-zA-Z_0-9]{4} - PDBID - PDB identifier - beta12orEarlier - - - - - - - - - - - AAindex ID - - beta12orEarlier - Identifier of an entry from the AAindex database. - - - - - - - - - - - BIND accession number - - Accession number of an entry from the BIND database. - beta12orEarlier - - - - - - - - - - - IntAct accession number - - EBI\-[0-9]+ - beta12orEarlier - Accession number of an entry from the IntAct database. - - - - - - - - - - - Protein family name - - - beta12orEarlier - Name of a protein family. - - - - - - - - - - - InterPro entry name - - - - - - - - beta12orEarlier - Name of an InterPro entry, usually indicating the type of protein matches for that entry. - - - - - - - - - - - InterPro accession - - - - - - - - Primary accession number of an InterPro entry. - InterPro primary accession - Every InterPro entry has a unique accession number to provide a persistent citation of database records. - beta12orEarlier - InterPro primary accession number - IPR015590 - IPR[0-9]{6} - - - - - - - - - - - InterPro secondary accession - - - - - - - - Secondary accession number of an InterPro entry. - beta12orEarlier - InterPro secondary accession number - - - - - - - - - - - Gene3D ID - - beta12orEarlier - Unique identifier of an entry from the Gene3D database. - - - - - - - - - - - PIRSF ID - - PIRSF[0-9]{6} - beta12orEarlier - Unique identifier of an entry from the PIRSF database. - - - - - - - - - - - PRINTS code - - beta12orEarlier - PR[0-9]{5} - The unique identifier of an entry in the PRINTS database. - - - - - - - - - - - Pfam accession number - - PF[0-9]{5} - Accession number of a Pfam entry. - beta12orEarlier - - - - - - - - - - - SMART accession number - - Accession number of an entry from the SMART database. - beta12orEarlier - SM[0-9]{5} - - - - - - - - - - - Superfamily hidden Markov model number - - Unique identifier (number) of a hidden Markov model from the Superfamily database. - beta12orEarlier - - - - - - - - - - - TIGRFam ID - - TIGRFam accession number - Accession number of an entry (family) from the TIGRFam database. - beta12orEarlier - - - - - - - - - - - ProDom accession number - - A ProDom domain family accession number. - PD[0-9]+ - beta12orEarlier - ProDom is a protein domain family database. - - - - - - - - - - - TRANSFAC accession number - - beta12orEarlier - Identifier of an entry from the TRANSFAC database. - - - - - - - - - - - ArrayExpress accession number - - Accession number of an entry from the ArrayExpress database. - beta12orEarlier - [AEP]-[a-zA-Z_0-9]{4}-[0-9]+ - ArrayExpress experiment ID - - - - - - - - - - - PRIDE experiment accession number - - [0-9]+ - beta12orEarlier - PRIDE experiment accession number. - - - - - - - - - - - EMDB ID - - beta12orEarlier - Identifier of an entry from the EMDB electron microscopy database. - - - - - - - - - - - GEO accession number - - Accession number of an entry from the GEO database. - o^GDS[0-9]+ - beta12orEarlier - - - - - - - - - - - GermOnline ID - - beta12orEarlier - Identifier of an entry from the GermOnline database. - - - - - - - - - - - EMAGE ID - - Identifier of an entry from the EMAGE database. - beta12orEarlier - - - - - - - - - - - Disease ID - - - - - - - - - Identifier of an entry from a database of disease. - beta12orEarlier - - - - - - - - - - - HGVbase ID - - Identifier of an entry from the HGVbase database. - beta12orEarlier - - - - - - - - - - - HIVDB identifier - - true - beta12orEarlier - Identifier of an entry from the HIVDB database. - beta12orEarlier - - - - - - - - - - OMIM ID - - beta12orEarlier - [*#+%^]?[0-9]{6} - Identifier of an entry from the OMIM database. - - - - - - - - - - - KEGG object identifier - - - beta12orEarlier - Unique identifier of an object from one of the KEGG databases (excluding the GENES division). - - - - - - - - - - - Pathway ID (reactome) - - Identifier of an entry from the Reactome database. - Reactome ID - beta12orEarlier - REACT_[0-9]+(\.[0-9]+)? - - - - - - - - - - - Pathway ID (aMAZE) - - beta12orEarlier - aMAZE ID - true - beta12orEarlier - Identifier of an entry from the aMAZE database. - - - - - - - - - - Pathway ID (BioCyc) - - - BioCyc pathway ID - beta12orEarlier - Identifier of an pathway from the BioCyc biological pathways database. - - - - - - - - - - - Pathway ID (INOH) - - beta12orEarlier - INOH identifier - Identifier of an entry from the INOH database. - - - - - - - - - - - Pathway ID (PATIKA) - - Identifier of an entry from the PATIKA database. - PATIKA ID - beta12orEarlier - - - - - - - - - - - Pathway ID (CPDB) - - This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined. - CPDB ID - Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB. - beta12orEarlier - - - - - - - - - - - Pathway ID (Panther) - - Identifier of a biological pathway from the Panther Pathways database. - beta12orEarlier - PTHR[0-9]{5} - Panther Pathways ID - - - - - - - - - - - MIRIAM identifier - - - - - - - - Unique identifier of a MIRIAM data resource. - MIR:00100005 - MIR:[0-9]{8} - beta12orEarlier - This is the identifier used internally by MIRIAM for a data type. - - - - - - - - - - - MIRIAM data type name - - - - - - - - beta12orEarlier - The name of a data type from the MIRIAM database. - - - - - - - - - - - MIRIAM URI - - - - - - - - - beta12orEarlier - The URI (URL or URN) of a data entity from the MIRIAM database. - identifiers.org synonym - urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 - A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term. - - - - - - - - - - - MIRIAM data type primary name - - beta12orEarlier - The primary name of a MIRIAM data type is taken from a controlled vocabulary. - UniProt|Enzyme Nomenclature - The primary name of a data type from the MIRIAM database. - - - - - - A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. - UniProt|Enzyme Nomenclature - - - - - - - - - - MIRIAM data type synonymous name - - A synonymous name of a data type from the MIRIAM database. - A synonymous name for a MIRIAM data type taken from a controlled vocabulary. - beta12orEarlier - - - - - - - - - - - Taverna workflow ID - - beta12orEarlier - Unique identifier of a Taverna workflow. - - - - - - - - - - - Biological model name - - - beta12orEarlier - Name of a biological (mathematical) model. - - - - - - - - - - - BioModel ID - - Unique identifier of an entry from the BioModel database. - beta12orEarlier - (BIOMD|MODEL)[0-9]{10} - - - - - - - - - - - PubChem CID - - - [0-9]+ - PubChem compound accession identifier - Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure. - beta12orEarlier - - - - - - - - - - - ChemSpider ID - - Identifier of an entry from the ChemSpider database. - beta12orEarlier - [0-9]+ - - - - - - - - - - - ChEBI ID - - Identifier of an entry from the ChEBI database. - ChEBI IDs - ChEBI identifier - CHEBI:[0-9]+ - beta12orEarlier - - - - - - - - - - - BioPax concept ID - - beta12orEarlier - An identifier of a concept from the BioPax ontology. - - - - - - - - - - - GO concept ID - - GO concept identifier - [0-9]{7}|GO:[0-9]{7} - beta12orEarlier - An identifier of a concept from The Gene Ontology. - - - - - - - - - - - MeSH concept ID - - beta12orEarlier - An identifier of a concept from the MeSH vocabulary. - - - - - - - - - - - HGNC concept ID - - beta12orEarlier - An identifier of a concept from the HGNC controlled vocabulary. - - - - - - - - - - - NCBI taxonomy ID - - - NCBI taxonomy identifier - [1-9][0-9]{0,8} - NCBI tax ID - A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database. - 9662|3483|182682 - beta12orEarlier - - - - - - - - - - - Plant Ontology concept ID - - An identifier of a concept from the Plant Ontology (PO). - beta12orEarlier - - - - - - - - - - - UMLS concept ID - - An identifier of a concept from the UMLS vocabulary. - beta12orEarlier - - - - - - - - - - - FMA concept ID - - An identifier of a concept from Foundational Model of Anatomy. - FMA:[0-9]+ - Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. - beta12orEarlier - - - - - - - - - - - EMAP concept ID - - beta12orEarlier - An identifier of a concept from the EMAP mouse ontology. - - - - - - - - - - - ChEBI concept ID - - beta12orEarlier - An identifier of a concept from the ChEBI ontology. - - - - - - - - - - - MGED concept ID - - beta12orEarlier - An identifier of a concept from the MGED ontology. - - - - - - - - - - - myGrid concept ID - - beta12orEarlier - The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. - An identifier of a concept from the myGrid ontology. - - - - - - - - - - - PubMed ID - - PMID - [1-9][0-9]{0,8} - PubMed unique identifier of an article. - beta12orEarlier - 4963447 - - - - - - - - - - - DOI - - beta12orEarlier - (doi\:)?[0-9]{2}\.[0-9]{4}/.* - Digital Object Identifier - Digital Object Identifier (DOI) of a published article. - - - - - - - - - - - Medline UI - - beta12orEarlier - Medline UI (unique identifier) of an article. - The use of Medline UI has been replaced by the PubMed unique identifier. - Medline unique identifier - - - - - - - - - - - Tool name - - The name of a computer package, application, method or function. - beta12orEarlier - - - - - - - - - - - Tool name (signature) - - beta12orEarlier - The unique name of a signature (sequence classifier) method. - Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. - - - - - - - - - - - Tool name (BLAST) - - This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. - The name of a BLAST tool. - beta12orEarlier - BLAST name - - - - - - - - - - - Tool name (FASTA) - - beta12orEarlier - The name of a FASTA tool. - This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. - - - - - - - - - - - Tool name (EMBOSS) - - The name of an EMBOSS application. - beta12orEarlier - - - - - - - - - - - Tool name (EMBASSY package) - - The name of an EMBASSY package. - beta12orEarlier - - - - - - - - - - - QSAR descriptor (constitutional) - - A QSAR constitutional descriptor. - beta12orEarlier - QSAR constitutional descriptor - - - - - - - - - - QSAR descriptor (electronic) - - beta12orEarlier - A QSAR electronic descriptor. - QSAR electronic descriptor - - - - - - - - - - QSAR descriptor (geometrical) - - QSAR geometrical descriptor - A QSAR geometrical descriptor. - beta12orEarlier - - - - - - - - - - QSAR descriptor (topological) - - beta12orEarlier - QSAR topological descriptor - A QSAR topological descriptor. - - - - - - - - - - QSAR descriptor (molecular) - - A QSAR molecular descriptor. - QSAR molecular descriptor - beta12orEarlier - - - - - - - - - - Sequence set (protein) - - Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. - beta12orEarlier - - - - - - - - - - Sequence set (nucleic acid) - - beta12orEarlier - Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. - - - - - - - - - - Sequence cluster - - - - - - - - - - - - - - A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information. - The cluster might include sequences identifiers, short descriptions, alignment and summary information. - beta12orEarlier - - - - - - - - - - Psiblast checkpoint file - - beta12orEarlier - A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. - beta12orEarlier - true - A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration. - - - - - - - - - - HMMER synthetic sequences set - - Sequences generated by HMMER package in FASTA-style format. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Proteolytic digest - - - - - - - - beta12orEarlier - A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. - - - - - - - - - - Restriction digest - - Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. - SO:0000412 - beta12orEarlier - - - - - - - - - - PCR primers - - beta12orEarlier - Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set. - - - - - - - - - - vectorstrip cloning vector definition file - - beta12orEarlier - true - File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format. - beta12orEarlier - - - - - - - - - - Primer3 internal oligo mishybridizing library - - true - beta12orEarlier - A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. - beta12orEarlier - - - - - - - - - - Primer3 mispriming library file - - true - A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format. - beta12orEarlier - beta12orEarlier - - - - - - - - - - primersearch primer pairs sequence record - - true - beta12orEarlier - beta12orEarlier - File of one or more pairs of primer sequences, as used by EMBOSS primersearch application. - - - - - - - - - - Sequence cluster (protein) - - - Protein sequence cluster - The sequences are typically related, for example a family of sequences. - beta12orEarlier - A cluster of protein sequences. - - - - - - - - - - Sequence cluster (nucleic acid) - - - A cluster of nucleotide sequences. - Nucleotide sequence cluster - beta12orEarlier - The sequences are typically related, for example a family of sequences. - - - - - - - - - - Sequence length - - beta12orEarlier - The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths. - - - - - - - - - - Word size - - Word size is used for example in word-based sequence database search methods. - Word length - 1.5 - Size of a sequence word. - true - beta12orEarlier - - - - - - - - - - Window size - - 1.5 - true - A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. - beta12orEarlier - Size of a sequence window. - - - - - - - - - - Sequence length range - - true - Specification of range(s) of length of sequences. - beta12orEarlier - 1.5 - - - - - - - - - - Sequence information report - - Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Sequence property - - beta12orEarlier - An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis. - Sequence properties report - - - - - - - - - - Sequence features - - Sequence features report - beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D058977 - SO:0000110 - This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. - General sequence features - Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence. - Features - Feature record - - - - - - - - - - Sequence features (comparative) - - Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc. - beta13 - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - true - beta12orEarlier - - - - - - - - - - Sequence property (protein) - - true - A report of general sequence properties derived from protein sequence data. - beta12orEarlier - beta12orEarlier - - - - - - - - - - Sequence property (nucleic acid) - - A report of general sequence properties derived from nucleotide sequence data. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Sequence complexity report - - A report on sequence complexity, for example low-complexity or repeat regions in sequences. - beta12orEarlier - Sequence property (complexity) - - - - - - - - - - Sequence ambiguity report - - A report on ambiguity in molecular sequence(s). - Sequence property (ambiguity) - beta12orEarlier - - - - - - - - - - Sequence composition report - - beta12orEarlier - A report (typically a table) on character or word composition / frequency of a molecular sequence(s). - Sequence property (composition) - - - - - - - - - - Peptide molecular weight hits - - A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. - beta12orEarlier - - - - - - - - - - Base position variability plot - - beta12orEarlier - A plot of third base position variability in a nucleotide sequence. - - - - - - - - - - Sequence composition table - - A table of character or word composition / frequency of a molecular sequence. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Base frequencies table - - - beta12orEarlier - A table of base frequencies of a nucleotide sequence. - - - - - - - - - - Base word frequencies table - - - A table of word composition of a nucleotide sequence. - beta12orEarlier - - - - - - - - - - Amino acid frequencies table - - - Sequence composition (amino acid frequencies) - A table of amino acid frequencies of a protein sequence. - beta12orEarlier - - - - - - - - - - Amino acid word frequencies table - - - A table of amino acid word composition of a protein sequence. - Sequence composition (amino acid words) - beta12orEarlier - - - - - - - - - - DAS sequence feature annotation - - beta12orEarlier - Annotation of a molecular sequence in DAS format. - beta12orEarlier - true - - - - - - - - - - Feature table - - Sequence feature table - beta12orEarlier - Annotation of positional sequence features, organized into a standard feature table. - - - - - - - - - - Map - - - - - - - - DNA map - beta12orEarlier - A map of (typically one) DNA sequence annotated with positional or non-positional features. - - - - - - - - - - Nucleic acid features - - - An informative report on intrinsic positional features of a nucleotide sequence. - beta12orEarlier - Genome features - This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. - Genomic features - Nucleic acid feature table - Feature table (nucleic acid) - - - - - - - - - - Protein features - - - An informative report on intrinsic positional features of a protein sequence. - beta12orEarlier - This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. - Feature table (protein) - Protein feature table - - - - - - - - - - Genetic map - - A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies. - beta12orEarlier - A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms. - Linkage map - Moby:GeneticMap - - - - - - - - - - Sequence map - - A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. - beta12orEarlier - A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs. - - - - - - - - - - Physical map - - A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them. - Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing. - beta12orEarlier - - - - - - - - - - Sequence signature map - - true - Image of a sequence with matches to signatures, motifs or profiles. - beta12orEarlier - beta12orEarlier - - - - - - - - - - Cytogenetic map - - beta12orEarlier - A map showing banding patterns derived from direct observation of a stained chromosome. - Cytologic map - Chromosome map - Cytogenic map - This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms. - - - - - - - - - - DNA transduction map - - beta12orEarlier - A gene map showing distances between loci based on relative cotransduction frequencies. - - - - - - - - - - Gene map - - Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene. - beta12orEarlier - - - - - - - - - - Plasmid map - - Sequence map of a plasmid (circular DNA). - beta12orEarlier - - - - - - - - - - Genome map - - beta12orEarlier - Sequence map of a whole genome. - - - - - - - - - - Restriction map - - - Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence. - beta12orEarlier - - - - - - - - - - InterPro compact match image - - beta12orEarlier - Image showing matches between protein sequence(s) and InterPro Entries. - The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches. - beta12orEarlier - true - - - - - - - - - - InterPro detailed match image - - beta12orEarlier - beta12orEarlier - Image showing detailed information on matches between protein sequence(s) and InterPro Entries. - The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. - true - - - - - - - - - - InterPro architecture image - - beta12orEarlier - beta12orEarlier - true - The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein. - Image showing the architecture of InterPro domains in a protein sequence. - - - - - - - - - - SMART protein schematic - - true - beta12orEarlier - beta12orEarlier - SMART protein schematic in PNG format. - - - - - - - - - - GlobPlot domain image - - beta12orEarlier - beta12orEarlier - true - Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. - - - - - - - - - - Sequence motif matches - - beta12orEarlier - Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences. - 1.8 - true - - - - - - - - - - Sequence features (repeats) - - beta12orEarlier - true - 1.5 - Repeat sequence map - The report might include derived data map such as classification, annotation, organization, periodicity etc. - Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. - - - - - - - - - - - Gene and transcript structure (report) - - 1.5 - beta12orEarlier - A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. - true - - - - - - - - - - Mobile genetic elements - - true - beta12orEarlier - regions of a nucleic acid sequence containing mobile genetic elements. - 1.8 - - - - - - - - - - Nucleic acid features report (PolyA signal or site) - - true - regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. - 1.8 - beta12orEarlier - - - - - - - - - - Nucleic acid features (quadruplexes) - - true - 1.5 - A report on quadruplex-forming motifs in a nucleotide sequence. - beta12orEarlier - - - - - - - - - - Nucleic acid features report (CpG island and isochore) - - 1.8 - CpG rich regions (isochores) in a nucleotide sequence. - beta12orEarlier - true - - - - - - - - - - Nucleic acid features report (restriction sites) - - beta12orEarlier - true - 1.8 - restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. - - - - - - - - - - Nucleosome exclusion sequences - - beta12orEarlier - true - Report on nucleosome formation potential or exclusion sequence(s). - 1.8 - - - - - - - - - - Nucleic acid features report (splice sites) - - splice sites in a nucleotide sequence or alternative RNA splicing events. - beta12orEarlier - true - 1.8 - - - - - - - - - - Nucleic acid features report (matrix/scaffold attachment sites) - - 1.8 - matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. - true - beta12orEarlier - - - - - - - - - - Gene features (exonic splicing enhancer) - - beta12orEarlier - beta13 - true - A report on exonic splicing enhancers (ESE) in an exon. - - - - - - - - - - Nucleic acid features (microRNA) - - true - beta12orEarlier - A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc. - 1.5 - - - - - - - - - - Gene features report (operon) - - true - operons (operators, promoters and genes) from a bacterial genome. - 1.8 - beta12orEarlier - - - - - - - - - - Nucleic acid features report (promoters) - - 1.8 - whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. - true - beta12orEarlier - - - - - - - - - - Coding region - - beta12orEarlier - protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. - 1.8 - true - - - - - - - - - - Gene features (SECIS element) - - beta12orEarlier - beta13 - A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. - true - - - - - - - - - - Transcription factor binding sites - - transcription factor binding sites (TFBS) in a DNA sequence. - beta12orEarlier - true - 1.8 - - - - - - - - - - Protein features (sites) - - true - beta12orEarlier - Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. - beta12orEarlier - A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites. - - - - - - - - - - Protein features report (signal peptides) - - true - signal peptides or signal peptide cleavage sites in protein sequences. - 1.8 - beta12orEarlier - - - - - - - - - - Protein features report (cleavage sites) - - true - 1.8 - cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. - beta12orEarlier - - - - - - - - - - Protein features (post-translation modifications) - - true - beta12orEarlier - post-translation modifications in a protein sequence, typically describing the specific sites involved. - 1.8 - - - - - - - - - - Protein features report (active sites) - - 1.8 - true - beta12orEarlier - catalytic residues (active site) of an enzyme. - - - - - - - - - - Protein features report (binding sites) - - beta12orEarlier - ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. - true - 1.8 - - - - - - - - - - Protein features (epitopes) - - A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data. - beta13 - beta12orEarlier - Epitope mapping is commonly done during vaccine design. - true - - - - - - - - - - Protein features report (nucleic acid binding sites) - - true - beta12orEarlier - 1.8 - RNA and DNA-binding proteins and binding sites in protein sequences. - - - - - - - - - - MHC Class I epitopes report - - beta12orEarlier - beta12orEarlier - true - A report on epitopes that bind to MHC class I molecules. - - - - - - - - - - MHC Class II epitopes report - - beta12orEarlier - beta12orEarlier - true - A report on predicted epitopes that bind to MHC class II molecules. - - - - - - - - - - Protein features (PEST sites) - - beta12orEarlier - A report or plot of PEST sites in a protein sequence. - true - beta13 - 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. - - - - - - - - - - Sequence database hits scores list - - Scores from a sequence database search (for example a BLAST search). - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Sequence database hits alignments list - - beta12orEarlier - Alignments from a sequence database search (for example a BLAST search). - beta12orEarlier - true - - - - - - - - - - Sequence database hits evaluation data - - beta12orEarlier - A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search). - beta12orEarlier - true - - - - - - - - - - MEME motif alphabet - - Alphabet for the motifs (patterns) that MEME will search for. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - MEME background frequencies file - - MEME background frequencies file. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - MEME motifs directive file - - beta12orEarlier - true - File of directives for ordering and spacing of MEME motifs. - beta12orEarlier - - - - - - - - - - Dirichlet distribution - - Dirichlet distribution used by hidden Markov model analysis programs. - beta12orEarlier - - - - - - - - - - HMM emission and transition counts - - Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states. - true - 1.4 - beta12orEarlier - - - - - - - - - - - Regular expression - - Regular expression pattern. - beta12orEarlier - - - - - - - - - - Sequence motif - - - - - - - - beta12orEarlier - Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence. - - - - - - - - - - Sequence profile - - - - - - - - Some type of statistical model representing a (typically multiple) sequence alignment. - http://semanticscience.org/resource/SIO_010531 - beta12orEarlier - - - - - - - - - - Protein signature - - An informative report about a specific or conserved protein sequence pattern. - InterPro entry - Protein repeat signature - Protein region signature - Protein site signature - beta12orEarlier - Protein family signature - Protein domain signature - - - - - - - - - - Prosite nucleotide pattern - - A nucleotide regular expression pattern from the Prosite database. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Prosite protein pattern - - A protein regular expression pattern from the Prosite database. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Position frequency matrix - - beta12orEarlier - PFM - A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position. - - - - - - - - - - Position weight matrix - - PWM - beta12orEarlier - A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position. - Contributions of individual sequences to the matrix might be uneven (weighted). - - - - - - - - - - Information content matrix - - beta12orEarlier - ICM - A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position. - - - - - - - - - - Hidden Markov model - - HMM - beta12orEarlier - A hidden Markov model representation of a set or alignment of sequences. - - - - - - - - - - Fingerprint - - beta12orEarlier - One or more fingerprints (sequence classifiers) as used in the PRINTS database. - - - - - - - - - - Domainatrix signature - - A protein signature of the type used in the EMBASSY Signature package. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - HMMER NULL hidden Markov model - - beta12orEarlier - beta12orEarlier - true - NULL hidden Markov model representation used by the HMMER package. - - - - - - - - - - Protein family signature - - Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures. - beta12orEarlier - true - 1.5 - A protein family signature (sequence classifier) from the InterPro database. - - - - - - - - - - Protein domain signature - - beta12orEarlier - 1.5 - true - A protein domain signature (sequence classifier) from the InterPro database. - Protein domain signatures identify structural or functional domains or other units with defined boundaries. - - - - - - - - - - Protein region signature - - A protein region signature (sequence classifier) from the InterPro database. - true - beta12orEarlier - 1.5 - A protein region signature defines a region which cannot be described as a protein family or domain signature. - - - - - - - - - - Protein repeat signature - - true - 1.5 - A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. - beta12orEarlier - A protein repeat signature (sequence classifier) from the InterPro database. - - - - - - - - - - Protein site signature - - A protein site signature is a classifier for a specific site in a protein. - beta12orEarlier - A protein site signature (sequence classifier) from the InterPro database. - true - 1.5 - - - - - - - - - - Protein conserved site signature - - 1.4 - true - A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. - A protein conserved site signature (sequence classifier) from the InterPro database. - beta12orEarlier - - - - - - - - - - Protein active site signature - - A protein active site signature (sequence classifier) from the InterPro database. - A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available. - true - 1.4 - beta12orEarlier - - - - - - - - - - Protein binding site signature - - 1.4 - A protein binding site signature (sequence classifier) from the InterPro database. - true - A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification. - beta12orEarlier - - - - - - - - - - Protein post-translational modification signature - - A protein post-translational modification signature (sequence classifier) from the InterPro database. - A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. - 1.4 - beta12orEarlier - true - - - - - - - - - - Sequence alignment (pair) - - http://semanticscience.org/resource/SIO_010068 - beta12orEarlier - Alignment of exactly two molecular sequences. - - - - - - - - - - Sequence alignment (multiple) - - beta12orEarlier - beta12orEarlier - Alignment of more than two molecular sequences. - true - - - - - - - - - - Sequence alignment (nucleic acid) - - beta12orEarlier - Alignment of multiple nucleotide sequences. - - - - - - - - - - Sequence alignment (protein) - - - Alignment of multiple protein sequences. - beta12orEarlier - - - - - - - - - - Sequence alignment (hybrid) - - Alignment of multiple molecular sequences of different types. - Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. - beta12orEarlier - - - - - - - - - - Sequence alignment (nucleic acid pair) - - - beta12orEarlier - Alignment of exactly two nucleotide sequences. - - - - - - - - - - Sequence alignment (protein pair) - - - Alignment of exactly two protein sequences. - beta12orEarlier - - - - - - - - - - Hybrid sequence alignment (pair) - - true - beta12orEarlier - beta12orEarlier - Alignment of exactly two molecular sequences of different types. - - - - - - - - - - Multiple nucleotide sequence alignment - - beta12orEarlier - Alignment of more than two nucleotide sequences. - true - beta12orEarlier - - - - - - - - - - Multiple protein sequence alignment - - true - beta12orEarlier - beta12orEarlier - Alignment of more than two protein sequences. - - - - - - - - - - Alignment score or penalty - - beta12orEarlier - A simple floating point number defining the penalty for opening or extending a gap in an alignment. - - - - - - - - - - Score end gaps control - - beta12orEarlier - beta12orEarlier - Whether end gaps are scored or not. - true - - - - - - - - - - Aligned sequence order - - beta12orEarlier - beta12orEarlier - true - Controls the order of sequences in an output sequence alignment. - - - - - - - - - - Gap opening penalty - - A penalty for opening a gap in an alignment. - beta12orEarlier - - - - - - - - - - Gap extension penalty - - A penalty for extending a gap in an alignment. - beta12orEarlier - - - - - - - - - - Gap separation penalty - - beta12orEarlier - A penalty for gaps that are close together in an alignment. - - - - - - - - - - Terminal gap penalty - - beta12orEarlier - A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. - true - beta12orEarlier - - - - - - - - - - - Match reward score - - beta12orEarlier - The score for a 'match' used in various sequence database search applications with simple scoring schemes. - - - - - - - - - - Mismatch penalty score - - beta12orEarlier - The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. - - - - - - - - - - Drop off score - - This is the threshold drop in score at which extension of word alignment is halted. - beta12orEarlier - - - - - - - - - - Gap opening penalty (integer) - - beta12orEarlier - true - A simple floating point number defining the penalty for opening a gap in an alignment. - beta12orEarlier - - - - - - - - - - Gap opening penalty (float) - - beta12orEarlier - beta12orEarlier - A simple floating point number defining the penalty for opening a gap in an alignment. - true - - - - - - - - - - Gap extension penalty (integer) - - true - A simple floating point number defining the penalty for extending a gap in an alignment. - beta12orEarlier - beta12orEarlier - - - - - - - - - - Gap extension penalty (float) - - beta12orEarlier - true - A simple floating point number defining the penalty for extending a gap in an alignment. - beta12orEarlier - - - - - - - - - - Gap separation penalty (integer) - - A simple floating point number defining the penalty for gaps that are close together in an alignment. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Gap separation penalty (float) - - beta12orEarlier - true - beta12orEarlier - A simple floating point number defining the penalty for gaps that are close together in an alignment. - - - - - - - - - - Terminal gap opening penalty - - beta12orEarlier - A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. - - - - - - - - - - Terminal gap extension penalty - - A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. - beta12orEarlier - - - - - - - - - - Sequence identity - - Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. - beta12orEarlier - - - - - - - - - - Sequence similarity - - beta12orEarlier - Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension. - Data Type is float probably. - - - - - - - - - - Sequence alignment metadata (quality report) - - beta12orEarlier - true - beta12orEarlier - Data on molecular sequence alignment quality (estimated accuracy). - - - - - - - - - - Sequence alignment report (site conservation) - - beta12orEarlier - Data on character conservation in a molecular sequence alignment. - 1.4 - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. - true - - - - - - - - - - Sequence alignment report (site correlation) - - 1.4 - beta12orEarlier - Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures. - true - - - - - - - - - - Sequence-profile alignment (Domainatrix signature) - - beta12orEarlier - Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment). - beta12orEarlier - true - - - - - - - - - - Sequence-profile alignment (HMM) - - beta12orEarlier - 1.5 - true - Alignment of molecular sequence(s) to a hidden Markov model(s). - - - - - - - - - - Sequence-profile alignment (fingerprint) - - Alignment of molecular sequences to a protein fingerprint from the PRINTS database. - 1.5 - beta12orEarlier - true - - - - - - - - - - Phylogenetic continuous quantitative data - - beta12orEarlier - Phylogenetic continuous quantitative characters - Quantitative traits - Continuous quantitative data that may be read during phylogenetic tree calculation. - - - - - - - - - - Phylogenetic discrete data - - Discrete characters - Character data with discrete states that may be read during phylogenetic tree calculation. - Phylogenetic discrete states - beta12orEarlier - Discretely coded characters - - - - - - - - - - Phylogenetic character cliques - - One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny. - Phylogenetic report (cliques) - beta12orEarlier - - - - - - - - - - Phylogenetic invariants - - - - - - - - Phylogenetic invariants data for testing alternative tree topologies. - beta12orEarlier - Phylogenetic report (invariants) - - - - - - - - - - Phylogenetic report - - beta12orEarlier - A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. - Phylogenetic tree report - 1.5 - Phylogenetic report - Phylogenetic tree-derived report - This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis. - true - - - - - - - - - - DNA substitution model - - Substitution model - Phylogenetic tree report (DNA substitution model) - Sequence alignment report (DNA substitution model) - beta12orEarlier - A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis. - - - - - - - - - - Phylogenetic tree report (tree shape) - - beta12orEarlier - true - 1.4 - Data about the shape of a phylogenetic tree. - - - - - - - - - - Phylogenetic tree report (tree evaluation) - - beta12orEarlier - true - 1.4 - Data on the confidence of a phylogenetic tree. - - - - - - - - - - Phylogenetic tree distances - - beta12orEarlier - Phylogenetic tree report (tree distances) - Distances, such as Branch Score distance, between two or more phylogenetic trees. - - - - - - - - - - Phylogenetic tree report (tree stratigraphic) - - beta12orEarlier - 1.4 - true - Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis. - - - - - - - - - - Phylogenetic character contrasts - - Phylogenetic report (character contrasts) - Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts. - beta12orEarlier - - - - - - - - - - Comparison matrix (integers) - - beta12orEarlier - Substitution matrix (integers) - beta12orEarlier - Matrix of integer numbers for sequence comparison. - true - - - - - - - - - - Comparison matrix (floats) - - beta12orEarlier - beta12orEarlier - true - Matrix of floating point numbers for sequence comparison. - Substitution matrix (floats) - - - - - - - - - - Comparison matrix (nucleotide) - - Matrix of integer or floating point numbers for nucleotide comparison. - beta12orEarlier - Nucleotide substitution matrix - - - - - - - - - - Comparison matrix (amino acid) - - - Amino acid comparison matrix - beta12orEarlier - Matrix of integer or floating point numbers for amino acid comparison. - Amino acid substitution matrix - - - - - - - - - - Nucleotide comparison matrix (integers) - - Nucleotide substitution matrix (integers) - beta12orEarlier - Matrix of integer numbers for nucleotide comparison. - true - beta12orEarlier - - - - - - - - - - Nucleotide comparison matrix (floats) - - beta12orEarlier - true - Matrix of floating point numbers for nucleotide comparison. - beta12orEarlier - Nucleotide substitution matrix (floats) - - - - - - - - - - Amino acid comparison matrix (integers) - - beta12orEarlier - Matrix of integer numbers for amino acid comparison. - Amino acid substitution matrix (integers) - true - beta12orEarlier - - - - - - - - - - Amino acid comparison matrix (floats) - - beta12orEarlier - Amino acid substitution matrix (floats) - beta12orEarlier - true - Matrix of floating point numbers for amino acid comparison. - - - - - - - - - - Protein features report (membrane regions) - - true - beta12orEarlier - 1.8 - trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. - - - - - - - - - - Nucleic acid structure - - - - - - - - 3D coordinate and associated data for a nucleic acid tertiary (3D) structure. - beta12orEarlier - - - - - - - - - - Protein structure - - - - - - - - Protein structures - 3D coordinate and associated data for a protein tertiary (3D) structure. - beta12orEarlier - - - - - - - - - - Protein-ligand complex - - The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule. - beta12orEarlier - This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead. - - - - - - - - - - Carbohydrate structure - - - - - - - - - - - - - - beta12orEarlier - 3D coordinate and associated data for a carbohydrate (3D) structure. - - - - - - - - - - Small molecule structure - - - - - - - - 3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound. - CHEBI:23367 - beta12orEarlier - - - - - - - - - - DNA structure - - beta12orEarlier - 3D coordinate and associated data for a DNA tertiary (3D) structure. - - - - - - - - - - RNA structure - - - - - - - - beta12orEarlier - 3D coordinate and associated data for an RNA tertiary (3D) structure. - - - - - - - - - - tRNA structure - - 3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc. - beta12orEarlier - - - - - - - - - - Protein chain - - beta12orEarlier - 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain. - - - - - - - - - - Protein domain - - - - - - - - 3D coordinate and associated data for the tertiary (3D) structure of a protein domain. - beta12orEarlier - - - - - - - - - - Protein structure (all atoms) - - beta12orEarlier - 1.5 - true - 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). - - - - - - - - - - C-alpha trace - - 3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only). - C-beta atoms from amino acid side-chains may be included. - Protein structure (C-alpha atoms) - beta12orEarlier - - - - - - - - - - Protein chain (all atoms) - - 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms). - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Protein chain (C-alpha atoms) - - true - 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only). - beta12orEarlier - beta12orEarlier - C-beta atoms from amino acid side-chains may be included. - - - - - - - - - - Protein domain (all atoms) - - 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms). - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Protein domain (C-alpha atoms) - - C-beta atoms from amino acid side-chains may be included. - true - 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only). - beta12orEarlier - beta12orEarlier - - - - - - - - - - Structure alignment (pair) - - Alignment (superimposition) of exactly two molecular tertiary (3D) structures. - beta12orEarlier - Pair structure alignment - - - - - - - - - - Structure alignment (multiple) - - beta12orEarlier - beta12orEarlier - true - Alignment (superimposition) of more than two molecular tertiary (3D) structures. - - - - - - - - - - Structure alignment (protein) - - - Protein structure alignment - beta12orEarlier - Alignment (superimposition) of protein tertiary (3D) structures. - - - - - - - - - - Structure alignment (nucleic acid) - - beta12orEarlier - Alignment (superimposition) of nucleic acid tertiary (3D) structures. - Nucleic acid structure alignment - - - - - - - - - - Structure alignment (protein pair) - - - Protein pair structural alignment - beta12orEarlier - Alignment (superimposition) of exactly two protein tertiary (3D) structures. - - - - - - - - - - Multiple protein tertiary structure alignment - - Alignment (superimposition) of more than two protein tertiary (3D) structures. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Structure alignment (protein all atoms) - - 1.5 - Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered). - beta12orEarlier - true - - - - - - - - - - Structure alignment (protein C-alpha atoms) - - Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered). - C-beta atoms from amino acid side-chains may be considered. - 1.5 - C-alpha trace - true - beta12orEarlier - - - - - - - - - - Pairwise protein tertiary structure alignment (all atoms) - - Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - Pairwise protein tertiary structure alignment (C-alpha atoms) - - C-beta atoms from amino acid side-chains may be included. - true - beta12orEarlier - Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). - beta12orEarlier - - - - - - - - - - Multiple protein tertiary structure alignment (all atoms) - - beta12orEarlier - true - Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). - beta12orEarlier - - - - - - - - - - Multiple protein tertiary structure alignment (C-alpha atoms) - - beta12orEarlier - Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). - true - beta12orEarlier - C-beta atoms from amino acid side-chains may be included. - - - - - - - - - - Structure alignment (nucleic acid pair) - - - beta12orEarlier - Nucleic acid pair structure alignment - Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. - - - - - - - - - - Multiple nucleic acid tertiary structure alignment - - beta12orEarlier - Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures. - true - beta12orEarlier - - - - - - - - - - Structure alignment (RNA) - - RNA structure alignment - Alignment (superimposition) of RNA tertiary (3D) structures. - beta12orEarlier - - - - - - - - - - Structural transformation matrix - - Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures. - beta12orEarlier - - - - - - - - - - DaliLite hit table - - DaliLite hit table of protein chain tertiary structure alignment data. - The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Molecular similarity score - - beta12orEarlier - A score reflecting structural similarities of two molecules. - true - beta12orEarlier - - - - - - - - - - Root-mean-square deviation - - RMSD - beta12orEarlier - Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates. - - - - - - - - - - Tanimoto similarity score - - beta12orEarlier - A measure of the similarity between two ligand fingerprints. - A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types. - - - - - - - - - - 3D-1D scoring matrix - - A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments. - beta12orEarlier - - - - - - - - - - Amino acid index - - - beta12orEarlier - A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids. - - - - - - - - - - Amino acid index (chemical classes) - - Chemical classes (amino acids) - Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids. - beta12orEarlier - - - - - - - - - - Amino acid pair-wise contact potentials - - Contact potentials (amino acid pair-wise) - Statistical protein contact potentials. - beta12orEarlier - - - - - - - - - - Amino acid index (molecular weight) - - Molecular weights of amino acids. - Molecular weight (amino acids) - beta12orEarlier - - - - - - - - - - Amino acid index (hydropathy) - - Hydrophobic, hydrophilic or charge properties of amino acids. - beta12orEarlier - Hydropathy (amino acids) - - - - - - - - - - Amino acid index (White-Wimley data) - - beta12orEarlier - White-Wimley data (amino acids) - Experimental free energy values for the water-interface and water-octanol transitions for the amino acids. - - - - - - - - - - Amino acid index (van der Waals radii) - - van der Waals radii (amino acids) - Van der Waals radii of atoms for different amino acid residues. - beta12orEarlier - - - - - - - - - - Enzyme report - - true - 1.5 - Protein report (enzyme) - beta12orEarlier - Enzyme report - An informative report on a specific enzyme. - - - - - - - - - - Restriction enzyme report - - An informative report on a specific restriction enzyme such as enzyme reference data. - Restriction enzyme pattern data - beta12orEarlier - 1.5 - This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. - Protein report (restriction enzyme) - Restriction enzyme report - true - - - - - - - - - - Peptide molecular weights - - beta12orEarlier - List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents. - The report might include associated data such as frequency of peptide fragment molecular weights. - - - - - - - - - - Peptide hydrophobic moment - - beta12orEarlier - Report on the hydrophobic moment of a polypeptide sequence. - Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. - - - - - - - - - - Protein aliphatic index - - The aliphatic index of a protein. - beta12orEarlier - The aliphatic index is the relative protein volume occupied by aliphatic side chains. - - - - - - - - - - Protein sequence hydropathy plot - - Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. - A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc. - beta12orEarlier - - - - - - - - - - Protein charge plot - - beta12orEarlier - A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence. - - - - - - - - - - Protein solubility - - beta12orEarlier - The solubility or atomic solvation energy of a protein sequence or structure. - Protein solubility data - - - - - - - - - - Protein crystallizability - - beta12orEarlier - Protein crystallizability data - Data on the crystallizability of a protein sequence. - - - - - - - - - - Protein globularity - - Protein globularity data - beta12orEarlier - Data on the stability, intrinsic disorder or globularity of a protein sequence. - - - - - - - - - - Protein titration curve - - - The titration curve of a protein. - beta12orEarlier - - - - - - - - - - Protein isoelectric point - - beta12orEarlier - The isoelectric point of one proteins. - - - - - - - - - - Protein pKa value - - The pKa value of a protein. - beta12orEarlier - - - - - - - - - - Protein hydrogen exchange rate - - beta12orEarlier - The hydrogen exchange rate of a protein. - - - - - - - - - - Protein extinction coefficient - - The extinction coefficient of a protein. - beta12orEarlier - - - - - - - - - - Protein optical density - - The optical density of a protein. - beta12orEarlier - - - - - - - - - - Protein subcellular localization - - Protein report (subcellular localization) - An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). - beta12orEarlier - true - beta13 - - - - - - - - - - Peptide immunogenicity data - - An report on allergenicity / immunogenicity of peptides and proteins. - Peptide immunogenicity report - beta12orEarlier - Peptide immunogenicity - This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. - - - - - - - - - - MHC peptide immunogenicity report - - A report on the immunogenicity of MHC class I or class II binding peptides. - beta13 - true - beta12orEarlier - - - - - - - - - - Protein structure report - - - Protein structural property - Protein structure-derived report - This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure). - Protein property (structural) - Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains. - beta12orEarlier - Protein report (structure) - Protein structure report (domain) - - - - - - - - - - Protein structural quality report - - Report on the quality of a protein three-dimensional model. - Protein structure report (quality evaluation) - Protein structure validation report - Protein property (structural quality) - Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. - Protein report (structural quality) - beta12orEarlier - - - - - - - - - - Protein residue interactions - - - - - - - - Residue interaction data - Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups. - beta12orEarlier - Atom interaction data - - - - - - - - - - Protein flexibility or motion report - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Protein property (flexibility or motion) - Informative report on flexibility or motion of a protein structure. - Protein flexibility or motion - beta12orEarlier - true - 1.4 - Protein structure report (flexibility or motion) - - - - - - - - - - Protein solvent accessibility - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. - beta12orEarlier - Data on the solvent accessible or buried surface area of a protein structure. - - - - - - - - - - Protein surface report - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Protein structure report (surface) - 1.4 - Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure. - beta12orEarlier - true - - - - - - - - - - Ramachandran plot - - beta12orEarlier - Phi/psi angle data or a Ramachandran plot of a protein structure. - - - - - - - - - - Protein dipole moment - - Data on the net charge distribution (dipole moment) of a protein structure. - beta12orEarlier - - - - - - - - - - Protein distance matrix - - beta12orEarlier - A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. - - - - - - - - - - Protein contact map - - An amino acid residue contact map for a protein structure. - beta12orEarlier - - - - - - - - - - Protein residue 3D cluster - - beta12orEarlier - Report on clusters of contacting residues in protein structures such as a key structural residue network. - - - - - - - - - - Protein hydrogen bonds - - Patterns of hydrogen bonding in protein structures. - beta12orEarlier - - - - - - - - - - Protein non-canonical interactions - - Protein non-canonical interactions report - true - Non-canonical atomic interactions in protein structures. - 1.4 - beta12orEarlier - - - - - - - - - - CATH node - - Information on a node from the CATH database. - The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links. - 1.5 - beta12orEarlier - true - CATH classification node report - - - - - - - - - - SCOP node - - true - SCOP classification node - Information on a node from the SCOP database. - 1.5 - beta12orEarlier - - - - - - - - - - EMBASSY domain classification - - beta12orEarlier - beta12orEarlier - true - An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format. - - - - - - - - - CATH class - - beta12orEarlier - 1.5 - Information on a protein 'class' node from the CATH database. - true - - - - - - - - - - CATH architecture - - beta12orEarlier - 1.5 - Information on a protein 'architecture' node from the CATH database. - true - - - - - - - - - - CATH topology - - true - 1.5 - Information on a protein 'topology' node from the CATH database. - beta12orEarlier - - - - - - - - - - CATH homologous superfamily - - 1.5 - true - beta12orEarlier - Information on a protein 'homologous superfamily' node from the CATH database. - - - - - - - - - - CATH structurally similar group - - 1.5 - true - beta12orEarlier - Information on a protein 'structurally similar group' node from the CATH database. - - - - - - - - - - CATH functional category - - Information on a protein 'functional category' node from the CATH database. - true - 1.5 - beta12orEarlier - - - - - - - - - - Protein fold recognition report - - Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. - beta12orEarlier - A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s). - true - beta12orEarlier - - - - - - - - - - Protein-protein interaction report - - protein-protein interaction(s), including interactions between protein domains. - beta12orEarlier - true - 1.8 - - - - - - - - - - Protein-ligand interaction report - - beta12orEarlier - An informative report on protein-ligand (small molecule) interaction(s). - - - - - - - - - - Protein-nucleic acid interactions report - - true - protein-DNA/RNA interaction(s). - beta12orEarlier - 1.8 - - - - - - - - - - Nucleic acid melting profile - - Nucleic acid stability profile - A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence. - Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating. - beta12orEarlier - - - - - - - - - - Nucleic acid enthalpy - - beta12orEarlier - Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). - - - - - - - - - - Nucleic acid entropy - - Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). - beta12orEarlier - - - - - - - - - - Nucleic acid melting temperature - - Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA). - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Nucleic acid stitch profile - - beta12orEarlier - Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA). - A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. - - - - - - - - - - DNA base pair stacking energies data - - DNA base pair stacking energies data. - beta12orEarlier - - - - - - - - - - DNA base pair twist angle data - - beta12orEarlier - DNA base pair twist angle data. - - - - - - - - - - DNA base trimer roll angles data - - beta12orEarlier - DNA base trimer roll angles data. - - - - - - - - - - Vienna RNA parameters - - RNA parameters used by the Vienna package. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - Vienna RNA structure constraints - - true - Structure constraints used by the Vienna package. - beta12orEarlier - beta12orEarlier - - - - - - - - - - Vienna RNA concentration data - - RNA concentration data used by the Vienna package. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Vienna RNA calculated energy - - beta12orEarlier - beta12orEarlier - true - RNA calculated energy data generated by the Vienna package. - - - - - - - - - - Base pairing probability matrix dotplot - - - beta12orEarlier - Such as generated by the Vienna package. - Dotplot of RNA base pairing probability matrix. - - - - - - - - - - Nucleic acid folding report - - Nucleic acid report (folding) - beta12orEarlier - Nucleic acid report (folding model) - RNA secondary structure folding probablities - A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc. - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - RNA secondary structure folding classification - - - - - - - - - - Codon usage table - - - - - - - - Table of codon usage data calculated from one or more nucleic acid sequences. - A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table. - beta12orEarlier - - - - - - - - - - Genetic code - - beta12orEarlier - A genetic code for an organism. - A genetic code need not include detailed codon usage information. - - - - - - - - - - Codon adaptation index - - true - A simple measure of synonymous codon usage bias often used to predict gene expression levels. - CAI - beta12orEarlier - beta12orEarlier - - - - - - - - - - Codon usage bias plot - - Synonymous codon usage statistic plot - beta12orEarlier - A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. - - - - - - - - - - Nc statistic - - true - beta12orEarlier - The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons. - beta12orEarlier - - - - - - - - - - Codon usage fraction difference - - The differences in codon usage fractions between two codon usage tables. - beta12orEarlier - - - - - - - - - - Pharmacogenomic test report - - beta12orEarlier - The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. - Data on the influence of genotype on drug response. - - - - - - - - - - Disease report - - - - - - - - An informative report on a specific disease. - For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. - beta12orEarlier - Disease report - - - - - - - - - - Linkage disequilibrium (report) - - true - A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). - 1.8 - beta12orEarlier - - - - - - - - - - Heat map - - - A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment. - beta12orEarlier - A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context. - - - - - - - - - - Affymetrix probe sets library file - - true - Affymetrix library file of information about which probes belong to which probe set. - CDF file - beta12orEarlier - beta12orEarlier - - - - - - - - - - Affymetrix probe sets information library file - - true - Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated. - GIN file - beta12orEarlier - beta12orEarlier - - - - - - - - - - Molecular weights standard fingerprint - - beta12orEarlier - Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS. - - - - - - - - - - Metabolic pathway report - - This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. - beta12orEarlier - A report typically including a map (diagram) of a metabolic pathway. - 1.8 - true - - - - - - - - - - Genetic information processing pathway report - - beta12orEarlier - 1.8 - true - genetic information processing pathways. - - - - - - - - - - Environmental information processing pathway report - - true - environmental information processing pathways. - beta12orEarlier - 1.8 - - - - - - - - - - Signal transduction pathway report - - A report typically including a map (diagram) of a signal transduction pathway. - 1.8 - true - beta12orEarlier - - - - - - - - - - Cellular process pathways report - - 1.8 - Topic concernning cellular process pathways. - true - beta12orEarlier - - - - - - - - - - Disease pathway or network report - - true - beta12orEarlier - disease pathways, typically of human disease. - 1.8 - - - - - - - - - - Drug structure relationship map - - A report typically including a map (diagram) of drug structure relationships. - beta12orEarlier - - - - - - - - - - Protein interaction networks - - 1.8 - networks of protein interactions. - true - beta12orEarlier - - - - - - - - - - MIRIAM datatype - - A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types. - An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources. - beta12orEarlier - true - 1.5 - - - - - - - - - - E-value - - An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score. - beta12orEarlier - A simple floating point number defining the lower or upper limit of an expectation value (E-value). - Expectation value - - - - - - - - - - Z-value - - beta12orEarlier - The z-value is the number of standard deviations a data value is above or below a mean value. - A z-value might be specified as a threshold for reporting hits from database searches. - - - - - - - - - - P-value - - beta12orEarlier - A z-value might be specified as a threshold for reporting hits from database searches. - The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true. - - - - - - - - - - Database version information - - true - Ontology version information - 1.5 - Information on a database (or ontology) version, for example name, version number and release date. - beta12orEarlier - - - - - - - - - - Tool version information - - beta12orEarlier - Information on an application version, for example name, version number and release date. - true - 1.5 - - - - - - - - - - CATH version information - - beta12orEarlier - beta12orEarlier - true - Information on a version of the CATH database. - - - - - - - - - - Swiss-Prot to PDB mapping - - Cross-mapping of Swiss-Prot codes to PDB identifiers. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Sequence database cross-references - - Cross-references from a sequence record to other databases. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Job status - - Metadata on the status of a submitted job. - beta12orEarlier - 1.5 - true - Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). - - - - - - - - - - Job ID - - 1.0 - The (typically numeric) unique identifier of a submitted job. - beta12orEarlier - true - - - - - - - - - Job type - - 1.5 - true - beta12orEarlier - A label (text token) describing the type of job, for example interactive or non-interactive. - - - - - - - - - - Tool log - - 1.5 - A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages. - true - beta12orEarlier - - - - - - - - - - DaliLite log file - - true - beta12orEarlier - DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. - beta12orEarlier - - - - - - - - - - STRIDE log file - - STRIDE log file. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - - NACCESS log file - - beta12orEarlier - beta12orEarlier - true - NACCESS log file. - - - - - - - - - - - EMBOSS wordfinder log file - - EMBOSS wordfinder log file. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - EMBOSS domainatrix log file - - beta12orEarlier - EMBOSS (EMBASSY) domainatrix application log file. - beta12orEarlier - true - - - - - - - - - - EMBOSS sites log file - - true - beta12orEarlier - beta12orEarlier - EMBOSS (EMBASSY) sites application log file. - - - - - - - - - - EMBOSS supermatcher error file - - EMBOSS (EMBASSY) supermatcher error file. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - EMBOSS megamerger log file - - beta12orEarlier - beta12orEarlier - EMBOSS megamerger log file. - true - - - - - - - - - - EMBOSS whichdb log file - - beta12orEarlier - true - EMBOSS megamerger log file. - beta12orEarlier - - - - - - - - - - EMBOSS vectorstrip log file - - true - beta12orEarlier - beta12orEarlier - EMBOSS vectorstrip log file. - - - - - - - - - - Username - - A username on a computer system. - beta12orEarlier - - - - - - - - - - - Password - - beta12orEarlier - A password on a computer system. - - - - - - - - - - - Email address - - beta12orEarlier - Moby:Email - A valid email address of an end-user. - Moby:EmailAddress - - - - - - - - - - - Person name - - beta12orEarlier - The name of a person. - - - - - - - - - - - Number of iterations - - 1.5 - Number of iterations of an algorithm. - true - beta12orEarlier - - - - - - - - - - Number of output entities - - Number of entities (for example database hits, sequences, alignments etc) to write to an output file. - 1.5 - beta12orEarlier - true - - - - - - - - - - Hit sort order - - Controls the order of hits (reported matches) in an output file from a database search. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - - Drug report - - - - - - - - An informative report on a specific drug. - beta12orEarlier - Drug annotation - - - - - - - - - - - Phylogenetic tree image - - beta12orEarlier - An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information. - See also 'Phylogenetic tree' - - - - - - - - - - RNA secondary structure image - - beta12orEarlier - Image of RNA secondary structure, knots, pseudoknots etc. - - - - - - - - - - Protein secondary structure image - - Image of protein secondary structure. - beta12orEarlier - - - - - - - - - - Structure image - - beta12orEarlier - Image of one or more molecular tertiary (3D) structures. - - - - - - - - - - Sequence alignment image - - beta12orEarlier - Image of two or more aligned molecular sequences possibly annotated with alignment features. - - - - - - - - - - Chemical structure image - - An image of the structure of a small chemical compound. - The molecular identifier and formula are typically included. - Small molecule structure image - beta12orEarlier - - - - - - - - - - Fate map - - - - - - - - - beta12orEarlier - A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development. - - - - - - - - - - Microarray spots image - - - beta12orEarlier - An image of spots from a microarray experiment. - - - - - - - - - - BioPax term - - beta12orEarlier - A term from the BioPax ontology. - beta12orEarlier - true - - - - - - - - - - GO - - beta12orEarlier - Gene Ontology term - Moby:Annotated_GO_Term - Moby:Annotated_GO_Term_With_Probability - true - A term definition from The Gene Ontology (GO). - beta12orEarlier - Moby:GO_Term - Moby:GOTerm - - - - - - - - - - MeSH - - true - A term from the MeSH vocabulary. - beta12orEarlier - beta12orEarlier - - - - - - - - - - HGNC - - beta12orEarlier - true - A term from the HGNC controlled vocabulary. - beta12orEarlier - - - - - - - - - - NCBI taxonomy vocabulary - - beta12orEarlier - beta12orEarlier - true - A term from the NCBI taxonomy vocabulary. - - - - - - - - - - Plant ontology term - - beta12orEarlier - true - beta12orEarlier - A term from the Plant Ontology (PO). - - - - - - - - - - UMLS - - beta12orEarlier - beta12orEarlier - A term from the UMLS vocabulary. - true - - - - - - - - - - FMA - - beta12orEarlier - Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. - beta12orEarlier - A term from Foundational Model of Anatomy. - true - - - - - - - - - - EMAP - - A term from the EMAP mouse ontology. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - ChEBI - - beta12orEarlier - A term from the ChEBI ontology. - true - beta12orEarlier - - - - - - - - - - MGED - - beta12orEarlier - true - A term from the MGED ontology. - beta12orEarlier - - - - - - - - - - myGrid - - The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. - beta12orEarlier - true - A term from the myGrid ontology. - beta12orEarlier - - - - - - - - - - GO (biological process) - - beta12orEarlier - true - beta12orEarlier - Data Type is an enumerated string. - A term definition for a biological process from the Gene Ontology (GO). - - - - - - - - - - GO (molecular function) - - A term definition for a molecular function from the Gene Ontology (GO). - beta12orEarlier - Data Type is an enumerated string. - true - beta12orEarlier - - - - - - - - - - GO (cellular component) - - beta12orEarlier - true - A term definition for a cellular component from the Gene Ontology (GO). - beta12orEarlier - Data Type is an enumerated string. - - - - - - - - - - Ontology relation type - - 1.5 - beta12orEarlier - true - A relation type defined in an ontology. - - - - - - - - - - Ontology concept definition - - beta12orEarlier - Ontology class definition - The definition of a concept from an ontology. - - - - - - - - - - Ontology concept comment - - beta12orEarlier - 1.4 - true - A comment on a concept from an ontology. - - - - - - - - - - Ontology concept reference - - beta12orEarlier - true - Reference for a concept from an ontology. - beta12orEarlier - - - - - - - - - - doc2loc document information - - beta12orEarlier - true - The doc2loc output includes the url, format, type and availability code of a document for every service provider. - beta12orEarlier - Information on a published article provided by the doc2loc program. - - - - - - - - - - PDB residue number - - WHATIF: pdb_number - PDBML:PDB_residue_no - beta12orEarlier - A residue identifier (a string) from a PDB file. - - - - - - - - - - Atomic coordinate - - Cartesian coordinate of an atom (in a molecular structure). - beta12orEarlier - Cartesian coordinate - - - - - - - - - - Atomic x coordinate - - WHATIF: PDBx_Cartn_x - Cartesian x coordinate - beta12orEarlier - PDBML:_atom_site.Cartn_x in PDBML - Cartesian x coordinate of an atom (in a molecular structure). - - - - - - - - - - Atomic y coordinate - - WHATIF: PDBx_Cartn_y - Cartesian y coordinate - beta12orEarlier - PDBML:_atom_site.Cartn_y in PDBML - Cartesian y coordinate of an atom (in a molecular structure). - - - - - - - - - - Atomic z coordinate - - PDBML:_atom_site.Cartn_z - WHATIF: PDBx_Cartn_z - Cartesian z coordinate of an atom (in a molecular structure). - beta12orEarlier - Cartesian z coordinate - - - - - - - - - - PDB atom name - - WHATIF: PDBx_type_symbol - beta12orEarlier - WHATIF: PDBx_auth_atom_id - WHATIF: alternate_atom - PDBML:pdbx_PDB_atom_name - WHATIF: atom_type - Identifier (a string) of a specific atom from a PDB file for a molecular structure. - - - - - - - - - - - Protein atom - - Atom data - CHEBI:33250 - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Data on a single atom from a protein structure. - beta12orEarlier - - - - - - - - - - Protein residue - - beta12orEarlier - Data on a single amino acid residue position in a protein structure. - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Residue - - - - - - - - - - Atom name - - - Name of an atom. - beta12orEarlier - - - - - - - - - - - PDB residue name - - Three-letter amino acid residue names as used in PDB files. - WHATIF: type - beta12orEarlier - - - - - - - - - - - PDB model number - - Identifier of a model structure from a PDB file. - beta12orEarlier - PDBML:pdbx_PDB_model_num - Model number - WHATIF: model_number - - - - - - - - - - - CATH domain report - - beta12orEarlier - true - beta13 - The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. - Summary of domain classification information for a CATH domain. - - - - - - - - - - CATH representative domain sequences (ATOM) - - beta12orEarlier - beta12orEarlier - FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity). - true - - - - - - - - - - CATH representative domain sequences (COMBS) - - true - FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). - beta12orEarlier - beta12orEarlier - - - - - - - - - - CATH domain sequences (ATOM) - - true - FASTA sequence database for all CATH domains (based on PDB ATOM records). - beta12orEarlier - beta12orEarlier - - - - - - - - - - CATH domain sequences (COMBS) - - FASTA sequence database for all CATH domains (based on COMBS sequence data). - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Sequence version - - beta12orEarlier - Information on an molecular sequence version. - Sequence version information - - - - - - - - - - Score - - A numerical value, that is some type of scored value arising for example from a prediction method. - beta12orEarlier - - - - - - - - - - Protein report (function) - - true - For properties that can be mapped to a sequence, use 'Sequence report' instead. - beta13 - Report on general functional properties of specific protein(s). - beta12orEarlier - - - - - - - - - - Gene name (ASPGD) - - 1.3 - beta12orEarlier - true - Name of a gene from Aspergillus Genome Database. - http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS - - - - - - - - - - Gene name (CGD) - - Name of a gene from Candida Genome Database. - true - http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS - beta12orEarlier - 1.3 - - - - - - - - - - Gene name (dictyBase) - - http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase - beta12orEarlier - 1.3 - true - Name of a gene from dictyBase database. - - - - - - - - - - Gene name (EcoGene primary) - - http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G - Primary name of a gene from EcoGene Database. - EcoGene primary gene name - 1.3 - true - beta12orEarlier - - - - - - - - - - Gene name (MaizeGDB) - - http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus - 1.3 - Name of a gene from MaizeGDB (maize genes) database. - true - beta12orEarlier - - - - - - - - - - Gene name (SGD) - - true - 1.3 - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS - Name of a gene from Saccharomyces Genome Database. - - - - - - - - - - Gene name (TGD) - - beta12orEarlier - 1.3 - Name of a gene from Tetrahymena Genome Database. - true - http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS - - - - - - - - - - Gene name (CGSC) - - beta12orEarlier - 1.3 - true - http://www.geneontology.org/doc/GO.xrf_abbs: CGSC - Symbol of a gene from E.coli Genetic Stock Center. - - - - - - - - - - Gene name (HGNC) - - beta12orEarlier - HUGO symbol - 1.3 - true - HGNC symbol - Official gene name - HUGO gene name - http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene - HGNC gene name - HUGO gene symbol - HGNC:[0-9]{1,5} - Gene name (HUGO) - HGNC gene symbol - Symbol of a gene approved by the HUGO Gene Nomenclature Committee. - - - - - - - - - - Gene name (MGD) - - MGI:[0-9]+ - Symbol of a gene from the Mouse Genome Database. - http://www.geneontology.org/doc/GO.xrf_abbs: MGD - 1.3 - true - beta12orEarlier - - - - - - - - - - Gene name (Bacillus subtilis) - - http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG - Symbol of a gene from Bacillus subtilis Genome Sequence Project. - beta12orEarlier - 1.3 - true - - - - - - - - - - Gene ID (PlasmoDB) - - Identifier of a gene from PlasmoDB Plasmodium Genome Resource. - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB - - - - - - - - - - - Gene ID (EcoGene) - - Identifier of a gene from EcoGene Database. - EcoGene Accession - EcoGene ID - beta12orEarlier - - - - - - - - - - - Gene ID (FlyBase) - - beta12orEarlier - Gene identifier from FlyBase database. - http://www.geneontology.org/doc/GO.xrf_abbs: FB - http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase - - - - - - - - - - - Gene ID (GeneDB Glossina morsitans) - - true - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans - beta13 - Gene identifier from Glossina morsitans GeneDB database. - beta12orEarlier - - - - - - - - - - Gene ID (GeneDB Leishmania major) - - Gene identifier from Leishmania major GeneDB database. - true - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor - beta12orEarlier - beta13 - - - - - - - - - - Gene ID (GeneDB Plasmodium falciparum) - - Gene identifier from Plasmodium falciparum GeneDB database. - true - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum - beta13 - beta12orEarlier - - - - - - - - - - Gene ID (GeneDB Schizosaccharomyces pombe) - - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe - beta12orEarlier - true - beta13 - Gene identifier from Schizosaccharomyces pombe GeneDB database. - - - - - - - - - - Gene ID (GeneDB Trypanosoma brucei) - - Gene identifier from Trypanosoma brucei GeneDB database. - true - beta13 - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei - - - - - - - - - - Gene ID (Gramene) - - http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE - Gene identifier from Gramene database. - - - - - - - - - - - Gene ID (Virginia microbial) - - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD - Gene identifier from Virginia Bioinformatics Institute microbial database. - http://www.geneontology.org/doc/GO.xrf_abbs: VMD - - - - - - - - - - - Gene ID (SGN) - - http://www.geneontology.org/doc/GO.xrf_abbs: SGN - Gene identifier from Sol Genomics Network. - beta12orEarlier - - - - - - - - - - - Gene ID (WormBase) - - - Gene identifier used by WormBase database. - WBGene[0-9]{8} - http://www.geneontology.org/doc/GO.xrf_abbs: WB - http://www.geneontology.org/doc/GO.xrf_abbs: WormBase - beta12orEarlier - - - - - - - - - - - Gene synonym - - Gene name synonym - true - Any name (other than the recommended one) for a gene. - beta12orEarlier - beta12orEarlier - - - - - - - - - - ORF name - - - beta12orEarlier - The name of an open reading frame attributed by a sequencing project. - - - - - - - - - - - Sequence assembly component - - A component of a larger sequence assembly. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - Chromosome annotation (aberration) - - beta12orEarlier - beta12orEarlier - true - A report on a chromosome aberration such as abnormalities in chromosome structure. - - - - - - - - - - Clone ID - - beta12orEarlier - An identifier of a clone (cloned molecular sequence) from a database. - - - - - - - - - - - PDB insertion code - - beta12orEarlier - WHATIF: insertion_code - PDBML:pdbx_PDB_ins_code - An insertion code (part of the residue number) for an amino acid residue from a PDB file. - - - - - - - - - - Atomic occupancy - - WHATIF: PDBx_occupancy - The fraction of an atom type present at a site in a molecular structure. - beta12orEarlier - The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. - - - - - - - - - - Isotropic B factor - - Isotropic B factor (atomic displacement parameter) for an atom from a PDB file. - WHATIF: PDBx_B_iso_or_equiv - beta12orEarlier - - - - - - - - - - Deletion map - - A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel. - beta12orEarlier - A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type. - Deletion-based cytogenetic map - - - - - - - - - - QTL map - - A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers. - beta12orEarlier - Quantitative trait locus map - - - - - - - - - - Haplotype map - - beta12orEarlier - Moby:Haplotyping_Study_obj - A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation. - - - - - - - - - - Map set data - - beta12orEarlier - Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped. - Moby:GCP_CorrelatedLinkageMapSet - Moby:GCP_CorrelatedMapSet - - - - - - - - - - Map feature - - beta12orEarlier - true - A feature which may mapped (positioned) on a genetic or other type of map. - Moby:MapFeature - beta12orEarlier - Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. - - - - - - - - - - - - Map type - - A designation of the type of map (genetic map, physical map, sequence map etc) or map set. - Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. - 1.5 - true - beta12orEarlier - - - - - - - - - - Protein fold name - - The name of a protein fold. - beta12orEarlier - - - - - - - - - - - Taxon - - Moby:PotentialTaxon - Taxonomy rank - beta12orEarlier - Taxonomic rank - For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. - The name of a group of organisms belonging to the same taxonomic rank. - Moby:BriefTaxonConcept - - - - - - - - - - - Organism identifier - - - - - - - - beta12orEarlier - A unique identifier of a (group of) organisms. - - - - - - - - - - - Genus name - - beta12orEarlier - The name of a genus of organism. - - - - - - - - - - - Taxonomic classification - - Moby:TaxonName - Moby:GCP_Taxon - beta12orEarlier - The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature. - Moby:iANT_organism-xml - Taxonomic name - Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included. - Taxonomic information - Moby:TaxonScientificName - Moby:TaxonTCS - - - - - - - - - - - iHOP organism ID - - beta12orEarlier - Moby_namespace:iHOPorganism - A unique identifier for an organism used in the iHOP database. - - - - - - - - - - - Genbank common name - - Common name for an organism as used in the GenBank database. - beta12orEarlier - - - - - - - - - - - NCBI taxon - - The name of a taxon from the NCBI taxonomy database. - beta12orEarlier - - - - - - - - - - - Synonym - - beta12orEarlier - Alternative name - beta12orEarlier - true - An alternative for a word. - - - - - - - - - - Misspelling - - A common misspelling of a word. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Acronym - - true - An abbreviation of a phrase or word. - beta12orEarlier - beta12orEarlier - - - - - - - - - - Misnomer - - A term which is likely to be misleading of its meaning. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Author ID - - Information on the authors of a published work. - Moby:Author - beta12orEarlier - - - - - - - - - - - DragonDB author identifier - - An identifier representing an author in the DragonDB database. - beta12orEarlier - - - - - - - - - - - Annotated URI - - beta12orEarlier - A URI along with annotation describing the data found at the address. - Moby:DescribedLink - - - - - - - - - - UniProt keywords - - true - beta12orEarlier - beta12orEarlier - A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database. - - - - - - - - - - Gene ID (GeneFarm) - - Moby_namespace:GENEFARM_GeneID - Identifier of a gene from the GeneFarm database. - beta12orEarlier - - - - - - - - - - - Blattner number - - beta12orEarlier - Moby_namespace:Blattner_number - The blattner identifier for a gene. - - - - - - - - - - - Gene ID (MIPS Maize) - - MIPS genetic element identifier (Maize) - Identifier for genetic elements in MIPS Maize database. - beta12orEarlier - Moby_namespace:MIPS_GE_Maize - beta13 - true - - - - - - - - - - Gene ID (MIPS Medicago) - - MIPS genetic element identifier (Medicago) - beta12orEarlier - beta13 - true - Moby_namespace:MIPS_GE_Medicago - Identifier for genetic elements in MIPS Medicago database. - - - - - - - - - - Gene name (DragonDB) - - true - The name of an Antirrhinum Gene from the DragonDB database. - beta12orEarlier - Moby_namespace:DragonDB_Gene - 1.3 - - - - - - - - - - Gene name (Arabidopsis) - - Moby_namespace:ArabidopsisGeneSymbol - true - A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name. - beta12orEarlier - 1.3 - - - - - - - - - - iHOP symbol - - - - A unique identifier of a protein or gene used in the iHOP database. - Moby_namespace:iHOPsymbol - beta12orEarlier - - - - - - - - - - - Gene name (GeneFarm) - - 1.3 - true - Name of a gene from the GeneFarm database. - Moby_namespace:GENEFARM_GeneName - GeneFarm gene ID - beta12orEarlier - - - - - - - - - - Locus ID - - - - - - - - - A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. - Locus name - beta12orEarlier - Locus identifier - - - - - - - - - - - Locus ID (AGI) - - AT[1-5]G[0-9]{5} - AGI ID - Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases) - http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode - Arabidopsis gene loci number - AGI locus code - beta12orEarlier - AGI identifier - - - - - - - - - - - Locus ID (ASPGD) - - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD - http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID - Identifier for loci from ASPGD (Aspergillus Genome Database). - - - - - - - - - - - Locus ID (MGG) - - Identifier for loci from Magnaporthe grisea Database at the Broad Institute. - http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG - beta12orEarlier - - - - - - - - - - - Locus ID (CGD) - - Identifier for loci from CGD (Candida Genome Database). - http://www.geneontology.org/doc/GO.xrf_abbs: CGDID - beta12orEarlier - CGDID - CGD locus identifier - http://www.geneontology.org/doc/GO.xrf_abbs: CGD - - - - - - - - - - - Locus ID (CMR) - - http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR - Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute. - http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR - beta12orEarlier - - - - - - - - - - - NCBI locus tag - - beta12orEarlier - Moby_namespace:LocusID - Locus ID (NCBI) - http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag - Identifier for loci from NCBI database. - - - - - - - - - - - Locus ID (SGD) - - - Identifier for loci from SGD (Saccharomyces Genome Database). - http://www.geneontology.org/doc/GO.xrf_abbs: SGDID - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: SGD - SGDID - - - - - - - - - - - Locus ID (MMP) - - Identifier of loci from Maize Mapping Project. - Moby_namespace:MMP_Locus - beta12orEarlier - - - - - - - - - - - Locus ID (DictyBase) - - Moby_namespace:DDB_gene - Identifier of locus from DictyBase (Dictyostelium discoideum). - beta12orEarlier - - - - - - - - - - - Locus ID (EntrezGene) - - Identifier of a locus from EntrezGene database. - beta12orEarlier - Moby_namespace:EntrezGene_ID - Moby_namespace:EntrezGene_EntrezGeneID - - - - - - - - - - - Locus ID (MaizeGDB) - - Identifier of locus from MaizeGDB (Maize genome database). - Moby_namespace:MaizeGDB_Locus - beta12orEarlier - - - - - - - - - - - Quantitative trait locus - - QTL - A QTL sometimes but does not necessarily correspond to a gene. - true - beta12orEarlier - beta12orEarlier - A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment). - Moby:SO_QTL - - - - - - - - - - Gene ID (KOME) - - Identifier of a gene from the KOME database. - beta12orEarlier - Moby_namespace:GeneId - - - - - - - - - - - Locus ID (Tropgene) - - Identifier of a locus from the Tropgene database. - Moby:Tropgene_locus - beta12orEarlier - - - - - - - - - - - Alignment - - An alignment of molecular sequences, structures or profiles derived from them. - beta12orEarlier - - - - - - - - - - Atomic property - - General atomic property - Data for an atom (in a molecular structure). - beta12orEarlier - - - - - - - - - - UniProt keyword - - beta12orEarlier - A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database. - Moby_namespace:SP_KW - http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW - - - - - - - - - - Ordered locus name - - beta12orEarlier - true - A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. - beta12orEarlier - - - - - - - - - - Sequence coordinates - - - - Map position - Moby:Position - Locus - Sequence co-ordinates - A position in a map (for example a genetic map), either a single position (point) or a region / interval. - Moby:GenePosition - This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position. - Moby:HitPosition - beta12orEarlier - Moby:MapPosition - Moby:Locus - Moby:GCP_MapInterval - Moby:GCP_MapPosition - Moby:GCP_MapPoint - PDBML:_atom_site.id - - - - - - - - - - Amino acid property - - Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids. - Amino acid data - beta12orEarlier - - - - - - - - - - Annotation - - beta12orEarlier - true - beta13 - This is a broad data type and is used a placeholder for other, more specific types. - A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. - - - - - - - - - - Map data - - - - - - - - Map attribute - beta12orEarlier - An attribute of a molecular map (genetic or physical), or data extracted from or derived from the analysis of such a map. - - - - - - - - - - Vienna RNA structural data - - true - Data used by the Vienna RNA analysis package. - beta12orEarlier - beta12orEarlier - - - - - - - - - - Sequence mask parameter - - beta12orEarlier - 1.5 - true - Data used to replace (mask) characters in a molecular sequence. - - - - - - - - - - Enzyme kinetics data - - - Data concerning chemical reaction(s) catalysed by enzyme(s). - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. - - - - - - - - - - Michaelis Menten plot - - A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent. - beta12orEarlier - - - - - - - - - - Hanes Woolf plot - - beta12orEarlier - A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v). - - - - - - - - - - Experimental data - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - true - Raw data from or annotation on laboratory experiments. - beta12orEarlier - Experimental measurement data - beta13 - - - - - - - - - - - Genome version information - - beta12orEarlier - true - Information on a genome version. - 1.5 - - - - - - - - - - Evidence - - Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc. - beta12orEarlier - - - - - - - - - - Sequence record lite - - beta12orEarlier - A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment. - true - 1.8 - - - - - - - - - - Sequence - - - - - - - - http://purl.bioontology.org/ontology/MSH/D008969 - Sequences - http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation - This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles. - beta12orEarlier - One or more molecular sequences, possibly with associated annotation. - - - - - - - - - - Nucleic acid sequence record (lite) - - beta12orEarlier - 1.8 - true - A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment. - - - - - - - - - - Protein sequence record (lite) - - 1.8 - Sequence record lite (protein) - beta12orEarlier - A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment. - true - - - - - - - - - - Report - - You can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing. - http://semanticscience.org/resource/SIO_000148 - Document - A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself. - beta12orEarlier - - - - - - - - - - Molecular property (general) - - General molecular property - General data for a molecule. - beta12orEarlier - - - - - - - - - - Structural data - - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier - true - Data concerning molecular structural data. - beta13 - - - - - - - - - - - Sequence motif (nucleic acid) - - Nucleic acid sequence motif - DNA sequence motif - A nucleotide sequence motif. - beta12orEarlier - RNA sequence motif - - - - - - - - - - Sequence motif (protein) - - beta12orEarlier - An amino acid sequence motif. - Protein sequence motif - - - - - - - - - - Search parameter - - beta12orEarlier - 1.5 - true - Some simple value controlling a search operation, typically a search of a database. - - - - - - - - - - Database search results - - beta12orEarlier - A report of hits from searching a database of some type. - Search results - Database hits - - - - - - - - - - Secondary structure - - 1.5 - true - beta12orEarlier - The secondary structure assignment (predicted or real) of a nucleic acid or protein. - - - - - - - - - - Matrix - - beta12orEarlier - Array - This is a broad data type and is used a placeholder for other, more specific types. - An array of numerical values. - - - - - - - - - - Alignment data - - beta12orEarlier - 1.8 - true - Data concerning, extracted from, or derived from the analysis of molecular alignment of some type. - This is a broad data type and is used a placeholder for other, more specific types. - Alignment report - - - - - - - - - - Nucleic acid report - - An informative human-readable report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data. - beta12orEarlier - - - - - - - - - - Structure report - - An informative report on general information, properties or features of one or more molecular tertiary (3D) structures. - beta12orEarlier - Structure-derived report - - - - - - - - - - Nucleic acid structure data - - Nucleic acid property (structural) - This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. - Nucleic acid structural property - beta12orEarlier - A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s). - - - - - - - - - - Molecular property - - beta12orEarlier - SO:0000400 - A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule. - Physicochemical property - - - - - - - - - - DNA base structural data - - Structural data for DNA base pairs or runs of bases, such as energy or angle data. - beta12orEarlier - - - - - - - - - - Database entry version information - - true - beta12orEarlier - 1.5 - Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on. - - - - - - - - - - Accession - - beta12orEarlier - http://semanticscience.org/resource/SIO_000731 - A persistent (stable) and unique identifier, typically identifying an object (entry) from a database. - http://semanticscience.org/resource/SIO_000675 - - - - - - - - - - - SNP - - single nucleotide polymorphism (SNP) in a DNA sequence. - true - beta12orEarlier - 1.8 - - - - - - - - - - Data reference - - A list of database accessions or identifiers are usually included. - Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology. - beta12orEarlier - - - - - - - - - - Job identifier - - http://wsio.org/data_009 - An identifier of a submitted job. - beta12orEarlier - - - - - - - - - - - Name - - http://semanticscience.org/resource/SIO_000116 - http://usefulinc.com/ns/doap#name - "http://www.w3.org/2000/01/rdf-schema#label - beta12orEarlier - A name of a thing, which need not necessarily uniquely identify it. - Symbolic name - - - - - - - Closely related, but focusing on labeling and human readability but not on identification. - - - - - - - - - - - Type - - A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values). - http://purl.org/dc/elements/1.1/type - 1.5 - beta12orEarlier - true - - - - - - - - - - User ID - - An identifier of a software end-user (typically a person). - beta12orEarlier - - - - - - - - - - - KEGG organism code - - - A three-letter code used in the KEGG databases to uniquely identify organisms. - beta12orEarlier - - - - - - - - - - - Gene name (KEGG GENES) - - beta12orEarlier - KEGG GENES entry name - [a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]* - Name of an entry (gene) from the KEGG GENES database. - Moby_namespace:GeneId - true - 1.3 - - - - - - - - - - BioCyc ID - - - Identifier of an object from one of the BioCyc databases. - beta12orEarlier - - - - - - - - - - - Compound ID (BioCyc) - - - BioCyc compound identifier - Identifier of a compound from the BioCyc chemical compounds database. - BioCyc compound ID - beta12orEarlier - - - - - - - - - - - Reaction ID (BioCyc) - - - - - - - - - beta12orEarlier - Identifier of a biological reaction from the BioCyc reactions database. - - - - - - - - - - - Enzyme ID (BioCyc) - - - BioCyc enzyme ID - beta12orEarlier - Identifier of an enzyme from the BioCyc enzymes database. - - - - - - - - - - - Reaction ID - - - - - - - - - beta12orEarlier - Identifier of a biological reaction from a database. - - - - - - - - - - - Identifier (hybrid) - - An identifier that is re-used for data objects of fundamentally different types (typically served from a single database). - beta12orEarlier - This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. - - - - - - - - - - - Molecular property identifier - - - - - - - - beta12orEarlier - Identifier of a molecular property. - - - - - - - - - - - Codon usage table ID - - - - - - - - - - - - - - Identifier of a codon usage table, for example a genetic code. - Codon usage table identifier - beta12orEarlier - - - - - - - - - - - FlyBase primary identifier - - beta12orEarlier - Primary identifier of an object from the FlyBase database. - - - - - - - - - - - WormBase identifier - - beta12orEarlier - Identifier of an object from the WormBase database. - - - - - - - - - - - WormBase wormpep ID - - - Protein identifier used by WormBase database. - CE[0-9]{5} - beta12orEarlier - - - - - - - - - - - Nucleic acid features (codon) - - beta12orEarlier - true - An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon. - beta12orEarlier - - - - - - - - - - Map identifier - - - - - - - - An identifier of a map of a molecular sequence. - beta12orEarlier - - - - - - - - - - - Person identifier - - An identifier of a software end-user (typically a person). - beta12orEarlier - - - - - - - - - - - Nucleic acid identifier - - - - - - - - Name or other identifier of a nucleic acid molecule. - beta12orEarlier - - - - - - - - - - - Translation frame specification - - beta12orEarlier - Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome). - - - - - - - - - - Genetic code identifier - - - - - - - - An identifier of a genetic code. - beta12orEarlier - - - - - - - - - - - Genetic code name - - - Informal name for a genetic code, typically an organism name. - beta12orEarlier - - - - - - - - - - - File format name - - - Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on. - beta12orEarlier - - - - - - - - - - - Sequence profile type - - true - 1.5 - A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc. - beta12orEarlier - - - - - - - - - - Operating system name - - beta12orEarlier - Name of a computer operating system such as Linux, PC or Mac. - - - - - - - - - - - Mutation type - - beta12orEarlier - true - beta12orEarlier - A type of point or block mutation, including insertion, deletion, change, duplication and moves. - - - - - - - - - - Logical operator - - beta12orEarlier - A logical operator such as OR, AND, XOR, and NOT. - - - - - - - - - - - Results sort order - - Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on. - beta12orEarlier - true - 1.5 - A control of the order of data that is output, for example the order of sequences in an alignment. - - - - - - - - - - Toggle - - beta12orEarlier - A simple parameter that is a toggle (boolean value), typically a control for a modal tool. - true - beta12orEarlier - - - - - - - - - - Sequence width - - true - beta12orEarlier - beta12orEarlier - The width of an output sequence or alignment. - - - - - - - - - - Gap penalty - - beta12orEarlier - A penalty for introducing or extending a gap in an alignment. - - - - - - - - - - Nucleic acid melting temperature - - beta12orEarlier - A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. - Melting temperature - - - - - - - - - - Concentration - - beta12orEarlier - The concentration of a chemical compound. - - - - - - - - - - Window step size - - 1.5 - beta12orEarlier - true - Size of the incremental 'step' a sequence window is moved over a sequence. - - - - - - - - - - EMBOSS graph - - beta12orEarlier - true - beta12orEarlier - An image of a graph generated by the EMBOSS suite. - - - - - - - - - - EMBOSS report - - An application report generated by the EMBOSS suite. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Sequence offset - - true - beta12orEarlier - 1.5 - An offset for a single-point sequence position. - - - - - - - - - - Threshold - - 1.5 - beta12orEarlier - true - A value that serves as a threshold for a tool (usually to control scoring or output). - - - - - - - - - - Protein report (transcription factor) - - beta13 - true - This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. - An informative report on a transcription factor protein. - Transcription factor binding site data - beta12orEarlier - - - - - - - - - - Database category name - - true - The name of a category of biological or bioinformatics database. - beta12orEarlier - beta12orEarlier - - - - - - - - - - Sequence profile name - - beta12orEarlier - Name of a sequence profile. - true - beta12orEarlier - - - - - - - - - - Color - - Specification of one or more colors. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Rendering parameter - - true - beta12orEarlier - 1.5 - A parameter that is used to control rendering (drawing) to a device or image. - Graphics parameter - Graphical parameter - - - - - - - - - - Sequence name - - - Any arbitrary name of a molecular sequence. - beta12orEarlier - - - - - - - - - - - Date - - 1.5 - A temporal date. - beta12orEarlier - true - - - - - - - - - - Word composition - - beta12orEarlier - Word composition data for a molecular sequence. - true - beta12orEarlier - - - - - - - - - - - Fickett testcode plot - - A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences. - beta12orEarlier - - - - - - - - - - Sequence similarity plot - - - Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. - beta12orEarlier - Sequence conservation report - Sequence similarity plot - A plot of sequence similarities identified from word-matching or character comparison. - - - - - - - - - - Helical wheel - - beta12orEarlier - An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties. - - - - - - - - - - Helical net - - beta12orEarlier - Useful for highlighting amphipathicity and other properties. - An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix. - - - - - - - - - - Protein sequence properties plot - - true - beta12orEarlier - beta12orEarlier - A plot of general physicochemical properties of a protein sequence. - - - - - - - - - - Protein ionization curve - - - beta12orEarlier - A plot of pK versus pH for a protein. - - - - - - - - - - Sequence composition plot - - - beta12orEarlier - A plot of character or word composition / frequency of a molecular sequence. - - - - - - - - - - Nucleic acid density plot - - - beta12orEarlier - Density plot (of base composition) for a nucleotide sequence. - - - - - - - - - - Sequence trace image - - Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases). - beta12orEarlier - - - - - - - - - - Nucleic acid features (siRNA) - - true - 1.5 - beta12orEarlier - A report on siRNA duplexes in mRNA. - - - - - - - - - - Sequence set (stream) - - beta12orEarlier - true - This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. - A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing. - beta12orEarlier - - - - - - - - - - FlyBase secondary identifier - - Secondary identifier of an object from the FlyBase database. - Secondary identifier are used to handle entries that were merged with or split from other entries in the database. - beta12orEarlier - - - - - - - - - - - Cardinality - - The number of a certain thing. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Exactly 1 - - beta12orEarlier - beta12orEarlier - A single thing. - true - - - - - - - - - 1 or more - - One or more things. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - Exactly 2 - - Exactly two things. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - 2 or more - - Two or more things. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - Sequence checksum - - A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing. - beta12orEarlier - Hash code - Hash sum - Hash - Hash value - - - - - - - - - - Protein features report (chemical modifications) - - 1.8 - beta12orEarlier - chemical modification of a protein. - true - - - - - - - - - - Error - - beta12orEarlier - Data on an error generated by computer system or tool. - 1.5 - true - - - - - - - - - - Database entry metadata - - beta12orEarlier - Basic information on any arbitrary database entry. - - - - - - - - - - Gene cluster - - beta13 - true - beta12orEarlier - A cluster of similar genes. - - - - - - - - - - Sequence record full - - true - beta12orEarlier - A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. - 1.8 - - - - - - - - - - Plasmid identifier - - An identifier of a plasmid in a database. - beta12orEarlier - - - - - - - - - - - Mutation ID - - - beta12orEarlier - A unique identifier of a specific mutation catalogued in a database. - - - - - - - - - - - Mutation annotation (basic) - - Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Mutation annotation (prevalence) - - beta12orEarlier - true - An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).. - beta12orEarlier - - - - - - - - - - Mutation annotation (prognostic) - - beta12orEarlier - An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study. - beta12orEarlier - true - - - - - - - - - - Mutation annotation (functional) - - An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - Codon number - - beta12orEarlier - The number of a codon, for instance, at which a mutation is located. - - - - - - - - - - Tumor annotation - - true - 1.4 - An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. - beta12orEarlier - - - - - - - - - - Server metadata - - Basic information about a server on the web, such as an SRS server. - beta12orEarlier - 1.5 - true - - - - - - - - - - Database field name - - The name of a field in a database. - beta12orEarlier - - - - - - - - - - - Sequence cluster ID (SYSTERS) - - SYSTERS cluster ID - Unique identifier of a sequence cluster from the SYSTERS database. - beta12orEarlier - - - - - - - - - - - Ontology metadata - - - - - - - - beta12orEarlier - Data concerning a biological ontology. - - - - - - - - - - Raw SCOP domain classification - - true - beta12orEarlier - Raw SCOP domain classification data files. - beta13 - These are the parsable data files provided by SCOP. - - - - - - - - - - Raw CATH domain classification - - Raw CATH domain classification data files. - These are the parsable data files provided by CATH. - true - beta13 - beta12orEarlier - - - - - - - - - - Heterogen annotation - - 1.4 - true - beta12orEarlier - An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. - - - - - - - - - - Phylogenetic property values - - beta12orEarlier - Phylogenetic property values data. - true - beta12orEarlier - - - - - - - - - - Sequence set (bootstrapped) - - 1.5 - beta12orEarlier - Bootstrapping is often performed in phylogenetic analysis. - true - A collection of sequences output from a bootstrapping (resampling) procedure. - - - - - - - - - - Phylogenetic consensus tree - - true - A consensus phylogenetic tree derived from comparison of multiple trees. - beta12orEarlier - beta12orEarlier - - - - - - - - - - Schema - - beta12orEarlier - true - A data schema for organising or transforming data of some type. - 1.5 - - - - - - - - - - DTD - - A DTD (document type definition). - true - beta12orEarlier - 1.5 - - - - - - - - - - XML Schema - - beta12orEarlier - XSD - An XML Schema. - true - 1.5 - - - - - - - - - - Relax-NG schema - - beta12orEarlier - 1.5 - A relax-NG schema. - true - - - - - - - - - - XSLT stylesheet - - 1.5 - beta12orEarlier - An XSLT stylesheet. - true - - - - - - - - - Data resource definition name - - - beta12orEarlier - The name of a data type. - - - - - - - - - - - OBO file format name - - Name of an OBO file format such as OBO-XML, plain and so on. - beta12orEarlier - - - - - - - - - - - Gene ID (MIPS) - - Identifier for genetic elements in MIPS database. - beta12orEarlier - MIPS genetic element identifier - - - - - - - - - - - Sequence identifier (protein) - - An identifier of protein sequence(s) or protein sequence database entries. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Sequence identifier (nucleic acid) - - An identifier of nucleotide sequence(s) or nucleotide sequence database entries. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - EMBL accession - - EMBL ID - beta12orEarlier - EMBL accession number - EMBL identifier - An accession number of an entry from the EMBL sequence database. - - - - - - - - - - - UniProt ID - - - - - - - - UniProtKB identifier - An identifier of a polypeptide in the UniProt database. - UniProtKB entry name - beta12orEarlier - UniProt identifier - UniProt entry name - - - - - - - - - - - GenBank accession - - GenBank ID - GenBank identifier - Accession number of an entry from the GenBank sequence database. - beta12orEarlier - GenBank accession number - - - - - - - - - - - Gramene secondary identifier - - beta12orEarlier - Gramene internal identifier - Gramene internal ID - Secondary (internal) identifier of a Gramene database entry. - Gramene secondary ID - - - - - - - - - - - Sequence variation ID - - - An identifier of an entry from a database of molecular sequence variation. - beta12orEarlier - - - - - - - - - - - Gene ID - - - Gene accession - beta12orEarlier - A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol. - Gene code - - - - - - - - - - - Gene name (AceView) - - AceView gene name - 1.3 - true - Name of an entry (gene) from the AceView genes database. - beta12orEarlier - - - - - - - - - - Gene ID (ECK) - - ECK accession - beta12orEarlier - E. coli K-12 gene identifier - Identifier of an E. coli K-12 gene from EcoGene Database. - http://www.geneontology.org/doc/GO.xrf_abbs: ECK - - - - - - - - - - - Gene ID (HGNC) - - HGNC ID - beta12orEarlier - Identifier for a gene approved by the HUGO Gene Nomenclature Committee. - - - - - - - - - - - Gene name - - - The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol. - Allele name - beta12orEarlier - - - - - - - - - - - Gene name (NCBI) - - beta12orEarlier - 1.3 - NCBI gene name - Name of an entry (gene) from the NCBI genes database. - true - - - - - - - - - - SMILES string - - A specification of a chemical structure in SMILES format. - beta12orEarlier - - - - - - - - - - STRING ID - - Unique identifier of an entry from the STRING database of protein-protein interactions. - beta12orEarlier - - - - - - - - - - - Virus annotation - - An informative report on a specific virus. - true - 1.4 - beta12orEarlier - - - - - - - - - - Virus annotation (taxonomy) - - An informative report on the taxonomy of a specific virus. - beta12orEarlier - true - 1.4 - - - - - - - - - - Reaction ID (SABIO-RK) - - Identifier of a biological reaction from the SABIO-RK reactions database. - beta12orEarlier - [0-9]+ - - - - - - - - - - - Carbohydrate report - - Annotation on or information derived from one or more specific carbohydrate 3D structure(s). - beta12orEarlier - - - - - - - - - - GI number - - beta12orEarlier - NCBI GI number - gi number - A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record. - Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. - - - - - - - - - - - NCBI version - - beta12orEarlier - NCBI accession.version - Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number. - An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number. - accession.version - - - - - - - - - - - Cell line name - - beta12orEarlier - The name of a cell line. - - - - - - - - - - - Cell line name (exact) - - beta12orEarlier - The name of a cell line. - - - - - - - - - - - Cell line name (truncated) - - The name of a cell line. - beta12orEarlier - - - - - - - - - - - Cell line name (no punctuation) - - The name of a cell line. - beta12orEarlier - - - - - - - - - - - Cell line name (assonant) - - The name of a cell line. - beta12orEarlier - - - - - - - - - - - Enzyme ID - - - beta12orEarlier - A unique, persistent identifier of an enzyme. - Enzyme accession - - - - - - - - - - - REBASE enzyme number - - Identifier of an enzyme from the REBASE enzymes database. - beta12orEarlier - - - - - - - - - - - DrugBank ID - - beta12orEarlier - DB[0-9]{5} - Unique identifier of a drug from the DrugBank database. - - - - - - - - - - - GI number (protein) - - beta12orEarlier - protein gi number - A unique identifier assigned to NCBI protein sequence records. - Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. - protein gi - - - - - - - - - - - Bit score - - A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system. - Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. - beta12orEarlier - - - - - - - - - - Translation phase specification - - beta12orEarlier - Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence. - Phase - - - - - - - - - - Resource metadata - - Data concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing. - This is a broad data type and is used a placeholder for other, more specific types. - Provenance metadata - beta12orEarlier - - - - - - - - - - Ontology identifier - - - - - - - - beta12orEarlier - Any arbitrary identifier of an ontology. - - - - - - - - - - - Ontology concept name - - - The name of a concept in an ontology. - beta12orEarlier - - - - - - - - - - - Genome build identifier - - beta12orEarlier - An identifier of a build of a particular genome. - - - - - - - - - - - Pathway or network name - - The name of a biological pathway or network. - beta12orEarlier - - - - - - - - - - - Pathway ID (KEGG) - - - Identifier of a pathway from the KEGG pathway database. - beta12orEarlier - [a-zA-Z_0-9]{2,3}[0-9]{5} - KEGG pathway ID - - - - - - - - - - - Pathway ID (NCI-Nature) - - beta12orEarlier - [a-zA-Z_0-9]+ - Identifier of a pathway from the NCI-Nature pathway database. - - - - - - - - - - - Pathway ID (ConsensusPathDB) - - - beta12orEarlier - Identifier of a pathway from the ConsensusPathDB pathway database. - - - - - - - - - - - Sequence cluster ID (UniRef) - - Unique identifier of an entry from the UniRef database. - UniRef cluster id - UniRef entry accession - beta12orEarlier - - - - - - - - - - - Sequence cluster ID (UniRef100) - - UniRef100 cluster id - beta12orEarlier - UniRef100 entry accession - Unique identifier of an entry from the UniRef100 database. - - - - - - - - - - - Sequence cluster ID (UniRef90) - - UniRef90 entry accession - beta12orEarlier - UniRef90 cluster id - Unique identifier of an entry from the UniRef90 database. - - - - - - - - - - - Sequence cluster ID (UniRef50) - - beta12orEarlier - UniRef50 cluster id - UniRef50 entry accession - Unique identifier of an entry from the UniRef50 database. - - - - - - - - - - - Ontology data - - - - - - - - Data concerning or derived from an ontology. - Ontological data - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. - - - - - - - - - - RNA family report - - beta12orEarlier - An informative report on a specific RNA family or other group of classified RNA sequences. - RNA family annotation - - - - - - - - - - RNA family identifier - - - - - - - - beta12orEarlier - Identifier of an RNA family, typically an entry from a RNA sequence classification database. - - - - - - - - - - - RFAM accession - - - Stable accession number of an entry (RNA family) from the RFAM database. - beta12orEarlier - - - - - - - - - - - Protein signature type - - beta12orEarlier - true - A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. - 1.5 - - - - - - - - - - Domain-nucleic acid interaction report - - 1.5 - true - An informative report on protein domain-DNA/RNA interaction(s). - beta12orEarlier - - - - - - - - - - Domain-domain interactions - - 1.8 - An informative report on protein domain-protein domain interaction(s). - beta12orEarlier - true - - - - - - - - - - Domain-domain interaction (indirect) - - true - beta12orEarlier - beta12orEarlier - Data on indirect protein domain-protein domain interaction(s). - - - - - - - - - - Sequence accession (hybrid) - - - - - - - - Accession number of a nucleotide or protein sequence database entry. - beta12orEarlier - - - - - - - - - - - 2D PAGE data - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - beta13 - beta12orEarlier - true - Data concerning two-dimensional polygel electrophoresis. - - - - - - - - - - - 2D PAGE report - - beta12orEarlier - two-dimensional gel electrophoresis experiments, gels or spots in a gel. - 1.8 - true - - - - - - - - - - Pathway or network accession - - - A persistent, unique identifier of a biological pathway or network (typically a database entry). - beta12orEarlier - - - - - - - - - - - Secondary structure alignment - - Alignment of the (1D representations of) secondary structure of two or more molecules. - beta12orEarlier - - - - - - - - - - ASTD ID - - - beta12orEarlier - Identifier of an object from the ASTD database. - - - - - - - - - - - ASTD ID (exon) - - beta12orEarlier - Identifier of an exon from the ASTD database. - - - - - - - - - - - ASTD ID (intron) - - beta12orEarlier - Identifier of an intron from the ASTD database. - - - - - - - - - - - ASTD ID (polya) - - Identifier of a polyA signal from the ASTD database. - beta12orEarlier - - - - - - - - - - - ASTD ID (tss) - - Identifier of a transcription start site from the ASTD database. - beta12orEarlier - - - - - - - - - - - 2D PAGE spot report - - 2D PAGE spot annotation - beta12orEarlier - An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. - 1.8 - true - - - - - - - - - - Spot ID - - - beta12orEarlier - Unique identifier of a spot from a two-dimensional (protein) gel. - - - - - - - - - - - Spot serial number - - Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database. - beta12orEarlier - - - - - - - - - - - Spot ID (HSC-2DPAGE) - - Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database. - beta12orEarlier - - - - - - - - - - - Protein-motif interaction - - beta13 - true - Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. - beta12orEarlier - - - - - - - - - - Strain identifier - - Identifier of a strain of an organism variant, typically a plant, virus or bacterium. - beta12orEarlier - - - - - - - - - - - CABRI accession - - - A unique identifier of an item from the CABRI database. - beta12orEarlier - - - - - - - - - - - Experiment report (genotyping) - - true - Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. - 1.8 - beta12orEarlier - - - - - - - - - - Genotype experiment ID - - - - - - - - - beta12orEarlier - Identifier of an entry from a database of genotype experiment metadata. - - - - - - - - - - - EGA accession - - beta12orEarlier - Identifier of an entry from the EGA database. - - - - - - - - - - - IPI protein ID - - Identifier of a protein entry catalogued in the International Protein Index (IPI) database. - IPI[0-9]{8} - beta12orEarlier - - - - - - - - - - - RefSeq accession (protein) - - RefSeq protein ID - Accession number of a protein from the RefSeq database. - beta12orEarlier - - - - - - - - - - - EPD ID - - beta12orEarlier - Identifier of an entry (promoter) from the EPD database. - EPD identifier - - - - - - - - - - - TAIR accession - - - beta12orEarlier - Identifier of an entry from the TAIR database. - - - - - - - - - - - TAIR accession (At gene) - - beta12orEarlier - Identifier of an Arabidopsis thaliana gene from the TAIR database. - - - - - - - - - - - UniSTS accession - - beta12orEarlier - Identifier of an entry from the UniSTS database. - - - - - - - - - - - UNITE accession - - beta12orEarlier - Identifier of an entry from the UNITE database. - - - - - - - - - - - UTR accession - - beta12orEarlier - Identifier of an entry from the UTR database. - - - - - - - - - - - UniParc accession - - beta12orEarlier - UPI[A-F0-9]{10} - Accession number of a UniParc (protein sequence) database entry. - UniParc ID - UPI - - - - - - - - - - - mFLJ/mKIAA number - - beta12orEarlier - Identifier of an entry from the Rouge or HUGE databases. - - - - - - - - - - - Fungi annotation - - true - beta12orEarlier - 1.4 - An informative report on a specific fungus. - - - - - - - - - - Fungi annotation (anamorph) - - beta12orEarlier - An informative report on a specific fungus anamorph. - 1.4 - true - - - - - - - - - - Gene features report (exon) - - true - exons in a nucleotide sequences. - 1.8 - beta12orEarlier - - - - - - - - - - Ensembl protein ID - - - Ensembl ID (protein) - beta12orEarlier - Protein ID (Ensembl) - Unique identifier for a protein from the Ensembl database. - - - - - - - - - - - Gene transcriptional features report - - 1.8 - beta12orEarlier - transcription of DNA into RNA including the regulation of transcription. - true - - - - - - - - - - Toxin annotation - - beta12orEarlier - An informative report on a specific toxin. - 1.4 - true - - - - - - - - - - Protein report (membrane protein) - - beta12orEarlier - true - An informative report on a membrane protein. - beta12orEarlier - - - - - - - - - - Protein-drug interaction report - - - - An informative report on tentative or known protein-drug interaction(s). - beta12orEarlier - - - - - - - - - - Map data - - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. - true - beta13 - Data concerning a map of molecular sequence(s). - - - - - - - - - - - Phylogenetic data - - Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. - Phylogenetic data - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier - - - - - - - - - - Protein data - - This is a broad data type and is used a placeholder for other, more specific types. - beta13 - Data concerning one or more protein molecules. - true - beta12orEarlier - - - - - - - - - - Nucleic acid data - - true - Data concerning one or more nucleic acid molecules. - beta13 - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. - - - - - - - - - - Article data - - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. - Article report - Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal. - - - - - - - - - - - Parameter - - http://semanticscience.org/resource/SIO_000144 - Tool-specific parameter - beta12orEarlier - http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter - Typically a simple numerical or string value that controls the operation of a tool. - Parameters - Tool parameter - - - - - - - - - - Molecular data - - Molecule-specific data - true - Data concerning a specific type of molecule. - beta13 - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. - - - - - - - - - - Molecule report - - An informative report on a specific molecule. - beta12orEarlier - Molecular report - 1.5 - true - - - - - - - - - - - Organism report - - An informative report on a specific organism. - beta12orEarlier - Organism annotation - - - - - - - - - - Experiment report - - Experiment metadata - beta12orEarlier - Experiment annotation - Annotation on a wet lab experiment, such as experimental conditions. - - - - - - - - - - Nucleic acid features report (mutation) - - DNA mutation. - 1.8 - true - beta12orEarlier - - - - - - - - - - Sequence attribute - - An attribute of a molecular sequence, possibly in reference to some other sequence. - Sequence parameter - beta12orEarlier - - - - - - - - - - Sequence tag profile - - SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from. - beta12orEarlier - Sequencing-based expression profile - Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed. - - - - - - - - - - Mass spectrometry data - - beta12orEarlier - Data concerning a mass spectrometry measurement. - - - - - - - - - - Protein structure raw data - - beta12orEarlier - Raw data from experimental methods for determining protein structure. - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - - - - - - - - - - Mutation identifier - - An identifier of a mutation. - beta12orEarlier - - - - - - - - - - - Alignment data - - This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles. - true - beta13 - Data concerning an alignment of two or more molecular sequences, structures or derived data. - beta12orEarlier - - - - - - - - - - - Data index data - - true - Data concerning an index of data. - beta12orEarlier - beta13 - Database index - This is a broad data type and is used a placeholder for other, more specific types. - - - - - - - - - - Amino acid name (single letter) - - beta12orEarlier - Single letter amino acid identifier, e.g. G. - - - - - - - - - - - Amino acid name (three letter) - - beta12orEarlier - Three letter amino acid identifier, e.g. GLY. - - - - - - - - - - - Amino acid name (full name) - - beta12orEarlier - Full name of an amino acid, e.g. Glycine. - - - - - - - - - - - Toxin identifier - - - - - - - - beta12orEarlier - Identifier of a toxin. - - - - - - - - - - - ArachnoServer ID - - Unique identifier of a toxin from the ArachnoServer database. - beta12orEarlier - - - - - - - - - - - Expressed gene list - - beta12orEarlier - true - 1.5 - Gene annotation (expressed gene list) - A simple summary of expressed genes. - - - - - - - - - - BindingDB Monomer ID - - Unique identifier of a monomer from the BindingDB database. - beta12orEarlier - - - - - - - - - - - GO concept name - - true - beta12orEarlier - beta12orEarlier - The name of a concept from the GO ontology. - - - - - - - - - - GO concept ID (biological process) - - [0-9]{7}|GO:[0-9]{7} - beta12orEarlier - An identifier of a 'biological process' concept from the the Gene Ontology. - - - - - - - - - - - GO concept ID (molecular function) - - beta12orEarlier - [0-9]{7}|GO:[0-9]{7} - An identifier of a 'molecular function' concept from the the Gene Ontology. - - - - - - - - - - - GO concept name (cellular component) - - The name of a concept for a cellular component from the GO ontology. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - Northern blot image - - beta12orEarlier - An image arising from a Northern Blot experiment. - - - - - - - - - - Blot ID - - - Unique identifier of a blot from a Northern Blot. - beta12orEarlier - - - - - - - - - - - BlotBase blot ID - - beta12orEarlier - Unique identifier of a blot from a Northern Blot from the BlotBase database. - - - - - - - - - - - Hierarchy - - beta12orEarlier - Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation. - Hierarchy annotation - - - - - - - - - - Hierarchy identifier - - Identifier of an entry from a database of biological hierarchies. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Brite hierarchy ID - - beta12orEarlier - Identifier of an entry from the Brite database of biological hierarchies. - - - - - - - - - - - Cancer type - - true - A type (represented as a string) of cancer. - beta12orEarlier - beta12orEarlier - - - - - - - - - - BRENDA organism ID - - A unique identifier for an organism used in the BRENDA database. - beta12orEarlier - - - - - - - - - - - UniGene taxon - - The name of a taxon using the controlled vocabulary of the UniGene database. - UniGene organism abbreviation - beta12orEarlier - - - - - - - - - - - UTRdb taxon - - beta12orEarlier - The name of a taxon using the controlled vocabulary of the UTRdb database. - - - - - - - - - - - Catalogue ID - - beta12orEarlier - An identifier of a catalogue of biological resources. - Catalogue identifier - - - - - - - - - - - CABRI catalogue name - - - The name of a catalogue of biological resources from the CABRI database. - beta12orEarlier - - - - - - - - - - - Secondary structure alignment metadata - - An informative report on protein secondary structure alignment-derived data or metadata. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Molecule interaction report - - An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules). - beta12orEarlier - Molecular interaction report - Molecular interaction data - - - - - - - - - Pathway or network - - - - - - - - Network - beta12orEarlier - Pathway - Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). - - - - - - - - - - Small molecule data - - true - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier - beta13 - Data concerning one or more small molecules. - - - - - - - - - - Genotype and phenotype data - - beta12orEarlier - true - beta13 - Data concerning a particular genotype, phenotype or a genotype / phenotype relation. - - - - - - - - - - Gene expression data - - - - - - - - beta12orEarlier - Image or hybridisation data for a microarray, typically a study of gene expression. - Microarray data - This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 - - - - - - - - - - Compound ID (KEGG) - - - C[0-9]+ - Unique identifier of a chemical compound from the KEGG database. - beta12orEarlier - KEGG compound ID - KEGG compound identifier - - - - - - - - - - - RFAM name - - - Name (not necessarily stable) an entry (RNA family) from the RFAM database. - beta12orEarlier - - - - - - - - - - - Reaction ID (KEGG) - - - Identifier of a biological reaction from the KEGG reactions database. - R[0-9]+ - beta12orEarlier - - - - - - - - - - - Drug ID (KEGG) - - - beta12orEarlier - Unique identifier of a drug from the KEGG Drug database. - D[0-9]+ - - - - - - - - - - - Ensembl ID - - - beta12orEarlier - ENS[A-Z]*[FPTG][0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database. - Ensembl IDs - - - - - - - - - - - ICD identifier - - - - - - - - An identifier of a disease from the International Classification of Diseases (ICD) database. - beta12orEarlier - [A-Z][0-9]+(\.[-[0-9]+])? - - - - - - - - - - - Sequence cluster ID (CluSTr) - - Unique identifier of a sequence cluster from the CluSTr database. - [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])? - CluSTr ID - beta12orEarlier - CluSTr cluster ID - - - - - - - - - - - KEGG Glycan ID - - - G[0-9]+ - Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND). - beta12orEarlier - - - - - - - - - - - TCDB ID - - beta12orEarlier - OBO file for regular expression. - TC number - [0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+ - A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins. - - - - - - - - - - - MINT ID - - MINT\-[0-9]{1,5} - Unique identifier of an entry from the MINT database of protein-protein interactions. - beta12orEarlier - - - - - - - - - - - DIP ID - - Unique identifier of an entry from the DIP database of protein-protein interactions. - beta12orEarlier - DIP[\:\-][0-9]{3}[EN] - - - - - - - - - - - Signaling Gateway protein ID - - beta12orEarlier - Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database. - A[0-9]{6} - - - - - - - - - - - Protein modification ID - - - beta12orEarlier - Identifier of a protein modification catalogued in a database. - - - - - - - - - - - RESID ID - - Identifier of a protein modification catalogued in the RESID database. - AA[0-9]{4} - beta12orEarlier - - - - - - - - - - - RGD ID - - - [0-9]{4,7} - beta12orEarlier - Identifier of an entry from the RGD database. - - - - - - - - - - - TAIR accession (protein) - - - - - - - - - AASequence:[0-9]{10} - Identifier of a protein sequence from the TAIR database. - beta12orEarlier - - - - - - - - - - - Compound ID (HMDB) - - HMDB[0-9]{5} - beta12orEarlier - HMDB ID - Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB). - - - - - - - - - - - LIPID MAPS ID - - beta12orEarlier - LM ID - Identifier of an entry from the LIPID MAPS database. - LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})? - - - - - - - - - - - PeptideAtlas ID - - Identifier of a peptide from the PeptideAtlas peptide databases. - PDBML:pdbx_PDB_strand_id - beta12orEarlier - PAp[0-9]{8} - - - - - - - - - - - Molecular interaction ID - - Identifier of a report of molecular interactions from a database (typically). - true - beta12orEarlier - 1.7 - - - - - - - - - - BioGRID interaction ID - - [0-9]+ - beta12orEarlier - A unique identifier of an interaction from the BioGRID database. - - - - - - - - - - - Enzyme ID (MEROPS) - - MEROPS ID - Unique identifier of a peptidase enzyme from the MEROPS database. - beta12orEarlier - S[0-9]{2}\.[0-9]{3} - - - - - - - - - - - Mobile genetic element ID - - - An identifier of a mobile genetic element. - beta12orEarlier - - - - - - - - - - - ACLAME ID - - beta12orEarlier - mge:[0-9]+ - An identifier of a mobile genetic element from the Aclame database. - - - - - - - - - - - SGD ID - - - PWY[a-zA-Z_0-9]{2}\-[0-9]{3} - beta12orEarlier - Identifier of an entry from the Saccharomyces genome database (SGD). - - - - - - - - - - - Book ID - - - beta12orEarlier - Unique identifier of a book. - - - - - - - - - - - ISBN - - beta12orEarlier - (ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X) - The International Standard Book Number (ISBN) is for identifying printed books. - - - - - - - - - - - Compound ID (3DMET) - - B[0-9]{5} - 3DMET ID - beta12orEarlier - Identifier of a metabolite from the 3DMET database. - - - - - - - - - - - MatrixDB interaction ID - - ([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*) - A unique identifier of an interaction from the MatrixDB database. - beta12orEarlier - - - - - - - - - - - cPath ID - - - [0-9]+ - These identifiers are unique within the cPath database, however, they are not stable between releases. - beta12orEarlier - A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database. - - - - - - - - - - - PubChem bioassay ID - - - Identifier of an assay from the PubChem database. - [0-9]+ - beta12orEarlier - - - - - - - - - - - PubChem ID - - - PubChem identifier - beta12orEarlier - Identifier of an entry from the PubChem database. - - - - - - - - - - - Reaction ID (MACie) - - beta12orEarlier - M[0-9]{4} - MACie entry number - Identifier of an enzyme reaction mechanism from the MACie database. - - - - - - - - - - - Gene ID (miRBase) - - beta12orEarlier - miRNA name - miRNA ID - Identifier for a gene from the miRBase database. - MI[0-9]{7} - miRNA identifier - - - - - - - - - - - Gene ID (ZFIN) - - Identifier for a gene from the Zebrafish information network genome (ZFIN) database. - beta12orEarlier - ZDB\-GENE\-[0-9]+\-[0-9]+ - - - - - - - - - - - Reaction ID (Rhea) - - [0-9]{5} - Identifier of an enzyme-catalysed reaction from the Rhea database. - beta12orEarlier - - - - - - - - - - - Pathway ID (Unipathway) - - UPA[0-9]{5} - upaid - beta12orEarlier - Identifier of a biological pathway from the Unipathway database. - - - - - - - - - - - Compound ID (ChEMBL) - - Identifier of a small molecular from the ChEMBL database. - ChEMBL ID - beta12orEarlier - [0-9]+ - - - - - - - - - - - LGICdb identifier - - Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database. - beta12orEarlier - [a-zA-Z_0-9]+ - - - - - - - - - - - Reaction kinetics ID (SABIO-RK) - - Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database. - [0-9]+ - beta12orEarlier - - - - - - - - - - - PharmGKB ID - - - beta12orEarlier - Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - PA[0-9]+ - - - - - - - - - - - Pathway ID (PharmGKB) - - - PA[0-9]+ - Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - beta12orEarlier - - - - - - - - - - - Disease ID (PharmGKB) - - - Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - beta12orEarlier - PA[0-9]+ - - - - - - - - - - - Drug ID (PharmGKB) - - - beta12orEarlier - Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - PA[0-9]+ - - - - - - - - - - - Drug ID (TTD) - - DAP[0-9]+ - Identifier of a drug from the Therapeutic Target Database (TTD). - beta12orEarlier - - - - - - - - - - - Target ID (TTD) - - TTDS[0-9]+ - Identifier of a target protein from the Therapeutic Target Database (TTD). - beta12orEarlier - - - - - - - - - - - Cell type identifier - - beta12orEarlier - Cell type ID - A unique identifier of a type or group of cells. - - - - - - - - - - - NeuronDB ID - - [0-9]+ - beta12orEarlier - A unique identifier of a neuron from the NeuronDB database. - - - - - - - - - - - NeuroMorpho ID - - beta12orEarlier - A unique identifier of a neuron from the NeuroMorpho database. - [a-zA-Z_0-9]+ - - - - - - - - - - - Compound ID (ChemIDplus) - - Identifier of a chemical from the ChemIDplus database. - ChemIDplus ID - [0-9]+ - beta12orEarlier - - - - - - - - - - - Pathway ID (SMPDB) - - beta12orEarlier - Identifier of a pathway from the Small Molecule Pathway Database (SMPDB). - SMP[0-9]{5} - - - - - - - - - - - BioNumbers ID - - Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. - [0-9]+ - beta12orEarlier - - - - - - - - - - - T3DB ID - - beta12orEarlier - T3D[0-9]+ - Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database. - - - - - - - - - - - Carbohydrate identifier - - - - - - - - - - - - - - beta12orEarlier - Identifier of a carbohydrate. - - - - - - - - - - - GlycomeDB ID - - Identifier of an entry from the GlycomeDB database. - beta12orEarlier - [0-9]+ - - - - - - - - - - - LipidBank ID - - beta12orEarlier - [a-zA-Z_0-9]+[0-9]+ - Identifier of an entry from the LipidBank database. - - - - - - - - - - - CDD ID - - beta12orEarlier - cd[0-9]{5} - Identifier of a conserved domain from the Conserved Domain Database. - - - - - - - - - - - MMDB ID - - [0-9]{1,5} - beta12orEarlier - An identifier of an entry from the MMDB database. - MMDB accession - - - - - - - - - - - iRefIndex ID - - Unique identifier of an entry from the iRefIndex database of protein-protein interactions. - beta12orEarlier - [0-9]+ - - - - - - - - - - - ModelDB ID - - Unique identifier of an entry from the ModelDB database. - [0-9]+ - beta12orEarlier - - - - - - - - - - - Pathway ID (DQCS) - - [0-9]+ - Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS). - beta12orEarlier - - - - - - - - - - - Ensembl ID (Homo sapiens) - - beta12orEarlier - true - beta12orEarlier - ENS([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division). - - - - - - - - - - Ensembl ID ('Bos taurus') - - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). - true - beta12orEarlier - ENSBTA([EGTP])[0-9]{11} - - - - - - - - - - Ensembl ID ('Canis familiaris') - - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). - true - ENSCAF([EGTP])[0-9]{11} - beta12orEarlier - - - - - - - - - - Ensembl ID ('Cavia porcellus') - - ENSCPO([EGTP])[0-9]{11} - true - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). - beta12orEarlier - - - - - - - - - - Ensembl ID ('Ciona intestinalis') - - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). - beta12orEarlier - beta12orEarlier - ENSCIN([EGTP])[0-9]{11} - - - - - - - - - - Ensembl ID ('Ciona savignyi') - - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division). - ENSCSAV([EGTP])[0-9]{11} - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Ensembl ID ('Danio rerio') - - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division). - true - beta12orEarlier - beta12orEarlier - ENSDAR([EGTP])[0-9]{11} - - - - - - - - - - Ensembl ID ('Dasypus novemcinctus') - - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division). - beta12orEarlier - beta12orEarlier - ENSDNO([EGTP])[0-9]{11} - true - - - - - - - - - - Ensembl ID ('Echinops telfairi') - - ENSETE([EGTP])[0-9]{11} - true - beta12orEarlier - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). - - - - - - - - - - Ensembl ID ('Erinaceus europaeus') - - true - ENSEEU([EGTP])[0-9]{11} - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). - beta12orEarlier - - - - - - - - - - Ensembl ID ('Felis catus') - - beta12orEarlier - true - ENSFCA([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division). - beta12orEarlier - - - - - - - - - - Ensembl ID ('Gallus gallus') - - ENSGAL([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Ensembl ID ('Gasterosteus aculeatus') - - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). - true - ENSGAC([EGTP])[0-9]{11} - beta12orEarlier - - - - - - - - - - Ensembl ID ('Homo sapiens') - - ENSHUM([EGTP])[0-9]{11} - beta12orEarlier - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division). - true - - - - - - - - - - Ensembl ID ('Loxodonta africana') - - beta12orEarlier - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). - ENSLAF([EGTP])[0-9]{11} - beta12orEarlier - - - - - - - - - - Ensembl ID ('Macaca mulatta') - - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division). - beta12orEarlier - ENSMMU([EGTP])[0-9]{11} - true - beta12orEarlier - - - - - - - - - - Ensembl ID ('Monodelphis domestica') - - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division). - true - ENSMOD([EGTP])[0-9]{11} - beta12orEarlier - - - - - - - - - - Ensembl ID ('Mus musculus') - - ENSMUS([EGTP])[0-9]{11} - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division). - beta12orEarlier - beta12orEarlier - - - - - - - - - - Ensembl ID ('Myotis lucifugus') - - beta12orEarlier - ENSMLU([EGTP])[0-9]{11} - true - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division). - - - - - - - - - - Ensembl ID ("Ornithorhynchus anatinus") - - beta12orEarlier - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). - ENSOAN([EGTP])[0-9]{11} - beta12orEarlier - - - - - - - - - - Ensembl ID ('Oryctolagus cuniculus') - - beta12orEarlier - ENSOCU([EGTP])[0-9]{11} - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division). - beta12orEarlier - - - - - - - - - - Ensembl ID ('Oryzias latipes') - - ENSORL([EGTP])[0-9]{11} - true - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division). - beta12orEarlier - - - - - - - - - - Ensembl ID ('Otolemur garnettii') - - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). - true - beta12orEarlier - ENSSAR([EGTP])[0-9]{11} - - - - - - - - - - Ensembl ID ('Pan troglodytes') - - beta12orEarlier - beta12orEarlier - ENSPTR([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division). - true - - - - - - - - - - Ensembl ID ('Rattus norvegicus') - - beta12orEarlier - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). - ENSRNO([EGTP])[0-9]{11} - beta12orEarlier - - - - - - - - - - Ensembl ID ('Spermophilus tridecemlineatus') - - true - beta12orEarlier - ENSSTO([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). - beta12orEarlier - - - - - - - - - - Ensembl ID ('Takifugu rubripes') - - beta12orEarlier - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). - ENSFRU([EGTP])[0-9]{11} - true - - - - - - - - - - Ensembl ID ('Tupaia belangeri') - - beta12orEarlier - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). - true - ENSTBE([EGTP])[0-9]{11} - - - - - - - - - - Ensembl ID ('Xenopus tropicalis') - - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division). - beta12orEarlier - beta12orEarlier - true - ENSXET([EGTP])[0-9]{11} - - - - - - - - - - CATH identifier - - beta12orEarlier - Identifier of a protein domain (or other node) from the CATH database. - - - - - - - - - - - CATH node ID (family) - - beta12orEarlier - A code number identifying a family from the CATH database. - 2.10.10.10 - - - - - - - - - - - Enzyme ID (CAZy) - - Identifier of an enzyme from the CAZy enzymes database. - beta12orEarlier - CAZy ID - - - - - - - - - - - Clone ID (IMAGE) - - I.M.A.G.E. cloneID - IMAGE cloneID - A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence). - beta12orEarlier - - - - - - - - - - - GO concept ID (cellular compartment) - - An identifier of a 'cellular compartment' concept from the Gene Ontology. - [0-9]{7}|GO:[0-9]{7} - beta12orEarlier - GO concept identifier (cellular compartment) - - - - - - - - - - - Chromosome name (BioCyc) - - Name of a chromosome as used in the BioCyc database. - beta12orEarlier - - - - - - - - - - - CleanEx entry name - - beta12orEarlier - An identifier of a gene expression profile from the CleanEx database. - - - - - - - - - - - CleanEx dataset code - - beta12orEarlier - An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database. - - - - - - - - - - - Genome report - - An informative report of general information concerning a genome as a whole. - beta12orEarlier - - - - - - - - - - Protein ID (CORUM) - - beta12orEarlier - CORUM complex ID - Unique identifier for a protein complex from the CORUM database. - - - - - - - - - - - CDD PSSM-ID - - beta12orEarlier - Unique identifier of a position-specific scoring matrix from the CDD database. - - - - - - - - - - - Protein ID (CuticleDB) - - CuticleDB ID - beta12orEarlier - Unique identifier for a protein from the CuticleDB database. - - - - - - - - - - - DBD ID - - Identifier of a predicted transcription factor from the DBD database. - beta12orEarlier - - - - - - - - - - - Oligonucleotide probe annotation - - - - - - - - beta12orEarlier - General annotation on an oligonucleotide probe. - - - - - - - - - - Oligonucleotide ID - - - Identifier of an oligonucleotide from a database. - beta12orEarlier - - - - - - - - - - - dbProbe ID - - Identifier of an oligonucleotide probe from the dbProbe database. - beta12orEarlier - - - - - - - - - - - Dinucleotide property - - beta12orEarlier - Physicochemical property data for one or more dinucleotides. - - - - - - - - - - DiProDB ID - - beta12orEarlier - Identifier of an dinucleotide property from the DiProDB database. - - - - - - - - - - - Protein features report (disordered structure) - - 1.8 - true - beta12orEarlier - disordered structure in a protein. - - - - - - - - - - Protein ID (DisProt) - - DisProt ID - beta12orEarlier - Unique identifier for a protein from the DisProt database. - - - - - - - - - - - Embryo report - - Annotation on an embryo or concerning embryological development. - true - Embryo annotation - beta12orEarlier - 1.5 - - - - - - - - - - Ensembl transcript ID - - - beta12orEarlier - Transcript ID (Ensembl) - Unique identifier for a gene transcript from the Ensembl database. - - - - - - - - - - - Inhibitor annotation - - 1.4 - beta12orEarlier - An informative report on one or more small molecules that are enzyme inhibitors. - true - - - - - - - - - - Promoter ID - - - beta12orEarlier - An identifier of a promoter of a gene that is catalogued in a database. - Moby:GeneAccessionList - - - - - - - - - - - EST accession - - Identifier of an EST sequence. - beta12orEarlier - - - - - - - - - - - COGEME EST ID - - beta12orEarlier - Identifier of an EST sequence from the COGEME database. - - - - - - - - - - - COGEME unisequence ID - - Identifier of a unisequence from the COGEME database. - A unisequence is a single sequence assembled from ESTs. - beta12orEarlier - - - - - - - - - - - Protein family ID (GeneFarm) - - GeneFarm family ID - beta12orEarlier - Accession number of an entry (family) from the TIGRFam database. - - - - - - - - - - - Family name - - beta12orEarlier - The name of a family of organism. - - - - - - - - - - - Genus name (virus) - - true - The name of a genus of viruses. - beta13 - beta12orEarlier - - - - - - - - - - Family name (virus) - - beta13 - The name of a family of viruses. - true - beta12orEarlier - - - - - - - - - - Database name (SwissRegulon) - - true - beta13 - The name of a SwissRegulon database. - beta12orEarlier - - - - - - - - - - Sequence feature ID (SwissRegulon) - - beta12orEarlier - A feature identifier as used in the SwissRegulon database. - This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end". - - - - - - - - - - - FIG ID - - A FIG ID consists of four parts: a prefix, genome id, locus type and id number. - A unique identifier of gene in the NMPDR database. - beta12orEarlier - - - - - - - - - - - Gene ID (Xenbase) - - A unique identifier of gene in the Xenbase database. - beta12orEarlier - - - - - - - - - - - Gene ID (Genolist) - - beta12orEarlier - A unique identifier of gene in the Genolist database. - - - - - - - - - - - Gene name (Genolist) - - beta12orEarlier - true - Genolist gene name - 1.3 - Name of an entry (gene) from the Genolist genes database. - - - - - - - - - - ABS ID - - ABS identifier - beta12orEarlier - Identifier of an entry (promoter) from the ABS database. - - - - - - - - - - - AraC-XylS ID - - Identifier of a transcription factor from the AraC-XylS database. - beta12orEarlier - - - - - - - - - - - Gene name (HUGO) - - beta12orEarlier - beta12orEarlier - true - Name of an entry (gene) from the HUGO database. - - - - - - - - - - Locus ID (PseudoCAP) - - beta12orEarlier - Identifier of a locus from the PseudoCAP database. - - - - - - - - - - - Locus ID (UTR) - - beta12orEarlier - Identifier of a locus from the UTR database. - - - - - - - - - - - MonosaccharideDB ID - - Unique identifier of a monosaccharide from the MonosaccharideDB database. - beta12orEarlier - - - - - - - - - - - Database name (CMD) - - beta12orEarlier - true - The name of a subdivision of the Collagen Mutation Database (CMD) database. - beta13 - - - - - - - - - - Database name (Osteogenesis) - - beta12orEarlier - true - beta13 - The name of a subdivision of the Osteogenesis database. - - - - - - - - - - Genome identifier - - An identifier of a particular genome. - beta12orEarlier - - - - - - - - - - - GenomeReviews ID - - beta12orEarlier - An identifier of a particular genome. - - - - - - - - - - - GlycoMap ID - - [0-9]+ - beta12orEarlier - Identifier of an entry from the GlycosciencesDB database. - - - - - - - - - - - Carbohydrate conformational map - - beta12orEarlier - A conformational energy map of the glycosidic linkages in a carbohydrate molecule. - - - - - - - - - - Gene features report (intron) - - introns in a nucleotide sequences. - true - beta12orEarlier - 1.8 - - - - - - - - - - Transcription factor name - - - The name of a transcription factor. - beta12orEarlier - - - - - - - - - - - TCID - - Identifier of a membrane transport proteins from the transport classification database (TCDB). - beta12orEarlier - - - - - - - - - - - Pfam domain name - - beta12orEarlier - Name of a domain from the Pfam database. - PF[0-9]{5} - - - - - - - - - - - Pfam clan ID - - beta12orEarlier - CL[0-9]{4} - Accession number of a Pfam clan. - - - - - - - - - - - Gene ID (VectorBase) - - VectorBase ID - beta12orEarlier - Identifier for a gene from the VectorBase database. - - - - - - - - - - - UTRSite ID - - Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs. - beta12orEarlier - - - - - - - - - - - Sequence signature report - - - - - - - - Sequence motif report - Sequence profile report - An informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc. - beta12orEarlier - - - - - - - - - - Locus annotation - - Locus report - true - beta12orEarlier - An informative report on a particular locus. - beta12orEarlier - - - - - - - - - - Protein name (UniProt) - - Official name of a protein as used in the UniProt database. - beta12orEarlier - - - - - - - - - - - Term ID list - - One or more terms from one or more controlled vocabularies which are annotations on an entity. - beta12orEarlier - true - The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included. - 1.5 - - - - - - - - - - HAMAP ID - - Name of a protein family from the HAMAP database. - beta12orEarlier - - - - - - - - - - - Identifier with metadata - - Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance. - beta12orEarlier - - - - - - - - - - Gene symbol annotation - - true - beta12orEarlier - Annotation about a gene symbol. - beta12orEarlier - - - - - - - - - - Transcript ID - - - - - - - - - Identifier of a RNA transcript. - beta12orEarlier - - - - - - - - - - - HIT ID - - Identifier of an RNA transcript from the H-InvDB database. - beta12orEarlier - - - - - - - - - - - HIX ID - - A unique identifier of gene cluster in the H-InvDB database. - beta12orEarlier - - - - - - - - - - - HPA antibody id - - beta12orEarlier - Identifier of a antibody from the HPA database. - - - - - - - - - - - IMGT/HLA ID - - Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database. - beta12orEarlier - - - - - - - - - - - Gene ID (JCVI) - - A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI). - beta12orEarlier - - - - - - - - - - - Kinase name - - beta12orEarlier - The name of a kinase protein. - - - - - - - - - - - ConsensusPathDB entity ID - - - Identifier of a physical entity from the ConsensusPathDB database. - beta12orEarlier - - - - - - - - - - - ConsensusPathDB entity name - - - beta12orEarlier - Name of a physical entity from the ConsensusPathDB database. - - - - - - - - - - - CCAP strain number - - The number of a strain of algae and protozoa from the CCAP database. - beta12orEarlier - - - - - - - - - - - Stock number - - - beta12orEarlier - An identifier of stock from a catalogue of biological resources. - - - - - - - - - - - Stock number (TAIR) - - beta12orEarlier - A stock number from The Arabidopsis information resource (TAIR). - - - - - - - - - - - REDIdb ID - - beta12orEarlier - Identifier of an entry from the RNA editing database (REDIdb). - - - - - - - - - - - SMART domain name - - Name of a domain from the SMART database. - beta12orEarlier - - - - - - - - - - - Protein family ID (PANTHER) - - beta12orEarlier - Panther family ID - Accession number of an entry (family) from the PANTHER database. - - - - - - - - - - - RNAVirusDB ID - - beta12orEarlier - Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. - A unique identifier for a virus from the RNAVirusDB database. - - - - - - - - - - - Virus ID - - - beta12orEarlier - An accession of annotation on a (group of) viruses (catalogued in a database). - - - - - - - - - - - NCBI Genome Project ID - - An identifier of a genome project assigned by NCBI. - beta12orEarlier - - - - - - - - - - - NCBI genome accession - - A unique identifier of a whole genome assigned by the NCBI. - beta12orEarlier - - - - - - - - - - - Sequence profile data - - 1.8 - Data concerning, extracted from, or derived from the analysis of a sequence profile, such as its name, length, technical details about the profile or it's construction, the biological role or annotation, and so on. - true - beta12orEarlier - - - - - - - - - - Protein ID (TopDB) - - beta12orEarlier - TopDB ID - Unique identifier for a membrane protein from the TopDB database. - - - - - - - - - - - Gel ID - - Gel identifier - Identifier of a two-dimensional (protein) gel. - beta12orEarlier - - - - - - - - - - - Reference map name (SWISS-2DPAGE) - - - beta12orEarlier - Name of a reference map gel from the SWISS-2DPAGE database. - - - - - - - - - - - Protein ID (PeroxiBase) - - PeroxiBase ID - beta12orEarlier - Unique identifier for a peroxidase protein from the PeroxiBase database. - - - - - - - - - - - SISYPHUS ID - - beta12orEarlier - Identifier of an entry from the SISYPHUS database of tertiary structure alignments. - - - - - - - - - - - ORF ID - - - beta12orEarlier - Accession of an open reading frame (catalogued in a database). - - - - - - - - - - - ORF identifier - - An identifier of an open reading frame. - beta12orEarlier - - - - - - - - - - - Linucs ID - - Identifier of an entry from the GlycosciencesDB database. - beta12orEarlier - - - - - - - - - - - Protein ID (LGICdb) - - beta12orEarlier - LGICdb ID - Unique identifier for a ligand-gated ion channel protein from the LGICdb database. - - - - - - - - - - - MaizeDB ID - - beta12orEarlier - Identifier of an EST sequence from the MaizeDB database. - - - - - - - - - - - Gene ID (MfunGD) - - beta12orEarlier - A unique identifier of gene in the MfunGD database. - - - - - - - - - - - Orpha number - - - - - - - - beta12orEarlier - An identifier of a disease from the Orpha database. - - - - - - - - - - - Protein ID (EcID) - - beta12orEarlier - Unique identifier for a protein from the EcID database. - - - - - - - - - - - Clone ID (RefSeq) - - - A unique identifier of a cDNA molecule catalogued in the RefSeq database. - beta12orEarlier - - - - - - - - - - - Protein ID (ConoServer) - - beta12orEarlier - Unique identifier for a cone snail toxin protein from the ConoServer database. - - - - - - - - - - - GeneSNP ID - - Identifier of a GeneSNP database entry. - beta12orEarlier - - - - - - - - - - - Lipid identifier - - - - - - - - - - - - - - Identifier of a lipid. - beta12orEarlier - - - - - - - - - - - Databank - - true - beta12orEarlier - A flat-file (textual) data archive. - beta12orEarlier - - - - - - - - - Web portal - - A web site providing data (web pages) on a common theme to a HTTP client. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - Gene ID (VBASE2) - - Identifier for a gene from the VBASE2 database. - beta12orEarlier - VBASE2 ID - - - - - - - - - - - DPVweb ID - - DPVweb virus ID - beta12orEarlier - A unique identifier for a virus from the DPVweb database. - - - - - - - - - - - Pathway ID (BioSystems) - - beta12orEarlier - Identifier of a pathway from the BioSystems pathway database. - [0-9]+ - - - - - - - - - - - Experimental data (proteomics) - - true - Data concerning a proteomics experiment. - beta12orEarlier - beta12orEarlier - - - - - - - - - - Abstract - - beta12orEarlier - An abstract of a scientific article. - - - - - - - - - - Lipid structure - - beta12orEarlier - 3D coordinate and associated data for a lipid structure. - - - - - - - - - - Drug structure - - beta12orEarlier - 3D coordinate and associated data for the (3D) structure of a drug. - - - - - - - - - - Toxin structure - - 3D coordinate and associated data for the (3D) structure of a toxin. - beta12orEarlier - - - - - - - - - - Position-specific scoring matrix - - - beta12orEarlier - PSSM - A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment. - - - - - - - - - - Distance matrix - - A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity. - beta12orEarlier - - - - - - - - - - Structural distance matrix - - Distances (values representing similarity) between a group of molecular structures. - beta12orEarlier - - - - - - - - - - Article metadata - - true - beta12orEarlier - Bibliographic data concerning scientific article(s). - 1.5 - - - - - - - - - - Ontology concept - - beta12orEarlier - This includes any fields from the concept definition such as concept name, definition, comments and so on. - A concept from a biological ontology. - - - - - - - - - - Codon usage bias - - A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences. - beta12orEarlier - - - - - - - - - - Northern blot report - - true - beta12orEarlier - 1.8 - Northern Blot experiments. - - - - - - - - - - Nucleic acid features report (VNTR) - - 1.8 - beta12orEarlier - true - variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. - - - - - - - - - - Nucleic acid features report (microsatellite) - - true - microsatellite polymorphism in a DNA sequence. - 1.8 - beta12orEarlier - - - - - - - - - - - Nucleic acid features report (RFLP) - - beta12orEarlier - true - 1.8 - restriction fragment length polymorphisms (RFLP) in a DNA sequence. - - - - - - - - - - Radiation hybrid map - - The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map. - A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome. - beta12orEarlier - RH map - - - - - - - - - - ID list - - A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data. - beta12orEarlier - - - - - - - - - - Phylogenetic gene frequencies data - - beta12orEarlier - Gene frequencies data that may be read during phylogenetic tree calculation. - - - - - - - - - - Sequence set (polymorphic) - - beta13 - beta12orEarlier - true - A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata. - - - - - - - - - - DRCAT resource - - 1.5 - An entry (resource) from the DRCAT bioinformatics resource catalogue. - beta12orEarlier - true - - - - - - - - - - Protein complex - - beta12orEarlier - 3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another. - - - - - - - - - - Protein structural motif - - beta12orEarlier - 3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role. - - - - - - - - - - Lipid report - - beta12orEarlier - Annotation on or information derived from one or more specific lipid 3D structure(s). - - - - - - - - - - Secondary structure image - - 1.4 - beta12orEarlier - Image of one or more molecular secondary structures. - true - - - - - - - - - - Secondary structure report - - Secondary structure-derived report - beta12orEarlier - true - An informative report on general information, properties or features of one or more molecular secondary structures. - 1.5 - - - - - - - - - - DNA features - - beta12orEarlier - DNA sequence-specific feature annotation (not in a feature table). - true - beta12orEarlier - - - - - - - - - - RNA features report - - true - beta12orEarlier - 1.5 - Features concerning RNA or regions of DNA that encode an RNA molecule. - RNA features - Nucleic acid features (RNA features) - - - - - - - - - - Plot - - beta12orEarlier - true - beta12orEarlier - Biological data that has been plotted as a graph of some type. - - - - - - - - - - Nucleic acid features report (polymorphism) - - true - DNA polymorphism. - beta12orEarlier - - - - - - - - - - Protein sequence record - - - A protein sequence and associated metadata. - beta12orEarlier - Protein sequence record - Sequence record (protein) - - - - - - - - - - Nucleic acid sequence record - - - RNA sequence record - Nucleotide sequence record - A nucleic acid sequence and associated metadata. - beta12orEarlier - DNA sequence record - Sequence record (nucleic acid) - - - - - - - - - - Protein sequence record (full) - - A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. - 1.8 - beta12orEarlier - true - - - - - - - - - - Nucleic acid sequence record (full) - - true - A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. - beta12orEarlier - 1.8 - - - - - - - - - - Biological model accession - - - beta12orEarlier - Accession of a mathematical model, typically an entry from a database. - - - - - - - - - - - Cell type name - - - The name of a type or group of cells. - beta12orEarlier - - - - - - - - - - - Cell type accession - - - beta12orEarlier - Accession of a type or group of cells (catalogued in a database). - - - - - - - - - - - Compound accession - - - Small molecule accession - Accession of an entry from a database of chemicals. - beta12orEarlier - Chemical compound accession - - - - - - - - - - - Drug accession - - - Accession of a drug. - beta12orEarlier - - - - - - - - - - - Toxin name - - - Name of a toxin. - beta12orEarlier - - - - - - - - - - - Toxin accession - - - beta12orEarlier - Accession of a toxin (catalogued in a database). - - - - - - - - - - - Monosaccharide accession - - - Accession of a monosaccharide (catalogued in a database). - beta12orEarlier - - - - - - - - - - - Drug name - - - beta12orEarlier - Common name of a drug. - - - - - - - - - - - Carbohydrate accession - - - Accession of an entry from a database of carbohydrates. - beta12orEarlier - - - - - - - - - - - Molecule accession - - - Accession of a specific molecule (catalogued in a database). - beta12orEarlier - - - - - - - - - - - Data resource definition accession - - - beta12orEarlier - Accession of a data definition (catalogued in a database). - - - - - - - - - - - Genome accession - - - An accession of a particular genome (in a database). - beta12orEarlier - - - - - - - - - - - Map accession - - - An accession of a map of a molecular sequence (deposited in a database). - beta12orEarlier - - - - - - - - - - - Lipid accession - - - beta12orEarlier - Accession of an entry from a database of lipids. - - - - - - - - - - - Peptide ID - - - beta12orEarlier - Accession of a peptide deposited in a database. - - - - - - - - - - - Protein accession - - - Protein accessions - beta12orEarlier - Accession of a protein deposited in a database. - - - - - - - - - - - Organism accession - - - An accession of annotation on a (group of) organisms (catalogued in a database). - beta12orEarlier - - - - - - - - - - - Organism name - - - Moby:Organism_Name - Moby:OrganismsShortName - Moby:OccurrenceRecord - Moby:BriefOccurrenceRecord - Moby:FirstEpithet - Moby:InfraspecificEpithet - beta12orEarlier - Moby:OrganismsLongName - The name of an organism (or group of organisms). - - - - - - - - - - - Protein family accession - - - beta12orEarlier - Accession of a protein family (that is deposited in a database). - - - - - - - - - - - Transcription factor accession - - - - beta12orEarlier - Accession of an entry from a database of transcription factors or binding sites. - - - - - - - - - - - Strain accession - - - - - - - - - beta12orEarlier - Identifier of a strain of an organism variant, typically a plant, virus or bacterium. - - - - - - - - - - - Virus identifier - - An accession of annotation on a (group of) viruses (catalogued in a database). - beta12orEarlier - - - - - - - - - - - Sequence features metadata - - beta12orEarlier - Metadata on sequence features. - - - - - - - - - - Gramene identifier - - beta12orEarlier - Identifier of a Gramene database entry. - - - - - - - - - - - DDBJ accession - - beta12orEarlier - DDBJ accession number - DDBJ identifier - DDBJ ID - An identifier of an entry from the DDBJ sequence database. - - - - - - - - - - - ConsensusPathDB identifier - - beta12orEarlier - An identifier of an entity from the ConsensusPathDB database. - - - - - - - - - - - Sequence data - - This is a broad data type and is used a placeholder for other, more specific types. - 1.8 - beta12orEarlier - true - Data concerning, extracted from, or derived from the analysis of molecular sequence(s). - - - - - - - - - - Codon usage - - beta12orEarlier - true - beta13 - Data concerning codon usage. - This is a broad data type and is used a placeholder for other, more specific types. - - - - - - - - - - Article report - - beta12orEarlier - 1.5 - Data derived from the analysis of a scientific text such as a full text article from a scientific journal. - true - - - - - - - - - - Sequence report - - An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties. - beta12orEarlier - Sequence-derived report - - - - - - - - - - Protein secondary structure report - - An informative report about the properties or features of one or more protein secondary structures. - beta12orEarlier - - - - - - - - - - Hopp and Woods plot - - - A Hopp and Woods plot of predicted antigenicity of a peptide or protein. - beta12orEarlier - - - - - - - - - - Nucleic acid melting curve - - - Shows the proportion of nucleic acid which are double-stranded versus temperature. - A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA). - beta12orEarlier - - - - - - - - - - Nucleic acid probability profile - - A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). - beta12orEarlier - Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature - - - - - - - - - - Nucleic acid temperature profile - - A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). - Plots melting temperature versus base position. - beta12orEarlier - Melting map - - - - - - - - - - Gene regulatory network report - - 1.8 - A report typically including a map (diagram) of a gene regulatory network. - true - beta12orEarlier - - - - - - - - - - 2D PAGE gel report - - An informative report on a two-dimensional (2D PAGE) gel. - 2D PAGE image report - 1.8 - true - 2D PAGE gel annotation - beta12orEarlier - 2D PAGE image annotation - - - - - - - - - - Oligonucleotide probe sets annotation - - beta12orEarlier - General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set. - - - - - - - - - - Microarray image - - 1.5 - beta12orEarlier - Gene expression image - An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. - true - - - - - - - - - - Image - - http://semanticscience.org/resource/SIO_000081 - Biological or biomedical data has been rendered into an image, typically for display on screen. - http://semanticscience.org/resource/SIO_000079 - Image data - beta12orEarlier - - - - - - - - - - Sequence image - - - Image of a molecular sequence, possibly with sequence features or properties shown. - beta12orEarlier - - - - - - - - - - Protein hydropathy data - - Protein hydropathy report - A report on protein properties concerning hydropathy. - beta12orEarlier - - - - - - - - - - Workflow data - - beta12orEarlier - beta13 - Data concerning a computational workflow. - true - - - - - - - - - - Workflow - - true - beta12orEarlier - 1.5 - A computational workflow. - - - - - - - - - - Secondary structure data - - beta13 - true - beta12orEarlier - Data concerning molecular secondary structure data. - - - - - - - - - - Protein sequence (raw) - - - Raw protein sequence - beta12orEarlier - Raw sequence (protein) - A raw protein sequence (string of characters). - - - - - - - - - - Nucleic acid sequence (raw) - - - Nucleic acid raw sequence - beta12orEarlier - Nucleotide sequence (raw) - Raw sequence (nucleic acid) - A raw nucleic acid sequence. - - - - - - - - - - Protein sequence - - One or more protein sequences, possibly with associated annotation. - Protein sequences - beta12orEarlier - http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation - - - - - - - - - - Nucleic acid sequence - - One or more nucleic acid sequences, possibly with associated annotation. - beta12orEarlier - DNA sequence - Nucleotide sequence - Nucleotide sequences - Nucleic acid sequences - http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation - - - - - - - - - - Reaction data - - Enzyme kinetics annotation - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier - Reaction annotation - Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction. - - - - - - - - - - Peptide property - - beta12orEarlier - Peptide data - Data concerning small peptides. - - - - - - - - - - Protein classification - - This is a broad data type and is used a placeholder for other, more specific types. - Protein classification data - An informative report concerning the classification of protein sequences or structures. - beta12orEarlier - - - - - - - - - Sequence motif data - - true - 1.8 - Data concerning specific or conserved pattern in molecular sequences. - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. - - - - - - - - - - Sequence profile data - - beta12orEarlier - true - This is a broad data type and is used a placeholder for other, more specific types. - beta13 - Data concerning models representing a (typically multiple) sequence alignment. - - - - - - - - - - Pathway or network data - - Data concerning a specific biological pathway or network. - beta13 - true - beta12orEarlier - - - - - - - - - - - Pathway or network report - - - - - - - - beta12orEarlier - An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation. - - - - - - - - - - Nucleic acid thermodynamic data - - Nucleic acid property (thermodynamic or kinetic) - A thermodynamic or kinetic property of a nucleic acid molecule. - Nucleic acid thermodynamic property - beta12orEarlier - - - - - - - - - - Nucleic acid classification - - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier - Data concerning the classification of nucleic acid sequences or structures. - Nucleic acid classification data - - - - - - - - - Classification report - - This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. - beta12orEarlier - true - Classification data - A report on a classification of molecular sequences, structures or other entities. - 1.5 - - - - - - - - - - Protein features report (key folding sites) - - beta12orEarlier - key residues involved in protein folding. - 1.8 - true - - - - - - - - - - Protein torsion angle data - - Torsion angle data - Torsion angle data for a protein structure. - beta12orEarlier - - - - - - - - - - Protein structure image - - - An image of protein structure. - beta12orEarlier - Structure image (protein) - - - - - - - - - - Phylogenetic character weights - - Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted. - beta12orEarlier - - - - - - - - - - Annotation track - - beta12orEarlier - Genomic track - Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser. - Genome annotation track - Genome-browser track - Genome track - Sequence annotation track - - - - - - - - - - UniProt accession - - - - - - - - UniProtKB accession number - beta12orEarlier - P43353|Q7M1G0|Q9C199|A5A6J6 - UniProt entry accession - [OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2} - Swiss-Prot entry accession - TrEMBL entry accession - Accession number of a UniProt (protein sequence) database entry. - UniProtKB accession - UniProt accession number - - - - - - - - - - - NCBI genetic code ID - - - Identifier of a genetic code in the NCBI list of genetic codes. - [1-9][0-9]? - 16 - beta12orEarlier - - - - - - - - - - - Ontology concept identifier - - - - - - - - Identifier of a concept in an ontology of biological or bioinformatics concepts and relations. - beta12orEarlier - - - - - - - - - - - GO concept name (biological process) - - true - The name of a concept for a biological process from the GO ontology. - beta12orEarlier - beta12orEarlier - - - - - - - - - - GO concept name (molecular function) - - true - beta12orEarlier - The name of a concept for a molecular function from the GO ontology. - beta12orEarlier - - - - - - - - - - Taxonomy - - - - - - - - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier - Data concerning the classification, identification and naming of organisms. - Taxonomic data - - - - - - - - - - Protein ID (EMBL/GenBank/DDBJ) - - beta13 - EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators. - This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. - - - - - - - - - - - Core data - - Core data entities typically have a format and may be identified by an accession number. - A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation. - 1.5 - true - beta13 - - - - - - - - - - Sequence feature identifier - - - - - - - - beta13 - Name or other identifier of molecular sequence feature(s). - - - - - - - - - - - Structure identifier - - - - - - - - beta13 - An identifier of a molecular tertiary structure, typically an entry from a structure database. - - - - - - - - - - - Matrix identifier - - - - - - - - An identifier of an array of numerical values, such as a comparison matrix. - beta13 - - - - - - - - - - - Protein sequence composition - - beta13 - 1.8 - true - A report (typically a table) on character or word composition / frequency of protein sequence(s). - - - - - - - - - - Nucleic acid sequence composition (report) - - 1.8 - A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s). - true - beta13 - - - - - - - - - - Protein domain classification node - - beta13 - A node from a classification of protein structural domain(s). - true - 1.5 - - - - - - - - - - CAS number - - beta13 - CAS registry number - Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service. - - - - - - - - - - - ATC code - - Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC). - beta13 - - - - - - - - - - - UNII - - beta13 - A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA). - Unique Ingredient Identifier - - - - - - - - - - - Geotemporal metadata - - 1.5 - beta13 - true - Basic information concerning geographical location or time. - - - - - - - - - - System metadata - - Metadata concerning the software, hardware or other aspects of a computer system. - beta13 - - - - - - - - - - Sequence feature name - - - A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. - beta13 - - - - - - - - - - - Experimental measurement - - beta13 - Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware. - Experimental measurement data - Measurement - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Measured data - Experimentally measured data - Measurement metadata - Measurement data - Raw experimental data - - - - - - - - - - Raw microarray data - - - beta13 - Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment. - Such data as found in Affymetrix CEL or GPR files. - - - - - - - - - - Processed microarray data - - - - - - - - Data generated from processing and analysis of probe set data from a microarray experiment. - Gene annotation (expression) - Microarray probe set data - beta13 - Gene expression report - Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. - - - - - - - - - - Gene expression matrix - - - This combines data from all hybridisations. - beta13 - Normalised microarray data - The final processed (normalised) data for a set of hybridisations in a microarray experiment. - Gene expression data matrix - - - - - - - - - - Sample annotation - - Annotation on a biological sample, for example experimental factors and their values. - This might include compound and dose in a dose response experiment. - beta13 - - - - - - - - - - Microarray metadata - - This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. - Annotation on the array itself used in a microarray experiment. - beta13 - - - - - - - - - - Microarray protocol annotation - - true - This might describe e.g. the normalisation methods used to process the raw data. - beta13 - 1.8 - Annotation on laboratory and/or data processing protocols used in an microarray experiment. - - - - - - - - - - Microarray hybridisation data - - Data concerning the hybridisations measured during a microarray experiment. - beta13 - - - - - - - - - - Protein features report (topological domains) - - 1.8 - beta13 - topological domains such as cytoplasmic regions in a protein. - true - - - - - - - - - - Sequence features (compositionally-biased regions) - - 1.5 - beta13 - true - A report of regions in a molecular sequence that are biased to certain characters. - - - - - - - - - - Nucleic acid features (difference and change) - - beta13 - A report on features in a nucleic acid sequence that indicate changes to or differences between sequences. - 1.5 - true - - - - - - - - - - Nucleic acid features report (expression signal) - - true - beta13 - regions within a nucleic acid sequence containing a signal that alters a biological function. - 1.8 - - - - - - - - - - Nucleic acid features report (binding) - - nucleic acids binding to some other molecule. - 1.8 - true - beta13 - This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). - - - - - - - - - - Nucleic acid repeats (report) - - true - repetitive elements within a nucleic acid sequence. - 1.8 - beta13 - - - - - - - - - - Nucleic acid features report (replication and recombination) - - beta13 - true - 1.8 - DNA replication or recombination. - - - - - - - - - - Nucleic acid structure report - - - A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures. - Stem loop (report) - d-loop (report) - Nucleic acid features (structure) - Quadruplexes (report) - beta13 - - - - - - - - - - Protein features report (repeats) - - 1.8 - short repetitive subsequences (repeat sequences) in a protein sequence. - beta13 - true - - - - - - - - - - Sequence motif matches (protein) - - Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences. - 1.8 - beta13 - true - - - - - - - - - - Sequence motif matches (nucleic acid) - - Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences. - beta13 - true - 1.8 - - - - - - - - - - Nucleic acid features (d-loop) - - beta13 - true - 1.5 - A report on displacement loops in a mitochondrial DNA sequence. - A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. - - - - - - - - - - Nucleic acid features (stem loop) - - beta13 - true - A report on stem loops in a DNA sequence. - 1.5 - A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. - - - - - - - - - - Gene transcript report - - This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). - Nucleic acid features (mRNA features) - beta13 - Transcript (report) - mRNA features - Gene transcript annotation - Clone or EST (report) - mRNA (report) - An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST. - - - - - - - - - - - Nucleic acid features report (signal or transit peptide) - - true - coding sequences for a signal or transit peptide. - 1.8 - beta13 - - - - - - - - - - Non-coding RNA - - beta13 - true - features of non-coding or functional RNA molecules, including tRNA and rRNA. - 1.8 - - - - - - - - - - Transcriptional features (report) - - 1.5 - true - This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. - Features concerning transcription of DNA into RNA including the regulation of transcription. - beta13 - - - - - - - - - - Nucleic acid features report (STS) - - sequence tagged sites (STS) in nucleic acid sequences. - 1.8 - true - beta13 - - - - - - - - - - Nucleic acid features (immunoglobulin gene structure) - - true - beta13 - 1.5 - A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments. - - - - - - - - - - SCOP class - - 1.5 - beta13 - true - Information on a 'class' node from the SCOP database. - - - - - - - - - - SCOP fold - - beta13 - Information on a 'fold' node from the SCOP database. - 1.5 - true - - - - - - - - - - SCOP superfamily - - beta13 - Information on a 'superfamily' node from the SCOP database. - 1.5 - true - - - - - - - - - - SCOP family - - 1.5 - true - Information on a 'family' node from the SCOP database. - beta13 - - - - - - - - - - SCOP protein - - Information on a 'protein' node from the SCOP database. - true - beta13 - 1.5 - - - - - - - - - - SCOP species - - 1.5 - true - beta13 - Information on a 'species' node from the SCOP database. - - - - - - - - - - Mass spectrometry experiment - - 1.8 - true - mass spectrometry experiments. - beta13 - - - - - - - - - - Gene family report - - An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene, or any other classification of nucleic acid sequences or structures that reflects gene structure. - This includes reports on on gene homologues between species. - beta13 - Gene annotation (homology information) - Homology information - Gene annotation (homology) - Nucleic acid classification - Gene family annotation - Gene homology (report) - - - - - - - - - - Protein image - - beta13 - An image of a protein. - - - - - - - - - - Protein alignment - - An alignment of protein sequences and/or structures. - beta13 - - - - - - - - - - NGS experiment - - 1.8 - 1.0 - sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. - true - - - - - - - - - - Sequence assembly report - - An informative report about a DNA sequence assembly. - 1.1 - This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc. - Assembly report - - - - - - - - - - Genome index - - 1.1 - Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. - An index of a genome sequence. - - - - - - - - - - GWAS report - - 1.8 - 1.1 - Report concerning genome-wide association study experiments. - true - Genome-wide association study - - - - - - - - - - Cytoband position - - 1.2 - The position of a cytogenetic band in a genome. - Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on. - - - - - - - - - - Cell type ontology ID - - - CL ID - Cell type ontology concept ID. - CL_[0-9]{7} - 1.2 - beta12orEarlier - - - - - - - - - - - Kinetic model - - 1.2 - Mathematical model of a network, that contains biochemical kinetics. - - - - - - - - - - COSMIC ID - - COSMIC identifier - cosmic ID - Identifier of a COSMIC database entry. - cosmic identifier - cosmic id - 1.3 - - - - - - - - - - - HGMD ID - - Identifier of a HGMD database entry. - hgmd ID - hgmd identifier - beta12orEarlier - hgmd id - HGMD identifier - - - - - - - - - - - Sequence assembly ID - - Sequence assembly version - Unique identifier of sequence assembly. - 1.3 - - - - - - - - - - - Sequence feature type - - true - A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory. - 1.3 - 1.5 - - - - - - - - - - Gene homology (report) - - beta12orEarlier - true - An informative report on gene homologues between species. - 1.5 - - - - - - - - - - Ensembl gene tree ID - - - ENSGT00390000003602 - Ensembl ID (gene tree) - Unique identifier for a gene tree from the Ensembl database. - 1.3 - - - - - - - - - - - Gene tree - - 1.3 - A phylogenetic tree that is an estimate of the character's phylogeny. - - - - - - - - - - Species tree - - A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled. - 1.3 - - - - - - - - - - Sample ID - - - - - - - - - 1.3 - Sample accession - Name or other identifier of an entry from a biosample database. - - - - - - - - - - - MGI accession - - - Identifier of an object from the MGI database. - 1.3 - - - - - - - - - - - Phenotype name - - - 1.3 - Name of a phenotype. - Phenotypes - Phenotype - - - - - - - - - - - Transition matrix - - A HMM transition matrix contains the probabilities of switching from one HMM state to another. - Consider for example an HMM with two states (AT-rich and GC-rich). The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa. - HMM transition matrix - 1.4 - - - - - - - - - Emission matrix - - A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM. - 1.4 - Consider for example an HMM with two states (AT-rich and GC-rich). The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state. - HMM emission matrix - - - - - - - - - Hidden Markov model - - A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. - 1.4 - - - - - - - - - Format identifier - - An identifier of a data format. - 1.4 - - - - - - - - - Raw image - - 1.5 - Amino acid data - http://semanticscience.org/resource/SIO_000081 - beta12orEarlier - Image data - Raw biological or biomedical image generated by some experimental technique. - - - - - - - - - - Carbohydrate property - - Carbohydrate data - Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates. - 1.5 - - - - - - - - - - Proteomics experiment report - - true - 1.8 - Report concerning proteomics experiments. - 1.5 - - - - - - - - - - RNAi report - - 1.5 - RNAi experiments. - true - 1.8 - - - - - - - - - - Simulation experiment report - - 1.5 - biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. - true - 1.8 - - - - - - - - - - MRI image - - - - - - - - MRT image - 1.7 - Magnetic resonance tomography image - Nuclear magnetic resonance imaging image - - Magnetic resonance imaging image - - NMRI image - An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. - - - - - - - - - - Cell migration track image - - - - - - - - 1.7 - An image from a cell migration track assay. - - - - - - - - - - Rate of association - - kon - 1.7 - Rate of association of a protein with another protein or some other molecule. - - - - - - - - - - Gene order - - Such data are often used for genome rearrangement tools and phylogenetic tree labeling. - Multiple gene identifiers in a specific order. - 1.7 - - - - - - - - - - Spectrum - - 1.7 - The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment. - Spectra - - - - - - - - - - NMR spectrum - - - - - - - - Spectral information for a molecule from a nuclear magnetic resonance experiment. - 1.7 - NMR spectra - - - - - - - - - - Chemical structure sketch - - Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software. - 1.8 - Small molecule sketch - A sketch of a small molecule made with some specialised drawing package. - - - - - - - - - - Nucleic acid signature - - 1.8 - An informative report about a specific or conserved nucleic acid sequence pattern. - - - - - - - - - - DNA sequence - - DNA sequences - 1.8 - A DNA sequence. - - - - - - - - - - RNA sequence - - A DNA sequence. - DNA sequences - RNA sequences - 1.8 - - - - - - - - - - RNA sequence (raw) - - - Raw sequence (RNA) - 1.8 - A raw RNA sequence. - RNA raw sequence - - - - - - - - - - DNA sequence (raw) - - - Raw sequence (DNA) - A raw DNA sequence. - 1.8 - DNA raw sequence - - - - - - - - - - Sequence variations - - - - - - - - 1.8 - Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects. - Gene sequence variations - Variations are stored along with a reference genome. - - - - - - - - - - Bibliography - - 1.8 - A list of publications such as scientic papers or books. - - - - - - - - - - Ontology mapping - - A mapping of supplied textual terms or phrases to ontology concepts (URIs). - beta12orEarlier - - - - - - - - - - Image metadata - - Image-associated data - This can include basic provenance and technical information about the image, scientific annotation and so on. - Any data concerning a specific biological or biomedical image. - 1.9 - Image data - Image-related data - - - - - - - - - - Clinical trial report - - Clinical trial information - A report concerning a clinical trial. - 1.9 - - - - - - - - - - Reference sample report - - 1.10 - A report about a biosample. - Biosample report - - - - - - - - - - Gene Expression Atlas Experiment ID - - Accession number of an entry from the Gene Expression Atlas. - 1.10 - - - - - - - - - - - SMILES - - - Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation. - beta12orEarlier - - - - - - - - - - - - - - InChI - - - Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. - beta12orEarlier - - - - - - - - - - mf - - - Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound. - beta12orEarlier - The general MF query format consists of a series of valid atomic symbols, with an optional number or range. - - - - - - - - - - inchikey - - - The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound. - beta12orEarlier - An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. - - - - - - - - - - smarts - - SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation. - beta12orEarlier - - - - - - - - - - unambiguous pure - - - beta12orEarlier - Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters. - - - - - - - - - - nucleotide - - - Non-sequence characters may be used for example for gaps. - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence - beta12orEarlier - Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters. - - - - - - - - - - protein - - - Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters. - beta12orEarlier - Non-sequence characters may be used for gaps and translation stop. - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence - - - - - - - - - - consensus - - - beta12orEarlier - Alphabet for the consensus of two or more molecular sequences. - - - - - - - - - - pure nucleotide - - - beta12orEarlier - Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters. - - - - - - - - - - unambiguous pure nucleotide - - - beta12orEarlier - Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters . - - - - - - - - - - dna - - beta12orEarlier - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence - Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters. - - - - - - - - - - rna - - Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters. - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence - beta12orEarlier - - - - - - - - - - unambiguous pure dna - - - Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters. - beta12orEarlier - - - - - - - - - - pure dna - - - Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters. - beta12orEarlier - - - - - - - - - - unambiguous pure rna sequence - - - Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters. - beta12orEarlier - - - - - - - - - - pure rna - - - Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters. - beta12orEarlier - - - - - - - - - - unambiguous pure protein - - - beta12orEarlier - Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters. - - - - - - - - - - pure protein - - - beta12orEarlier - Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters. - - - - - - - - - - UniGene entry format - - beta12orEarlier - Format of an entry from UniGene. - A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. - beta12orEarlier - true - - - - - - - - - - COG sequence cluster format - - beta12orEarlier - true - beta12orEarlier - Format of an entry from the COG database of clusters of (related) protein sequences. - - - - - - - - - - EMBL feature location - - - beta12orEarlier - Feature location - Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database. - - - - - - - - - - quicktandem - - - Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program). - beta12orEarlier - - - - - - - - - - Sanger inverted repeats - - - beta12orEarlier - Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program). - - - - - - - - - - EMBOSS repeat - - - Report format for tandem repeats in a sequence (an EMBOSS report format). - beta12orEarlier - - - - - - - - - - est2genome format - - - beta12orEarlier - Format of a report on exon-intron structure generated by EMBOSS est2genome. - - - - - - - - - - restrict format - - - Report format for restriction enzyme recognition sites used by EMBOSS restrict program. - beta12orEarlier - - - - - - - - - - restover format - - - beta12orEarlier - Report format for restriction enzyme recognition sites used by EMBOSS restover program. - - - - - - - - - - REBASE restriction sites - - - beta12orEarlier - Report format for restriction enzyme recognition sites used by REBASE database. - - - - - - - - - - FASTA search results format - - - Format of results of a sequence database search using FASTA. - beta12orEarlier - This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) - - - - - - - - - - BLAST results - - - Format of results of a sequence database search using some variant of BLAST. - beta12orEarlier - This includes score data, alignment data and summary table. - - - - - - - - - - mspcrunch - - - beta12orEarlier - Format of results of a sequence database search using some variant of MSPCrunch. - - - - - - - - - - Smith-Waterman format - - - beta12orEarlier - Format of results of a sequence database search using some variant of Smith Waterman. - - - - - - - - - - dhf - - - The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. - beta12orEarlier - Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information. - - - - - - - - - - lhf - - - beta12orEarlier - Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information. - The hits are putative ligand-binding sequences and are found from a search of a sequence database. - - - - - - - - - - InterPro hits format - - - Results format for searches of the InterPro database. - beta12orEarlier - - - - - - - - - - InterPro protein view report format - - Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries. - The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. - beta12orEarlier - - - - - - - - - - InterPro match table format - - Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry. - beta12orEarlier - The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated. - - - - - - - - - - HMMER Dirichlet prior - - - beta12orEarlier - Dirichlet distribution HMMER format. - - - - - - - - - - MEME Dirichlet prior - - - beta12orEarlier - Dirichlet distribution MEME format. - - - - - - - - - - HMMER emission and transition - - - Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model. - beta12orEarlier - - - - - - - - - - prosite-pattern - - - Format of a regular expression pattern from the Prosite database. - beta12orEarlier - - - - - - - - - - EMBOSS sequence pattern - - - Format of an EMBOSS sequence pattern. - beta12orEarlier - - - - - - - - - - meme-motif - - - A motif in the format generated by the MEME program. - beta12orEarlier - - - - - - - - - - prosite-profile - - - Sequence profile (sequence classifier) format used in the PROSITE database. - beta12orEarlier - - - - - - - - - - JASPAR format - - - beta12orEarlier - A profile (sequence classifier) in the format used in the JASPAR database. - - - - - - - - - - MEME background Markov model - - - Format of the model of random sequences used by MEME. - beta12orEarlier - - - - - - - - - - HMMER format - - - Format of a hidden Markov model representation used by the HMMER package. - beta12orEarlier - - - - - - - - - - HMMER-aln - - - - beta12orEarlier - FASTA-style format for multiple sequences aligned by HMMER package to an HMM. - - - - - - - - - - DIALIGN format - - - Format of multiple sequences aligned by DIALIGN package. - beta12orEarlier - - - - - - - - - - daf - - - The format is clustal-like and includes annotation of domain family classification information. - EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family. - beta12orEarlier - - - - - - - - - - Sequence-MEME profile alignment - - - beta12orEarlier - Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package. - - - - - - - - - - HMMER profile alignment (sequences versus HMMs) - - - Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database. - beta12orEarlier - - - - - - - - - - HMMER profile alignment (HMM versus sequences) - - - Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database. - beta12orEarlier - - - - - - - - - - Phylip distance matrix - - - Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). - beta12orEarlier - Format of PHYLIP phylogenetic distance matrix data. - - - - - - - - - - ClustalW dendrogram - - - beta12orEarlier - Dendrogram (tree file) format generated by ClustalW. - - - - - - - - - - Phylip tree raw - - - Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted. - beta12orEarlier - - - - - - - - - - Phylip continuous quantitative characters - - - beta12orEarlier - PHYLIP file format for continuous quantitative character data. - - - - - - - - - - Phylogenetic property values format - - Format of phylogenetic property data. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Phylip character frequencies format - - - beta12orEarlier - PHYLIP file format for phylogenetics character frequency data. - - - - - - - - - - Phylip discrete states format - - - Format of PHYLIP discrete states data. - beta12orEarlier - - - - - - - - - - Phylip cliques format - - - beta12orEarlier - Format of PHYLIP cliques data. - - - - - - - - - - Phylip tree format - - - Phylogenetic tree data format used by the PHYLIP program. - beta12orEarlier - - - - - - - - - - TreeBASE format - - - beta12orEarlier - The format of an entry from the TreeBASE database of phylogenetic data. - - - - - - - - - - TreeFam format - - - beta12orEarlier - The format of an entry from the TreeFam database of phylogenetic data. - - - - - - - - - - Phylip tree distance format - - - Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package. - beta12orEarlier - - - - - - - - - - dssp - - - beta12orEarlier - The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. - Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins). - - - - - - - - - - hssp - - - Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins). - beta12orEarlier - - - - - - - - - - Dot-bracket format - - - beta12orEarlier - Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server. - Vienna RNA secondary structure format - Vienna RNA format - - - - - - - - - - Vienna local RNA secondary structure format - - - Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server. - beta12orEarlier - - - - - - - - - - PDB database entry format - - - - - - - - beta12orEarlier - PDB entry format - Format of an entry (or part of an entry) from the PDB database. - - - - - - - - - - PDB - - - PDB format - beta12orEarlier - Entry format of PDB database in PDB format. - - - - - - - - - - mmCIF - - - Chemical MIME (http://www.ch.ic.ac.uk/chemime): chemical/x-mmcif - Entry format of PDB database in mmCIF format. - beta12orEarlier - mmcif - - - - - - - - - - PDBML - - - Entry format of PDB database in PDBML (XML) format. - beta12orEarlier - - - - - - - - - - Domainatrix 3D-1D scoring matrix format - - beta12orEarlier - true - beta12orEarlier - Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications. - - - - - - - - - aaindex - - - Amino acid index format used by the AAindex database. - beta12orEarlier - - - - - - - - - - IntEnz enzyme report format - - beta12orEarlier - beta12orEarlier - Format of an entry from IntEnz (The Integrated Relational Enzyme Database). - IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. - true - - - - - - - - - - BRENDA enzyme report format - - true - Format of an entry from the BRENDA enzyme database. - beta12orEarlier - beta12orEarlier - - - - - - - - - - KEGG REACTION enzyme report format - - true - beta12orEarlier - Format of an entry from the KEGG REACTION database of biochemical reactions. - beta12orEarlier - - - - - - - - - - KEGG ENZYME enzyme report format - - beta12orEarlier - true - Format of an entry from the KEGG ENZYME database. - beta12orEarlier - - - - - - - - - - REBASE proto enzyme report format - - Format of an entry from the proto section of the REBASE enzyme database. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - REBASE withrefm enzyme report format - - beta12orEarlier - true - beta12orEarlier - Format of an entry from the withrefm section of the REBASE enzyme database. - - - - - - - - - - Pcons report format - - - Format of output of the Pcons Model Quality Assessment Program (MQAP). - beta12orEarlier - Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality. - - - - - - - - - - ProQ report format - - - beta12orEarlier - ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. - Format of output of the ProQ protein model quality predictor. - - - - - - - - - - SMART domain assignment report format - - beta12orEarlier - true - Format of SMART domain assignment data. - The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues. - beta12orEarlier - - - - - - - - - - BIND entry format - - Entry format for the BIND database of protein interaction. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - IntAct entry format - - beta12orEarlier - beta12orEarlier - Entry format for the IntAct database of protein interaction. - true - - - - - - - - - - InterPro entry format - - Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences. - true - beta12orEarlier - This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry. - beta12orEarlier - - - - - - - - - - InterPro entry abstract format - - true - beta12orEarlier - References are included and a functional inference is made where possible. - beta12orEarlier - Entry format for the textual abstract of signatures in an InterPro entry and its protein matches. - - - - - - - - - - Gene3D entry format - - Entry format for the Gene3D protein secondary database. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - PIRSF entry format - - beta12orEarlier - Entry format for the PIRSF protein secondary database. - true - beta12orEarlier - - - - - - - - - - PRINTS entry format - - beta12orEarlier - beta12orEarlier - true - Entry format for the PRINTS protein secondary database. - - - - - - - - - - Panther Families and HMMs entry format - - beta12orEarlier - beta12orEarlier - Entry format for the Panther library of protein families and subfamilies. - true - - - - - - - - - - Pfam entry format - - Entry format for the Pfam protein secondary database. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - SMART entry format - - true - beta12orEarlier - Entry format for the SMART protein secondary database. - beta12orEarlier - - - - - - - - - - Superfamily entry format - - Entry format for the Superfamily protein secondary database. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - TIGRFam entry format - - beta12orEarlier - true - Entry format for the TIGRFam protein secondary database. - beta12orEarlier - - - - - - - - - - ProDom entry format - - Entry format for the ProDom protein domain classification database. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - FSSP entry format - - Entry format for the FSSP database. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - findkm - - - beta12orEarlier - A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax). - - - - - - - - - - Ensembl gene report format - - beta12orEarlier - Entry format of Ensembl genome database. - beta12orEarlier - true - - - - - - - - - - DictyBase gene report format - - true - beta12orEarlier - Entry format of DictyBase genome database. - beta12orEarlier - - - - - - - - - - CGD gene report format - - beta12orEarlier - true - beta12orEarlier - Entry format of Candida Genome database. - - - - - - - - - - DragonDB gene report format - - beta12orEarlier - Entry format of DragonDB genome database. - beta12orEarlier - true - - - - - - - - - - EcoCyc gene report format - - Entry format of EcoCyc genome database. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - FlyBase gene report format - - true - beta12orEarlier - beta12orEarlier - Entry format of FlyBase genome database. - - - - - - - - - - Gramene gene report format - - beta12orEarlier - beta12orEarlier - Entry format of Gramene genome database. - true - - - - - - - - - - KEGG GENES gene report format - - true - beta12orEarlier - Entry format of KEGG GENES genome database. - beta12orEarlier - - - - - - - - - - MaizeGDB gene report format - - beta12orEarlier - beta12orEarlier - true - Entry format of the Maize genetics and genomics database (MaizeGDB). - - - - - - - - - - MGD gene report format - - Entry format of the Mouse Genome Database (MGD). - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - RGD gene report format - - true - beta12orEarlier - Entry format of the Rat Genome Database (RGD). - beta12orEarlier - - - - - - - - - - SGD gene report format - - true - beta12orEarlier - beta12orEarlier - Entry format of the Saccharomyces Genome Database (SGD). - - - - - - - - - - GeneDB gene report format - - Entry format of the Sanger GeneDB genome database. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - TAIR gene report format - - beta12orEarlier - beta12orEarlier - Entry format of The Arabidopsis Information Resource (TAIR) genome database. - true - - - - - - - - - - WormBase gene report format - - Entry format of the WormBase genomes database. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - ZFIN gene report format - - beta12orEarlier - beta12orEarlier - true - Entry format of the Zebrafish Information Network (ZFIN) genome database. - - - - - - - - - - TIGR gene report format - - true - Entry format of the TIGR genome database. - beta12orEarlier - beta12orEarlier - - - - - - - - - - dbSNP polymorphism report format - - beta12orEarlier - Entry format for the dbSNP database. - true - beta12orEarlier - - - - - - - - - - OMIM entry format - - beta12orEarlier - true - beta12orEarlier - Format of an entry from the OMIM database of genotypes and phenotypes. - - - - - - - - - - HGVbase entry format - - true - Format of a record from the HGVbase database of genotypes and phenotypes. - beta12orEarlier - beta12orEarlier - - - - - - - - - - HIVDB entry format - - beta12orEarlier - beta12orEarlier - true - Format of a record from the HIVDB database of genotypes and phenotypes. - - - - - - - - - - KEGG DISEASE entry format - - beta12orEarlier - Format of an entry from the KEGG DISEASE database. - true - beta12orEarlier - - - - - - - - - - Primer3 primer - - - Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program. - beta12orEarlier - - - - - - - - - - ABI - - - A format of raw sequence read data from an Applied Biosystems sequencing machine. - beta12orEarlier - - - - - - - - - - mira - - - Format of MIRA sequence trace information file. - beta12orEarlier - - - - - - - - - - CAF - - - Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata. - beta12orEarlier - - - - - - - - - - - - exp - - - Sequence assembly project file EXP format. - beta12orEarlier - - - - - - - - - - SCF - - - Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata. - beta12orEarlier - - - - - - - - - - - - PHD - - - beta12orEarlier - PHD sequence trace format to store serialised chromatogram data (reads). - - - - - - - - - - - - dat - - - - - - - - - beta12orEarlier - Format of Affymetrix data file of raw image data. - Affymetrix image data file format - - - - - - - - - - cel - - - - - - - - - beta12orEarlier - Affymetrix probe raw data format - Format of Affymetrix data file of information about (raw) expression levels of the individual probes. - - - - - - - - - - affymetrix - - - Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering. - beta12orEarlier - - - - - - - - - - ArrayExpress entry format - - beta12orEarlier - true - Entry format for the ArrayExpress microarrays database. - beta12orEarlier - - - - - - - - - - affymetrix-exp - - - Affymetrix data file format for information about experimental conditions and protocols. - Affymetrix experimental conditions data file format - beta12orEarlier - - - - - - - - - - CHP - - - - - - - - - Affymetrix probe normalised data format - beta12orEarlier - Format of Affymetrix data file of information about (normalised) expression levels of the individual probes. - - - - - - - - - - EMDB entry format - - beta12orEarlier - Format of an entry from the Electron Microscopy DataBase (EMDB). - true - beta12orEarlier - - - - - - - - - - KEGG PATHWAY entry format - - beta12orEarlier - beta12orEarlier - The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks. - true - - - - - - - - - - MetaCyc entry format - - true - beta12orEarlier - The format of an entry from the MetaCyc metabolic pathways database. - beta12orEarlier - - - - - - - - - - HumanCyc entry format - - The format of a report from the HumanCyc metabolic pathways database. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - INOH entry format - - beta12orEarlier - true - The format of an entry from the INOH signal transduction pathways database. - beta12orEarlier - - - - - - - - - - PATIKA entry format - - beta12orEarlier - The format of an entry from the PATIKA biological pathways database. - beta12orEarlier - true - - - - - - - - - - Reactome entry format - - beta12orEarlier - The format of an entry from the reactome biological pathways database. - true - beta12orEarlier - - - - - - - - - - aMAZE entry format - - beta12orEarlier - true - The format of an entry from the aMAZE biological pathways and molecular interactions database. - beta12orEarlier - - - - - - - - - - CPDB entry format - - The format of an entry from the CPDB database. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Panther Pathways entry format - - beta12orEarlier - true - beta12orEarlier - The format of an entry from the Panther Pathways database. - - - - - - - - - - Taverna workflow format - - - Format of Taverna workflows. - beta12orEarlier - - - - - - - - - - BioModel mathematical model format - - beta12orEarlier - beta12orEarlier - Format of mathematical models from the BioModel database. - true - Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. - - - - - - - - - - KEGG LIGAND entry format - - The format of an entry from the KEGG LIGAND chemical database. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - KEGG COMPOUND entry format - - beta12orEarlier - The format of an entry from the KEGG COMPOUND database. - true - beta12orEarlier - - - - - - - - - - KEGG PLANT entry format - - beta12orEarlier - beta12orEarlier - The format of an entry from the KEGG PLANT database. - true - - - - - - - - - - KEGG GLYCAN entry format - - true - beta12orEarlier - The format of an entry from the KEGG GLYCAN database. - beta12orEarlier - - - - - - - - - - PubChem entry format - - beta12orEarlier - The format of an entry from PubChem. - true - beta12orEarlier - - - - - - - - - - ChemSpider entry format - - beta12orEarlier - The format of an entry from a database of chemical structures and property predictions. - beta12orEarlier - true - - - - - - - - - - ChEBI entry format - - beta12orEarlier - beta12orEarlier - The format of an entry from Chemical Entities of Biological Interest (ChEBI). - true - ChEBI includes an ontological classification defining relations between entities or classes of entities. - - - - - - - - - - MSDchem ligand dictionary entry format - - The format of an entry from the MSDchem ligand dictionary. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - HET group dictionary entry format - - - The format of an entry from the HET group dictionary (HET groups from PDB files). - beta12orEarlier - - - - - - - - - - KEGG DRUG entry format - - The format of an entry from the KEGG DRUG database. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - PubMed citation - - - beta12orEarlier - Format of bibliographic reference as used by the PubMed database. - - - - - - - - - - Medline Display Format - - - beta12orEarlier - Format for abstracts of scientific articles from the Medline database. - Bibliographic reference information including citation information is included - - - - - - - - - - CiteXplore-core - - - beta12orEarlier - CiteXplore 'core' citation format including title, journal, authors and abstract. - - - - - - - - - - CiteXplore-all - - - CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references. - beta12orEarlier - - - - - - - - - - pmc - - - beta12orEarlier - Article format of the PubMed Central database. - - - - - - - - - - iHOP text mining abstract format - - - beta12orEarlier - iHOP abstract format. - - - - - - - - - - Oscar3 - - - Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document. - Text mining abstract format from the Oscar 3 application. - beta12orEarlier - - - - - - - - - - PDB atom record format - - true - beta13 - beta12orEarlier - Format of an ATOM record (describing data for an individual atom) from a PDB file. - - - - - - - - - - CATH chain report format - - The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain. - beta12orEarlier - Format of CATH domain classification information for a polypeptide chain. - beta12orEarlier - true - - - - - - - - - - CATH PDB report format - - beta12orEarlier - beta12orEarlier - true - Format of CATH domain classification information for a protein PDB file. - The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file. - - - - - - - - - - NCBI gene report format - - true - Entry (gene) format of the NCBI database. - beta12orEarlier - beta12orEarlier - - - - - - - - - - GeneIlluminator gene report format - - Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service. - This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. - beta12orEarlier - beta12orEarlier - Moby:GI_Gene - true - - - - - - - - - - BacMap gene card format - - Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database. - true - beta12orEarlier - beta12orEarlier - Moby:BacMapGeneCard - - - - - - - - - - ColiCard report format - - Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB). - true - beta12orEarlier - Moby:ColiCard - beta12orEarlier - - - - - - - - - - PlasMapper TextMap - - - beta12orEarlier - Map of a plasmid (circular DNA) in PlasMapper TextMap format. - - - - - - - - - - newick - - - nh - beta12orEarlier - Phylogenetic tree Newick (text) format. - - - - - - - - - - TreeCon format - - - beta12orEarlier - Phylogenetic tree TreeCon (text) format. - - - - - - - - - - Nexus format - - - Phylogenetic tree Nexus (text) format. - beta12orEarlier - - - - - - - - - - Format - - - - http://en.wikipedia.org/wiki/File_format - http://purl.org/biotop/biotop.owl#MachineLanguage - File format - Data model - http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure - Exchange format - "http://purl.obolibrary.org/obo/IAO_0000098" - http://semanticscience.org/resource/SIO_000612 - http://semanticscience.org/resource/SIO_000618 - beta12orEarlier - http://www.ifomis.org/bfo/1.1/snap#Continuant - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality - "http://purl.org/dc/elements/1.1/format" - http://wsio.org/compression_004 - A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. - http://en.wikipedia.org/wiki/List_of_file_formats - http://www.ifomis.org/bfo/1.1/snap#Quality - Data format - http://purl.org/biotop/biotop.owl#Quality - The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. - http://www.onto-med.de/ontologies/gfo.owl#Perpetuant - - - - - A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) - Data model - - - - - File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. - File format - - - - - - - - - - Atomic data format - - beta12orEarlier - beta13 - Data format for an individual atom. - true - - - - - - - - - - Sequence record format - - - - - - - - Data format for a molecular sequence record. - beta12orEarlier - - - - - - - - - - Sequence feature annotation format - - - - - - - - beta12orEarlier - Data format for molecular sequence feature information. - - - - - - - - - - Alignment format - - - - - - - - Data format for molecular sequence alignment information. - beta12orEarlier - - - - - - - - - - acedb - - beta12orEarlier - ACEDB sequence format. - - - - - - - - - - clustal sequence format - - true - beta12orEarlier - Clustalw output format. - beta12orEarlier - - - - - - - - - - codata - - - Codata entry format. - beta12orEarlier - - - - - - - - - - dbid - - beta12orEarlier - Fasta format variant with database name before ID. - - - - - - - - - - EMBL format - - - EMBL entry format. - EMBL sequence format - EMBL - beta12orEarlier - - - - - - - - - - Staden experiment format - - - Staden experiment file format. - beta12orEarlier - - - - - - - - - - FASTA - - - beta12orEarlier - FASTA format - FASTA sequence format - FASTA format including NCBI-style IDs. - - - - - - - - - - FASTQ - - FASTQ short read format ignoring quality scores. - beta12orEarlier - FASTAQ - fq - - - - - - - - - - FASTQ-illumina - - FASTQ Illumina 1.3 short read format. - beta12orEarlier - - - - - - - - - - FASTQ-sanger - - FASTQ short read format with phred quality. - beta12orEarlier - - - - - - - - - - FASTQ-solexa - - FASTQ Solexa/Illumina 1.0 short read format. - beta12orEarlier - - - - - - - - - - fitch program - - - Fitch program format. - beta12orEarlier - - - - - - - - - - GCG - - - GCG SSF - beta12orEarlier - GCG SSF (single sequence file) file format. - GCG sequence file format. - - - - - - - - - - GenBank format - - - beta12orEarlier - Genbank entry format. - - - - - - - - - - genpept - - beta12orEarlier - Genpept protein entry format. - Currently identical to refseqp format - - - - - - - - - - GFF2-seq - - - GFF feature file format with sequence in the header. - beta12orEarlier - - - - - - - - - - GFF3-seq - - - GFF3 feature file format with sequence. - beta12orEarlier - - - - - - - - - - giFASTA format - - FASTA sequence format including NCBI-style GIs. - beta12orEarlier - - - - - - - - - - hennig86 - - - beta12orEarlier - Hennig86 output sequence format. - - - - - - - - - - ig - - - Intelligenetics sequence format. - beta12orEarlier - - - - - - - - - - igstrict - - - beta12orEarlier - Intelligenetics sequence format (strict version). - - - - - - - - - - jackknifer - - - Jackknifer interleaved and non-interleaved sequence format. - beta12orEarlier - - - - - - - - - - mase format - - - beta12orEarlier - Mase program sequence format. - - - - - - - - - - mega-seq - - - beta12orEarlier - Mega interleaved and non-interleaved sequence format. - - - - - - - - - - MSF - - GCG MSF - beta12orEarlier - GCG MSF (multiple sequence file) file format. - - - - - - - - - - nbrf/pir - - NBRF/PIR entry sequence format. - nbrf - beta12orEarlier - pir - - - - - - - - - - nexus-seq - - - - beta12orEarlier - Nexus/paup interleaved sequence format. - - - - - - - - - - pdbatom - - - - pdb format in EMBOSS. - beta12orEarlier - PDB sequence format (ATOM lines). - - - - - - - - - - pdbatomnuc - - - - beta12orEarlier - pdbnuc format in EMBOSS. - PDB nucleotide sequence format (ATOM lines). - - - - - - - - - - pdbseqresnuc - - - - pdbnucseq format in EMBOSS. - PDB nucleotide sequence format (SEQRES lines). - beta12orEarlier - - - - - - - - - - pdbseqres - - - - PDB sequence format (SEQRES lines). - beta12orEarlier - pdbseq format in EMBOSS. - - - - - - - - - - Pearson format - - beta12orEarlier - Plain old FASTA sequence format (unspecified format for IDs). - - - - - - - - - - phylip sequence format - - beta12orEarlier - Phylip interleaved sequence format. - true - beta12orEarlier - - - - - - - - - - phylipnon sequence format - - true - Phylip non-interleaved sequence format. - beta12orEarlier - beta12orEarlier - - - - - - - - - - raw - - - beta12orEarlier - Raw sequence format with no non-sequence characters. - - - - - - - - - - refseqp - - - beta12orEarlier - Refseq protein entry sequence format. - Currently identical to genpept format - - - - - - - - - - selex sequence format - - beta12orEarlier - true - beta12orEarlier - Selex sequence format. - - - - - - - - - - Staden format - - - beta12orEarlier - Staden suite sequence format. - - - - - - - - - - - - - - Stockholm format - - - Stockholm multiple sequence alignment format (used by Pfam and Rfam). - beta12orEarlier - - - - - - - - - - - - strider format - - - DNA strider output sequence format. - beta12orEarlier - - - - - - - - - - UniProtKB format - - UniProt format - SwissProt format - beta12orEarlier - UniProtKB entry sequence format. - - - - - - - - - - plain text format (unformatted) - - - beta12orEarlier - Plain text sequence format (essentially unformatted). - - - - - - - - - - treecon sequence format - - true - beta12orEarlier - beta12orEarlier - Treecon output sequence format. - - - - - - - - - - ASN.1 sequence format - - - NCBI ASN.1-based sequence format. - beta12orEarlier - - - - - - - - - - DAS format - - - das sequence format - DAS sequence (XML) format (any type). - beta12orEarlier - - - - - - - - - - dasdna - - - beta12orEarlier - DAS sequence (XML) format (nucleotide-only). - The use of this format is deprecated. - - - - - - - - - - debug-seq - - - EMBOSS debugging trace sequence format of full internal data content. - beta12orEarlier - - - - - - - - - - jackknifernon - - - beta12orEarlier - Jackknifer output sequence non-interleaved format. - - - - - - - - - - meganon sequence format - - beta12orEarlier - beta12orEarlier - Mega non-interleaved output sequence format. - true - - - - - - - - - - NCBI format - - NCBI FASTA sequence format with NCBI-style IDs. - beta12orEarlier - There are several variants of this. - - - - - - - - - - nexusnon - - - - Nexus/paup non-interleaved sequence format. - beta12orEarlier - - - - - - - - - - GFF2 - - beta12orEarlier - General Feature Format (GFF) of sequence features. - - - - - - - - - - - - GFF3 - - beta12orEarlier - Generic Feature Format version 3 (GFF3) of sequence features. - - - - - - - - - - - - pir - - true - 1.7 - PIR feature format. - beta12orEarlier - - - - - - - - - - swiss feature - - true - Swiss-Prot feature format. - beta12orEarlier - beta12orEarlier - - - - - - - - - - DASGFF - - - DAS GFF (XML) feature format. - das feature - DASGFF feature - beta12orEarlier - - - - - - - - - - debug-feat - - - EMBOSS debugging trace feature format of full internal data content. - beta12orEarlier - - - - - - - - - - EMBL feature - - beta12orEarlier - EMBL feature format. - true - beta12orEarlier - - - - - - - - - - GenBank feature - - beta12orEarlier - Genbank feature format. - beta12orEarlier - true - - - - - - - - - - ClustalW format - - - clustal - beta12orEarlier - ClustalW format for (aligned) sequences. - - - - - - - - - - debug - - - EMBOSS alignment format for debugging trace of full internal data content. - beta12orEarlier - - - - - - - - - - FASTA-aln - - - beta12orEarlier - Fasta format for (aligned) sequences. - - - - - - - - - - markx0 - - beta12orEarlier - Pearson MARKX0 alignment format. - - - - - - - - - - markx1 - - Pearson MARKX1 alignment format. - beta12orEarlier - - - - - - - - - - markx10 - - beta12orEarlier - Pearson MARKX10 alignment format. - - - - - - - - - - markx2 - - beta12orEarlier - Pearson MARKX2 alignment format. - - - - - - - - - - markx3 - - beta12orEarlier - Pearson MARKX3 alignment format. - - - - - - - - - - match - - - Alignment format for start and end of matches between sequence pairs. - beta12orEarlier - - - - - - - - - - mega - - Mega format for (typically aligned) sequences. - beta12orEarlier - - - - - - - - - - meganon - - Mega non-interleaved format for (typically aligned) sequences. - beta12orEarlier - - - - - - - - - - msf alignment format - - true - beta12orEarlier - beta12orEarlier - MSF format for (aligned) sequences. - - - - - - - - - - nexus alignment format - - Nexus/paup format for (aligned) sequences. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - nexusnon alignment format - - beta12orEarlier - true - Nexus/paup non-interleaved format for (aligned) sequences. - beta12orEarlier - - - - - - - - - - pair - - EMBOSS simple sequence pair alignment format. - beta12orEarlier - - - - - - - - - - PHYLIP format - - phy - beta12orEarlier - ph - http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format - PHYLIP interleaved format - Phylip format for (aligned) sequences. - - - - - - - - - - phylipnon - - http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format - beta12orEarlier - PHYLIP sequential format - Phylip non-interleaved format for (aligned) sequences. - - - - - - - - - - scores format - - - Alignment format for score values for pairs of sequences. - beta12orEarlier - - - - - - - - - - selex - - - - beta12orEarlier - SELEX format for (aligned) sequences. - - - - - - - - - - EMBOSS simple format - - - EMBOSS simple multiple alignment format. - beta12orEarlier - - - - - - - - - - srs format - - - beta12orEarlier - Simple multiple sequence (alignment) format for SRS. - - - - - - - - - - srspair - - - beta12orEarlier - Simple sequence pair (alignment) format for SRS. - - - - - - - - - - T-Coffee format - - - T-Coffee program alignment format. - beta12orEarlier - - - - - - - - - - TreeCon-seq - - - - Treecon format for (aligned) sequences. - beta12orEarlier - - - - - - - - - - Phylogenetic tree format - - - - - - - - Data format for a phylogenetic tree. - beta12orEarlier - - - - - - - - - - Biological pathway or network format - - - - - - - - beta12orEarlier - Data format for a biological pathway or network. - - - - - - - - - - Sequence-profile alignment format - - - - - - - - beta12orEarlier - Data format for a sequence-profile alignment. - - - - - - - - - - Sequence-profile alignment (HMM) format - - beta12orEarlier - beta12orEarlier - true - Data format for a sequence-HMM profile alignment. - - - - - - - - - - Amino acid index format - - - - - - - - Data format for an amino acid index. - beta12orEarlier - - - - - - - - - - Article format - - - - - - - - beta12orEarlier - Literature format - Data format for a full-text scientific article. - - - - - - - - - - Text mining report format - - - - - - - - beta12orEarlier - Data format for an abstract (report) from text mining. - - - - - - - - - - Enzyme kinetics report format - - - - - - - - Data format for reports on enzyme kinetics. - beta12orEarlier - - - - - - - - - - Small molecule report format - - - - - - - - beta12orEarlier - Chemical compound annotation format - Format of a report on a chemical compound. - - - - - - - - - - Gene annotation format - - - - - - - - Format of a report on a particular locus, gene, gene system or groups of genes. - beta12orEarlier - Gene features format - - - - - - - - - - Workflow format - - beta12orEarlier - Format of a workflow. - - - - - - - - - - Tertiary structure format - - beta12orEarlier - Data format for a molecular tertiary structure. - - - - - - - - - - Biological model format - - Data format for a biological model. - beta12orEarlier - 1.2 - true - - - - - - - - - - Chemical formula format - - - - - - - - beta12orEarlier - Text format of a chemical formula. - - - - - - - - - - Phylogenetic character data format - - - - - - - - beta12orEarlier - Format of raw (unplotted) phylogenetic data. - - - - - - - - - - Phylogenetic continuous quantitative character format - - - - - - - - Format of phylogenetic continuous quantitative character data. - beta12orEarlier - - - - - - - - - - Phylogenetic discrete states format - - - - - - - - Format of phylogenetic discrete states data. - beta12orEarlier - - - - - - - - - - Phylogenetic tree report (cliques) format - - - - - - - - Format of phylogenetic cliques data. - beta12orEarlier - - - - - - - - - - Phylogenetic tree report (invariants) format - - - - - - - - beta12orEarlier - Format of phylogenetic invariants data. - - - - - - - - - - Electron microscopy model format - - beta12orEarlier - true - beta12orEarlier - Annotation format for electron microscopy models. - - - - - - - - - - Phylogenetic tree report (tree distances) format - - - - - - - - Format for phylogenetic tree distance data. - beta12orEarlier - - - - - - - - - - Polymorphism report format - - beta12orEarlier - true - 1.0 - Format for sequence polymorphism data. - - - - - - - - - Protein family report format - - - - - - - - beta12orEarlier - Format for reports on a protein family. - - - - - - - - - - Protein interaction format - - - - - - - - beta12orEarlier - Format for molecular interaction data. - Molecular interaction format - - - - - - - - - - Sequence assembly format - - - - - - - - beta12orEarlier - Format for sequence assembly data. - - - - - - - - - - Microarray experiment data format - - Format for information about a microarray experimental per se (not the data generated from that experiment). - beta12orEarlier - - - - - - - - - - Sequence trace format - - - - - - - - Format for sequence trace data (i.e. including base call information). - beta12orEarlier - - - - - - - - - - Gene expression report format - - - - - - - - Gene expression data format - Format of a file of gene expression data, e.g. a gene expression matrix or profile. - beta12orEarlier - - - - - - - - - - Genotype and phenotype annotation format - - beta12orEarlier - true - Format of a report on genotype / phenotype information. - beta12orEarlier - - - - - - - - - - Map format - - - - - - - - Format of a map of (typically one) molecular sequence annotated with features. - beta12orEarlier - - - - - - - - - - Nucleic acid features (primers) format - - beta12orEarlier - Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence. - - - - - - - - - - Protein report format - - - - - - - - Format of a report of general information about a specific protein. - beta12orEarlier - - - - - - - - - - Protein report (enzyme) format - - Format of a report of general information about a specific enzyme. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - 3D-1D scoring matrix format - - - - - - - - beta12orEarlier - Format of a matrix of 3D-1D scores (amino acid environment probabilities). - - - - - - - - - - Protein structure report (quality evaluation) format - - - - - - - - Format of a report on the quality of a protein three-dimensional model. - beta12orEarlier - - - - - - - - - - Database hits (sequence) format - - - - - - - - Format of a report on sequence hits and associated data from searching a sequence database. - beta12orEarlier - - - - - - - - - - Sequence distance matrix format - - - - - - - - beta12orEarlier - Format of a matrix of genetic distances between molecular sequences. - - - - - - - - - - Sequence motif format - - - - - - - - Format of a sequence motif. - beta12orEarlier - - - - - - - - - - Sequence profile format - - - - - - - - Format of a sequence profile. - beta12orEarlier - - - - - - - - - - Hidden Markov model format - - - - - - - - beta12orEarlier - Format of a hidden Markov model. - - - - - - - - - - Dirichlet distribution format - - - - - - - - Data format of a dirichlet distribution. - beta12orEarlier - - - - - - - - - - HMM emission and transition counts format - - - - - - - - - - - - - - Data format for the emission and transition counts of a hidden Markov model. - beta12orEarlier - - - - - - - - - - RNA secondary structure format - - - - - - - - beta12orEarlier - Format for secondary structure (predicted or real) of an RNA molecule. - - - - - - - - - - Protein secondary structure format - - Format for secondary structure (predicted or real) of a protein molecule. - beta12orEarlier - - - - - - - - - - Sequence range format - - - - - - - - beta12orEarlier - Format used to specify range(s) of sequence positions. - - - - - - - - - - pure - - - Alphabet for molecular sequence with possible unknown positions but without non-sequence characters. - beta12orEarlier - - - - - - - - - - unpure - - - Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters. - beta12orEarlier - - - - - - - - - - unambiguous sequence - - - Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters. - beta12orEarlier - - - - - - - - - - ambiguous - - - beta12orEarlier - Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters. - - - - - - - - - - Sequence features (repeats) format - - beta12orEarlier - Format used for map of repeats in molecular (typically nucleotide) sequences. - - - - - - - - - - Nucleic acid features (restriction sites) format - - beta12orEarlier - Format used for report on restriction enzyme recognition sites in nucleotide sequences. - - - - - - - - - - Gene features (coding region) format - - beta12orEarlier - Format used for report on coding regions in nucleotide sequences. - true - 1.10 - - - - - - - - - - Sequence cluster format - - - - - - - - beta12orEarlier - Format used for clusters of molecular sequences. - - - - - - - - - - Sequence cluster format (protein) - - Format used for clusters of protein sequences. - beta12orEarlier - - - - - - - - - - Sequence cluster format (nucleic acid) - - Format used for clusters of nucleotide sequences. - beta12orEarlier - - - - - - - - - - Gene cluster format - - true - beta13 - beta12orEarlier - Format used for clusters of genes. - - - - - - - - - - EMBL-like (text) - - - This concept may be used for the many non-standard EMBL-like text formats. - beta12orEarlier - A text format resembling EMBL entry format. - - - - - - - - - - FASTQ-like format (text) - - - A text format resembling FASTQ short read format. - This concept may be used for non-standard FASTQ short read-like formats. - beta12orEarlier - - - - - - - - - - EMBLXML - - XML format for EMBL entries. - beta12orEarlier - - - - - - - - - - cdsxml - - XML format for EMBL entries. - beta12orEarlier - - - - - - - - - - insdxml - - beta12orEarlier - XML format for EMBL entries. - - - - - - - - - - geneseq - - Geneseq sequence format. - beta12orEarlier - - - - - - - - - - UniProt-like (text) - - - A text sequence format resembling uniprotkb entry format. - beta12orEarlier - - - - - - - - - - UniProt format - - beta12orEarlier - true - UniProt entry sequence format. - 1.8 - - - - - - - - - - ipi - - 1.8 - beta12orEarlier - ipi sequence format. - true - - - - - - - - - - medline - - - Abstract format used by MedLine database. - beta12orEarlier - - - - - - - - - - Ontology format - - - - - - - - Format used for ontologies. - beta12orEarlier - - - - - - - - - - OBO format - - beta12orEarlier - A serialisation format conforming to the Open Biomedical Ontologies (OBO) model. - - - - - - - - - - OWL format - - - A serialisation format conforming to the Web Ontology Language (OWL) model. - beta12orEarlier - - - - - - - - - - FASTA-like (text) - - - This concept may also be used for the many non-standard FASTA-like formats. - http://filext.com/file-extension/FASTA - beta12orEarlier - A text format resembling FASTA format. - - - - - - - - - - Sequence record full format - - 1.8 - beta12orEarlier - Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database. - true - - - - - - - - - - Sequence record lite format - - true - 1.8 - beta12orEarlier - Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment. - - - - - - - - - - EMBL format (XML) - - beta12orEarlier - An XML format for EMBL entries. - This is a placeholder for other more specific concepts. It should not normally be used for annotation. - - - - - - - - - - GenBank-like format (text) - - - A text format resembling GenBank entry (plain text) format. - This concept may be used for the non-standard GenBank-like text formats. - beta12orEarlier - - - - - - - - - - Sequence feature table format (text) - - Text format for a sequence feature table. - beta12orEarlier - - - - - - - - - - Strain data format - - Format of a report on organism strain data / cell line. - beta12orEarlier - true - 1.0 - - - - - - - - - CIP strain data format - - Format for a report of strain data as used for CIP database entries. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - phylip property values - - true - PHYLIP file format for phylogenetic property data. - beta12orEarlier - beta12orEarlier - - - - - - - - - - STRING entry format (HTML) - - beta12orEarlier - true - beta12orEarlier - Entry format (HTML) for the STRING database of protein interaction. - - - - - - - - - - STRING entry format (XML) - - - Entry format (XML) for the STRING database of protein interaction. - beta12orEarlier - - - - - - - - - - GFF - - - GFF feature format (of indeterminate version). - beta12orEarlier - - - - - - - - - - GTF - - Gene Transfer Format (GTF), a restricted version of GFF. - beta12orEarlier - - - - - - - - - - - - - FASTA-HTML - - - FASTA format wrapped in HTML elements. - beta12orEarlier - - - - - - - - - - EMBL-HTML - - - EMBL entry format wrapped in HTML elements. - beta12orEarlier - - - - - - - - - - BioCyc enzyme report format - - true - beta12orEarlier - beta12orEarlier - Format of an entry from the BioCyc enzyme database. - - - - - - - - - - ENZYME enzyme report format - - Format of an entry from the Enzyme nomenclature database (ENZYME). - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - PseudoCAP gene report format - - true - beta12orEarlier - beta12orEarlier - Format of a report on a gene from the PseudoCAP database. - - - - - - - - - - GeneCards gene report format - - Format of a report on a gene from the GeneCards database. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Textual format - - http://filext.com/file-extension/TSV - http://www.iana.org/assignments/media-types/text/plain - Textual format. - Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual). - txt - http://filext.com/file-extension/TXT - Plain text - http://www.iana.org/assignments/media-types/media-types.xhtml#text - beta12orEarlier - - - - - - - - - - HTML - - - - - - - - HTML format. - beta12orEarlier - http://filext.com/file-extension/HTML - Hypertext Markup Language - - - - - - - - - - XML - - Data in XML format can be serialised into text, or binary format. - eXtensible Markup Language (XML) format. - beta12orEarlier - http://filext.com/file-extension/XML - Extensible Markup Language - - - - - - - - - - Binary format - - Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. - beta12orEarlier - Binary format. - - - - - - - - - - URI format - - beta13 - true - Typical textual representation of a URI. - beta12orEarlier - - - - - - - - - - NCI-Nature pathway entry format - - beta12orEarlier - true - The format of an entry from the NCI-Nature pathways database. - beta12orEarlier - - - - - - - - - - Format (typed) - - This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. - beta12orEarlier - A broad class of format distinguished by the scientific nature of the data that is identified. - - - - - - - - - - BioXSD - - - - - - - - - - - - - - - - - - - - - - - - BioXSD XML format - beta12orEarlier - BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). - - - - - - - - - - - - RDF format - - - beta12orEarlier - A serialisation format conforming to the Resource Description Framework (RDF) model. - - - - - - - - - - GenBank-HTML - - - beta12orEarlier - Genbank entry format wrapped in HTML elements. - - - - - - - - - - Protein features (domains) format - - beta12orEarlier - true - beta12orEarlier - Format of a report on protein features (domain composition). - - - - - - - - - - EMBL-like format - - beta12orEarlier - A format resembling EMBL entry (plain text) format. - This concept may be used for the many non-standard EMBL-like formats. - - - - - - - - - - FASTQ-like format - - A format resembling FASTQ short read format. - This concept may be used for non-standard FASTQ short read-like formats. - beta12orEarlier - - - - - - - - - - FASTA-like - - This concept may be used for the many non-standard FASTA-like formats. - beta12orEarlier - A format resembling FASTA format. - - - - - - - - - - uniprotkb-like format - - - beta12orEarlier - A sequence format resembling uniprotkb entry format. - - - - - - - - - - Sequence feature table format - - - - - - - - Format for a sequence feature table. - beta12orEarlier - - - - - - - - - - OBO - - - beta12orEarlier - OBO ontology text format. - - - - - - - - - - OBO-XML - - - beta12orEarlier - OBO ontology XML format. - - - - - - - - - - Sequence record format (text) - - Data format for a molecular sequence record. - beta12orEarlier - - - - - - - - - - Sequence record format (XML) - - beta12orEarlier - Data format for a molecular sequence record. - - - - - - - - - - Sequence feature table format (XML) - - XML format for a sequence feature table. - beta12orEarlier - - - - - - - - - - Alignment format (text) - - Text format for molecular sequence alignment information. - beta12orEarlier - - - - - - - - - - Alignment format (XML) - - XML format for molecular sequence alignment information. - beta12orEarlier - - - - - - - - - - Phylogenetic tree format (text) - - beta12orEarlier - Text format for a phylogenetic tree. - - - - - - - - - - Phylogenetic tree format (XML) - - beta12orEarlier - XML format for a phylogenetic tree. - - - - - - - - - - EMBL-like (XML) - - - An XML format resembling EMBL entry format. - This concept may be used for the any non-standard EMBL-like XML formats. - beta12orEarlier - - - - - - - - - - GenBank-like format - - A format resembling GenBank entry (plain text) format. - beta12orEarlier - This concept may be used for the non-standard GenBank-like formats. - - - - - - - - - - STRING entry format - - beta12orEarlier - Entry format for the STRING database of protein interaction. - beta12orEarlier - true - - - - - - - - - - Sequence assembly format (text) - - beta12orEarlier - Text format for sequence assembly data. - - - - - - - - - - Amino acid identifier format - - beta13 - Text format (representation) of amino acid residues. - true - beta12orEarlier - - - - - - - - - - completely unambiguous - - - beta12orEarlier - Alphabet for a molecular sequence without any unknown positions or ambiguity characters. - - - - - - - - - - completely unambiguous pure - - - beta12orEarlier - Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters. - - - - - - - - - - completely unambiguous pure nucleotide - - - Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters . - beta12orEarlier - - - - - - - - - - completely unambiguous pure dna - - - beta12orEarlier - Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters. - - - - - - - - - - completely unambiguous pure rna sequence - - - Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters. - beta12orEarlier - - - - - - - - - - Raw sequence format - - - - - - - - http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence - beta12orEarlier - Format of a raw molecular sequence (i.e. the alphabet used). - - - - - - - - - - BAM - - - - beta12orEarlier - BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. - - - - - - - - - - - - SAM - - - - The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project. - beta12orEarlier - Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. - - - - - - - - - - - - SBML - - - Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation. - beta12orEarlier - - - - - - - - - - - - completely unambiguous pure protein - - - beta12orEarlier - Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters. - - - - - - - - - - Bibliographic reference format - - - - - - - - - - - - - - Format of a bibliographic reference. - beta12orEarlier - - - - - - - - - - Sequence annotation track format - - - - - - - - Format of a sequence annotation track. - beta12orEarlier - - - - - - - - - - Alignment format (pair only) - - - - - - - - beta12orEarlier - Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences. - - - - - - - - - - Sequence variation annotation format - - - - - - - - Format of sequence variation annotation. - beta12orEarlier - - - - - - - - - - markx0 variant - - - Some variant of Pearson MARKX alignment format. - beta12orEarlier - - - - - - - - - - mega variant - - - - Some variant of Mega format for (typically aligned) sequences. - beta12orEarlier - - - - - - - - - - Phylip format variant - - - - beta12orEarlier - Some variant of Phylip format for (aligned) sequences. - - - - - - - - - - AB1 - - - beta12orEarlier - AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. - AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). - - - - - - - - - - ACE - - - ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards). - beta12orEarlier - - - - - - - - - - - - BED - - - beta12orEarlier - BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track). - Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser. - - - - - - - - - - - - bigBed - - - beta12orEarlier - bigBed format for large sequence annotation tracks, similar to textual BED format. - - - - - - - - - - - - WIG - - - Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser. - beta12orEarlier - - - - - - - - - - - - bigWig - - - beta12orEarlier - bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format. - - - - - - - - - - - - PSL - - - - PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track. - beta12orEarlier - - - - - - - - - - - - MAF - - - - Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth. - Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format. - beta12orEarlier - - - - - - - - - - - - 2bit - - - beta12orEarlier - 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. - - - - - - - - - - - - - .nib - - - beta12orEarlier - .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. - - - - - - - - - - - - genePred - - - genePred table format for gene prediction tracks. - genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables. - beta12orEarlier - - - - - - - - - - - - pgSnp - - - Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser. - beta12orEarlier - - - - - - - - - - - - axt - - - beta12orEarlier - axt format of alignments, typically produced from BLASTZ. - - - - - - - - - - - - LAV - - - beta12orEarlier - LAV format of alignments generated by BLASTZ and LASTZ. - - - - - - - - - - - - Pileup - - - beta12orEarlier - Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s). - - - - - - - - - - - - VCF - - - beta12orEarlier - Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). - - - - - - - - - - - - SRF - - - Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. - beta12orEarlier - - - - - - - - - - - - ZTR - - - ZTR format for storing chromatogram data from DNA sequencing instruments. - beta12orEarlier - - - - - - - - - - - - GVF - - - Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation. - beta12orEarlier - - - - - - - - - - - - BCF - - - beta12orEarlier - BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). - - - - - - - - - - - Matrix format - - - - - - - - Format of a matrix (array) of numerical values. - beta13 - - - - - - - - - - Protein domain classification format - - - - - - - - Format of data concerning the classification of the sequences and/or structures of protein structural domain(s). - beta13 - - - - - - - - - - Raw SCOP domain classification format - - Format of raw SCOP domain classification data files. - These are the parsable data files provided by SCOP. - beta13 - - - - - - - - - - Raw CATH domain classification format - - These are the parsable data files provided by CATH. - beta13 - Format of raw CATH domain classification data files. - - - - - - - - - - CATH domain report format - - Format of summary of domain classification information for a CATH domain. - beta13 - The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. - - - - - - - - - - SBRML - - - 1.0 - Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models. - - - - - - - - - - - - BioPAX - - BioPAX is an exchange format for pathway data, with its data model defined in OWL. - 1.0 - - - - - - - - - - - - EBI Application Result XML - - - - EBI Application Result XML is a format returned by sequence similarity search Web services at EBI. - 1.0 - - - - - - - - - - - - PSI MI XML (MIF) - - - 1.0 - XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI. - MIF - - - - - - - - - - - - phyloXML - - - phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data. - 1.0 - - - - - - - - - - - - NeXML - - - 1.0 - NeXML is a standardised XML format for rich phyloinformatic data. - - - - - - - - - - - - MAGE-ML - - - - - - - - - 1.0 - MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED). - - - - - - - - - - - - MAGE-TAB - - - - - - - - - MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED). - 1.0 - - - - - - - - - - - - GCDML - - - GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC). - 1.0 - - - - - - - - - - - - GTrack - - - 1.0 - GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG). - - - - - - - - - - - - Biological pathway or network report format - - - - - - - - Data format for a report of information derived from a biological pathway or network. - beta12orEarlier - - - - - - - - - - Experiment annotation format - - - - - - - - beta12orEarlier - Data format for annotation on a laboratory experiment. - - - - - - - - - - Cytoband format - - - - - - - - - 1.2 - Cytoband format for chromosome cytobands. - Reflects a UCSC Browser DB table. - - - - - - - - - - - - CopasiML - - - - 1.2 - CopasiML, the native format of COPASI. - - - - - - - - - - - - CellML - - - CellML, the format for mathematical models of biological and other networks. - 1.2 - - - - - - - - - - - - PSI MI TAB (MITAB) - - - 1.2 - Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI. - - - - - - - - - - - - PSI-PAR - - Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema. - 1.2 - - - - - - - - - - - - mzML - - - mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center. - 1.2 - mzML format for raw spectrometer output data, standardised by HUPO PSI MSS. - - - - - - - - - - - - Mass spectrometry data format - - - - - - - - 1.2 - Format for mass spectrometry data. - - - - - - - - - - TraML - - - TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS. - 1.2 - - - - - - - - - - - - mzIdentML - - - mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines. - 1.2 - - - - - - - - - - - - mzQuantML - - - mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics. - 1.2 - - - - - - - - - - - - GelML - - - 1.2 - GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. - - - - - - - - - - - - spML - - - 1.2 - spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics. - - - - - - - - - - - - OWL Functional Syntax - - - A human-readable encoding for the Web Ontology Language (OWL). - 1.2 - - - - - - - - - - Manchester OWL Syntax - - - A syntax for writing OWL class expressions. - 1.2 - This format was influenced by the OWL Abstract Syntax and the DL style syntax. - - - - - - - - - - KRSS2 Syntax - - - This format is used in Protege 4. - A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort". - 1.2 - - - - - - - - - - Turtle - - - The SPARQL Query Language incorporates a very similar syntax. - 1.2 - The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs. - - - - - - - - - - N-Triples - - - N-Triples should not be confused with Notation 3 which is a superset of Turtle. - 1.2 - A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format. - - - - - - - - - - Notation3 - - - N3 - A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind. - - - - - - - - - - RDF/XML - - - - RDF - Resource Description Framework (RDF) XML format. - 1.2 - http://www.ebi.ac.uk/SWO/data/SWO_3000006 - RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. - - - - - - - - - - OWL/XML - - - OWL ontology XML serialisation format. - 1.2 - OWL - - - - - - - - - - A2M - - - The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA. - 1.3 - - - - - - - - - - - - SFF - - - Standard flowgram format - Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. - 1.3 - - - - - - - - - - - - MAP - - The MAP file describes SNPs and is used by the Plink package. - 1.3 - Plink MAP - - - - - - - - - - - PED - - Plink PED - 1.3 - The PED file describes individuals and genetic data and is used by the Plink package. - - - - - - - - - - - Individual genetic data format - - Data format for a metadata on an individual and their genetic data. - 1.3 - - - - - - - - - - PED/MAP - - - The PED/MAP file describes data used by the Plink package. - Plink PED/MAP - 1.3 - - - - - - - - - - - CT - - - File format of a CT (Connectivity Table) file from the RNAstructure package. - beta12orEarlier - Connect format - Connectivity Table file format - - - - - - - - - - - - SS - - - beta12orEarlier - XRNA old input style format. - - - - - - - - - - - RNAML - - - - RNA Markup Language. - beta12orEarlier - - - - - - - - - - - GDE - - - Format for the Genetic Data Environment (GDE). - beta12orEarlier - - - - - - - - - - - BLC - - 1.3 - Block file format - A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge. - - - - - - - - - - - Data index format - - - - - - - - - 1.3 - - - - - - - - - - BAI - - - - - - - - 1.3 - BAM indexing format - - - - - - - - - - - HMMER2 - - HMMER profile HMM file for HMMER versions 2.x - 1.3 - - - - - - - - - - - HMMER3 - - 1.3 - HMMER profile HMM file for HMMER versions 3.x - - - - - - - - - - - PO - - EMBOSS simple sequence pair alignment format. - 1.3 - - - - - - - - - - - BLAST XML results format - - - XML format as produced by the NCBI Blast package - 1.3 - - - - - - - - - - CRAM - - - Reference-based compression of alignment format - http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf - http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf - 1.7 - - - - - - - - - - JSON - - 1.7 - Javascript Object Notation format; a lightweight, text-based format to represent structured data using key-value pairs. - - - - - - - - - - EPS - - Encapsulated PostScript format - 1.7 - - - - - - - - - - GIF - - 1.7 - Graphics Interchange Format. - - - - - - - - - - xls - - - Microsoft Excel spreadsheet format. - Microsoft Excel format - 1.7 - - - - - - - - - - TSV - - Tabular format - http://filext.com/file-extension/CSV - http://www.iana.org/assignments/media-types/text/csv - Tabular data represented as tab-separated values in a text file. - 1.7 - http://filext.com/file-extension/TSV - CSV - - - - - - - - - - Gene expression data format - - true - 1.10 - 1.7 - Format of a file of gene expression data, e.g. a gene expression matrix or profile. - - - - - - - - - - Cytoscape input file format - - - Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments. - 1.7 - - - - - - - - - - ebwt - - - - - - - - https://github.com/BenLangmead/bowtie/blob/master/MANUAL - Bowtie index format - 1.7 - Bowtie format for indexed reference genome for "small" genomes. - - - - - - - - - - RSF - - http://www.molbiol.ox.ac.uk/tutorials/Seqlab_GCG.pdf - RSF-format files contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information (from the GCG manual). - Rich sequence format. - 1.7 - GCG RSF - - - - - - - - - - GCG format variant - - - - 1.7 - Some format based on the GCG format. - - - - - - - - - - BSML - - - http://rothlab.ucdavis.edu/genhelp/chapter_2_using_sequences.html#_Creating_and_Editing_Single_Sequenc - Bioinformatics Sequence Markup Language format. - 1.7 - - - - - - - - - - ebwtl - - - - - - - - 1.7 - https://github.com/BenLangmead/bowtie/blob/master/MANUAL - Bowtie long index format - Bowtie format for indexed reference genome for "large" genomes. - - - - - - - - - - Ensembl variation file format - - - Ensembl standard format for variation data. - 1.8 - - - - - - - - - - - docx - - - 1.8 - Microsoft Word format - doc - Microsoft Word format. - - - - - - - - - - Document format - - Portable Document Format - Microsoft Word format - Format of documents including word processor, spreadsheet and presentation. - 1.8 - doc - - - - - - - - - - PDF - - - 1.8 - Portable Document Format - - - - - - - - - - Image format - - - - - - - - Format used for images and image metadata. - 1.9 - - - - - - - - - - DICOM format - - - 1.9 - Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard. - - - - - - - - - - - - - nii - - - Medical image and metadata format of the Neuroimaging Informatics Technology Initiative. - - - NIfTI-1 format - 1.9 - - - - - - - - - - - mhd - - - Metalmage format - 1.9 - Text-based tagged file format for medical images generated using the MetaImage software package. - - - - - - - - - - - nrrd - - - 1.9 - Nearly Raw Rasta Data format designed to support scientific visualization and image processing involving N-dimensional raster data. - - - - - - - - - - - R file format - - File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics. - - 1.9 - - - - - - - - - - SPSS - - 1.9 - File format used for scripts for the Statistical Package for the Social Sciences. - - - - - - - - - - - MHT - MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on. - - EMBL entry format wrapped in HTML elements. - 1.9 - MHTML - - - - - - - - - - IDAT - - - - - - - - - Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array. - 1.10 - - - - - - - - - - JPG - - - 1.10 - Joint Picture Group file format for lossy graphics file. - - Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type. - - - - - - - - - - - rcc - - - 1.10 - Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts. - - - - - - - - - - arff - - ARFF (Attribute-Relation File Format) is an ASCII text file format that describes a list of instances sharing a set of attributes. - 1.11 - This file format is for machine learning. - - - - - - - - - - - - afg - - - 1.11 - AFG is a single text-based file assembly format that holds read and consensus information together - - - - - - - - - - - - bedgraph - - - Holds a tab-delimited chromosome /start /end / datavalue dataset. - 1.11 - The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data - - - - - - - - - - - - bedstrict - - Browser Extensible Data (BED) format of sequence annotation track that strictly does not contain non-standard fields beyond the first 3 columns. - Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not. - 1.11 - - - - - - - - - - - - bed6 - - Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6 - BED file format where each feature is described by chromosome, start, end, name, score, and strand. - 1.11 - - - - - - - - - - - - bed12 - - 1.11 - Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12 - A BED file where each feature is described by all twelve columns. - - - - - - - - - - - - chrominfo - - - 1.11 - Tabular format of chromosome names and sizes used by Galaxy. - Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not. - - - - - - - - - - - - customtrack - - - 1.11 - Custom Sequence annotation track format used by Galaxy. - Used for tracks/track views within galaxy. - - - - - - - - - - - - csfasta - - - Color space FASTA format sequence variant. - 1.3 - FASTA format extended for color space information. - - - - - - - - - - - - hdf5 - - An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. H5py uses straightforward NumPy and Python metaphors, like dictionary and NumPy array syntax. - 1.11 - h5 - Binary format used by Galaxy for hierarchical data. - - - - - - - - - - - - tiff - - - The TIFF format is perhaps the most versatile and diverse bitmap format in existence. Its extensible nature and support for numerous data compression schemes allow developers to customize the TIFF format to fit any peculiar data storage needs. - - A versatile bitmap format. - 1.11 - - - - - - - - - - - bmp - - - Standard bitmap storage format in the Microsoft Windows environment. - 1.11 - Although it is based on Windows internal bitmap data structures, it is supported by many non-Windows and non-PC applications. - - - - - - - - - - - im - - - IM is a format used by LabEye and other applications based on the IFUNC image processing library. - IFUNC library reads and writes most uncompressed interchange versions of this format. - - 1.11 - - - - - - - - - - - pcd - - - PCD was developed by Kodak. A PCD file contains five different resolution (ranging from low to high) of a slide or film negative. Due to it PCD is often used by many photographers and graphics professionals for high-end printed applications. - 1.11 - Photo CD format, which is the highest resolution format for images on a CD. - - - - - - - - - - - pcx - - - 1.11 - PCX is an image file format that uses a simple form of run-length encoding. It is lossless. - - - - - - - - - - - - ppm - - - The PPM format is a lowest common denominator color image file format. - - 1.11 - - - - - - - - - - - psd - - - 1.11 - PSD (Photoshop Document) is a proprietary file that allows the user to work with the images’ individual layers even after the file has been saved. - - - - - - - - - - - xbm - - - The XBM format was replaced by XPM for X11 in 1989. - 1.11 - X BitMap is a plain text binary image format used by the X Window System used for storing cursor and icon bitmaps used in the X GUI. - - - - - - - - - - - xpm - - - 1.11 - Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type. - X PixMap (XPM) is an image file format used by the X Window System, it is intended primarily for creating icon pixmaps, and supports transparent pixels. - - - - - - - - - - - - rgb - - - 1.11 - RGB file format is the native raster graphics file format for Silicon Graphics workstations. - - - - - - - - - - - - pbm - - - 1.11 - The PBM format is a lowest common denominator monochrome file format. It serves as the common language of a large family of bitmap image conversion filters. - - - - - - - - - - - - pgm - - - It is designed to be extremely easy to learn and write programs for. - The PGM format is a lowest common denominator grayscale file format. - - 1.11 - - - - - - - - - - - png - - - 1.11 - PNG is a file format for image compression. - - It iis expected to replace the Graphics Interchange Format (GIF). - - - - - - - - - - - svg - - - The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999. - Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation. - 1.11 - - - - - - - - - - - rast - - - Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems - 1.11 - The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999. - - - - - - - - - - - Sequence quality report format (text) - - - - - - - - - Textual report format for sequence quality for reports from sequencing machines. - 1.11 - - - - - - - - - - qual - - - http://en.wikipedia.org/wiki/Phred_quality_score - 1.11 - Phred quality scores are defined as a property which is logarithmically related to the base-calling error probabilities. - FASTQ format subset for Phred sequencing quality score data only (no sequences). - - - - - - - - - - qualsolexa - - - Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected) - 1.11 - FASTQ format subset for Phred sequencing quality score data only (no sequences) for Solexa/Illumina 1.0 format. - - - - - - - - - - qualillumina - - - Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 "B", is used also at the end of reads as a Read Segment Quality Control Indicator. - FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8. - 1.11 - http://en.wikipedia.org/wiki/Phred_quality_score - - - - - - - - - - qualsolid - - For SOLiD data, the sequence is in color space, except the first position. The quality values are those of the Sanger format. - FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data. - 1.11 - http://en.wikipedia.org/wiki/Phred_quality_score - - - - - - - - - - qual454 - - http://en.wikipedia.org/wiki/Phred_quality_score - 1.11 - FASTQ format subset for Phred sequencing quality score data only (no sequences) from 454 sequencers. - - - - - - - - - - ENCODE peak format - - 1.11 - Human ENCODE peak format. - Format that covers both the broad peak format and narrow peak format from ENCODE. - - - - - - - - - - - - ENCODE narrow peak format - - 1.11 - Human ENCODE narrow peak format. - Format that covers both the broad peak format and narrow peak format from ENCODE. - - - - - - - - - - - - ENCODE broad peak format - - 1.11 - Human ENCODE broad peak format. - - - - - - - - - - - - bgzip - - - BAM files are compressed using a variant of GZIP (GNU ZIP), into a format called BGZF (Blocked GNU Zip Format). - Blocked GNU Zip format. - 1.11 - - - - - - - - - - - tabix - - - TAB-delimited genome position file index format. - 1.11 - - - - - - - - - - - - Graph format - - Data format for graph data. - 1.11 - - - - - - - - - - xgmml - - XML-based format used to store graph descriptions within Galaxy. - 1.11 - - - - - - - - - - - sif - - 1.11 - SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape. - - - - - - - - - - - xlsx - - - 1.11 - MS Excel spreadsheet format consisting of a set of XML documents stored in a ZIP-compressed file. - - - - - - - - - - SQLite - - https://www.sqlite.org/fileformat2.html - Data format used by the SQLite database. - 1.11 - - - - - - - - - - GeminiSQLite - - https://gemini.readthedocs.org/en/latest/content/quick_start.html - 1.11 - Data format used by the SQLite database conformant to the Gemini schema. - - - - - - - - - - Index format - - - - - - - - - Format of a data index of some type. - 1.11 - - - - - - - - - - snpeffdb - - An index of a genome database, indexed for use by the snpeff tool. - 1.11 - - - - - - - - - - Operation - - - http://www.onto-med.de/ontologies/gfo.owl#Perpetuant - Computational tool - A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state. - Function - http://purl.org/biotop/biotop.owl#Function - http://www.ifomis.org/bfo/1.1/snap#Function - http://en.wikipedia.org/wiki/Function_(mathematics) - Computational method - http://semanticscience.org/resource/SIO_000017 - http://www.ebi.ac.uk/swo/SWO_0000003 - Mathematical operation - sumo:Function - beta12orEarlier - Process - Computational operation - Computational subroutine - http://semanticscience.org/resource/SIO_000649 - http://www.ifomis.org/bfo/1.1/span#Process - http://www.ifomis.org/bfo/1.1/snap#Continuant - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method - Computational procedure - Mathematical function - Lambda abstraction - Function (programming) - http://www.onto-med.de/ontologies/gfo.owl#Process - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality - http://wsio.org/operation_001 - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process - http://www.ifomis.org/bfo/1.1/snap#Quality - http://www.onto-med.de/ontologies/gfo.owl#Function - http://en.wikipedia.org/wiki/Function_(computer_science) - http://en.wikipedia.org/wiki/Subroutine - - - - - Process - Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. - - - - - Computational tool provides one or more operations. - Computational tool - - - - - Function - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. - - - - - - - - - - Query and retrieval - - - - - - - - - - - - - - beta12orEarlier - Query - Retrieval - Search or query a data resource and retrieve entries and / or annotation. - Database retrieval - Search - - - - - - - - - - Data retrieval (database cross-reference) - - beta12orEarlier - Search database to retrieve all relevant references to a particular entity or entry. - true - beta13 - - - - - - - - - - Annotation - - - - - - - - - - - - - - Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. - beta12orEarlier - This is a broad concept and is used a placeholder for other, more specific concepts. - - - - - - - - - - Indexing - - - - - - - - Data indexing - beta12orEarlier - Generate an index of (typically a file of) biological data. - Database indexing - - - - - - - - - - Data index analysis - - Database index analysis - Analyse an index of biological data. - beta12orEarlier - true - 1.6 - - - - - - - - - - Annotation retrieval (sequence) - - true - beta12orEarlier - Retrieve basic information about a molecular sequence. - beta12orEarlier - - - - - - - - - - Sequence generation - - - beta12orEarlier - Generate a molecular sequence by some means. - - - - - - - - - - Sequence editing - - - Edit or change a molecular sequence, either randomly or specifically. - beta12orEarlier - - - - - - - - - - Sequence merging - - beta12orEarlier - Merge two or more (typically overlapping) molecular sequences. - Sequence splicing - - - - - - - - - - Sequence conversion - - - Convert a molecular sequence from one type to another. - beta12orEarlier - - - - - - - - - - Sequence complexity calculation - - - - - - - - - - - - - - beta12orEarlier - Calculate sequence complexity, for example to find low-complexity regions in sequences. - - - - - - - - - - Sequence ambiguity calculation - - - - - - - - - - - - - - Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes. - beta12orEarlier - - - - - - - - - - Sequence composition calculation - - - - - - - - - - - - - - - beta12orEarlier - Calculate character or word composition or frequency of a molecular sequence. - - - - - - - - - - Repeat sequence analysis - - - - - - - - Find and/or analyse repeat sequences in (typically nucleotide) sequences. - beta12orEarlier - Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. - - - - - - - - - - Sequence motif discovery - - - - - - - - - - - - - - Motifs and patterns might be conserved or over-represented (occur with improbable frequency). - beta12orEarlier - Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery). - Motif discovery - - - - - - - - - - Sequence signature recognition - - - - - - - - - - - - - - beta12orEarlier - Motif search - Sequence motif search - Protein secondary database search - Motif detection - Sequence motif recognition - Sequence signature detection - Sequence profile search - Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s). - Sequence motif detection - Motif recognition - - - - - - - - - - Sequence motif comparison - - - - - - - - - - - - - - beta12orEarlier - Find motifs shared by molecular sequences. - - - - - - - - - - Transcription regulatory sequence analysis - - beta12orEarlier - beta13 - Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. - For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. - true - - - - - - - - - - Conserved transcription regulatory sequence identification - - - For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes. - beta12orEarlier - Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites). - - - - - - - - - - Protein property calculation (from structure) - - - - - - - - - - - - - - - This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. - Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure. - beta12orEarlier - Protein structural property calculation - - - - - - - - - - Protein flexibility and motion analysis - - - beta12orEarlier - Analyse flexibility and motion in protein structure. - Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. - - - - - - - - - - Protein structural motif recognition - - - - - - - - - Identify or screen for 3D structural motifs in protein structure(s). - This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc. - beta12orEarlier - Protein structural feature identification - - - - - - - - - - Protein domain recognition - - - - - - - - - beta12orEarlier - Identify structural domains in a protein structure from first principles (for example calculations on structural compactness). - - - - - - - - - - Protein architecture analysis - - beta12orEarlier - Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s). - - - - - - - - - - Residue interaction calculation - - - - - - - - - - - - - - WHATIF: SymShellTenXML - WHATIF:ListContactsRelaxed - WHATIF: SymShellTwoXML - WHATIF:ListSideChainContactsRelaxed - beta12orEarlier - WHATIF:ListSideChainContactsNormal - WHATIF:ListContactsNormal - Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s). - WHATIF: SymShellFiveXML - WHATIF: SymShellOneXML - - - - - - - - - - Torsion angle calculation - - - - - - - - beta12orEarlier - Calculate, visualise or analyse phi/psi angles of a protein structure. - - - - - - - - - - Protein property calculation - - - - - - - - - - - - - - - - Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. - This includes methods to render and visualise the properties of a protein sequence. - beta12orEarlier - Protein property rendering - - - - - - - - - - Peptide immunogenicity prediction - - - - - - - - - - - - - - - beta12orEarlier - This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. - Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins. - - - - - - - - - - Sequence feature detection - - - - - - - - - - - - - - - Sequence feature prediction - Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. - Sequence feature recognition - beta12orEarlier - Motif database search - SO:0000110 - - - - - - - - - - Data retrieval (feature table) - - beta13 - Extract a sequence feature table from a sequence database entry. - true - beta12orEarlier - - - - - - - - - - Feature table query - - 1.6 - beta12orEarlier - true - Query the features (in a feature table) of molecular sequence(s). - - - - - - - - - - Sequence feature comparison - - - - - - - - - - - - - - - - - - - - - beta12orEarlier - Compare the feature tables of two or more molecular sequences. - Feature comparison - Feature table comparison - - - - - - - - - - Data retrieval (sequence alignment) - - beta12orEarlier - true - beta13 - Display basic information about a sequence alignment. - - - - - - - - - - Sequence alignment analysis - - - - - - - - Analyse a molecular sequence alignment. - beta12orEarlier - - - - - - - - - - Sequence alignment comparison - - - Compare (typically by aligning) two molecular sequence alignments. - beta12orEarlier - See also 'Sequence profile alignment'. - - - - - - - - - - Sequence alignment conversion - - - beta12orEarlier - Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence). - - - - - - - - - - Nucleic acid property processing - - beta12orEarlier - true - Process (read and / or write) physicochemical property data of nucleic acids. - beta13 - - - - - - - - - - Nucleic acid property calculation - - - - - - - - - beta12orEarlier - Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence. - - - - - - - - - - Splice transcript prediction - - - - - - - - beta12orEarlier - Predict splicing alternatives or transcript isoforms from analysis of sequence data. - - - - - - - - - - Frameshift detection - - - - - - - - - Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects. - Frameshift error detection - beta12orEarlier - Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. - - - - - - - - - - Vector sequence detection - - - beta12orEarlier - Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences. - - - - - - - - - - Protein secondary structure prediction - - - - - - - - - - Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. - Predict secondary structure of protein sequences. - Secondary structure prediction (protein) - beta12orEarlier - - - - - - - - - - Protein super-secondary structure prediction - - - - - - - - beta12orEarlier - Predict super-secondary structure of protein sequence(s). - Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. - - - - - - - - - - Transmembrane protein prediction - - - Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences. - beta12orEarlier - - - - - - - - - - Transmembrane protein analysis - - - - - - - - beta12orEarlier - Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions. - Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). - - - - - - - - - - Structure prediction - - - - - - - - - - - - - - - Predict tertiary structure of a molecular (biopolymer) sequence. - beta12orEarlier - - - - - - - - - - Residue interaction prediction - - - - - - - - - Methods usually involve multiple sequence alignment analysis. - Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences. - beta12orEarlier - - - - - - - - - - Protein interaction raw data analysis - - - - - - - - - - - - - - Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. - beta12orEarlier - - - - - - - - - - Protein-protein interaction prediction (from protein sequence) - - - beta12orEarlier - Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences. - - - - - - - - - - Protein-protein interaction prediction (from protein structure) - - - - beta12orEarlier - Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures. - - - - - - - - - - Protein interaction network analysis - - - - - - - - - - - - - - - beta12orEarlier - Analyse a network of protein interactions. - - - - - - - - - - Protein interaction network comparison - - - beta12orEarlier - Compare two or more networks of protein interactions. - - - - - - - - - - RNA secondary structure prediction - - - - - - - - - - - - - - - - Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc). - beta12orEarlier - Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). - - - - - - - - - - Nucleic acid folding prediction - - - - - - - - - - - - - - - - beta12orEarlier - Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data. - Nucleic acid folding modelling - Nucleic acid folding - - - - - - - - - - Data retrieval (restriction enzyme annotation) - - beta13 - Restriction enzyme information retrieval - true - Retrieve information on restriction enzymes or restriction enzyme sites. - beta12orEarlier - - - - - - - - - - Genetic marker identification - - true - beta12orEarlier - beta13 - Identify genetic markers in DNA sequences. - A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. - - - - - - - - - - Genetic mapping - - - - - - - - - beta12orEarlier - QTL mapping - This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). - Linkage mapping - Genetic map generation - Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. - Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances. - Genetic map construction - Functional mapping - - - - - - - - - - Linkage analysis - - - - - - - - - - - - - - beta12orEarlier - For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. - Analyse genetic linkage. - - - - - - - - - - Codon usage table generation - - - - - - - - - Calculate codon usage statistics and create a codon usage table. - beta12orEarlier - Codon usage table construction - - - - - - - - - - Codon usage table comparison - - - beta12orEarlier - Compare two or more codon usage tables. - - - - - - - - - - Codon usage analysis - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - beta12orEarlier - synon: Codon usage data analysis - Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences. - synon: Codon usage table analysis - - - - - - - - - - Base position variability plotting - - - - - - - - - - - - - - - Identify and plot third base position variability in a nucleotide sequence. - beta12orEarlier - - - - - - - - - - Sequence word comparison - - Find exact character or word matches between molecular sequences without full sequence alignment. - beta12orEarlier - - - - - - - - - - Sequence distance matrix generation - - - - - - - - - - - - - - - Sequence distance matrix construction - Phylogenetic distance matrix generation - beta12orEarlier - Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences. - - - - - - - - - - Sequence redundancy removal - - - - - - - - beta12orEarlier - Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria. - - - - - - - - - - Sequence clustering - - - - - - - - - - - - - - - - The clusters may be output or used internally for some other purpose. - Sequence cluster construction - beta12orEarlier - Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences. - Sequence cluster generation - - - - - - - - - - Sequence alignment - - - - - - - - - - Sequence alignment construction - beta12orEarlier - Align (identify equivalent sites within) molecular sequences. - Sequence alignment generation - Sequence alignment computation - - - - - - - - - - Hybrid sequence alignment construction - - Hybrid sequence alignment - true - beta13 - beta12orEarlier - Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA). - Hybrid sequence alignment generation - - - - - - - - - - Structure-based sequence alignment - - Structure-based sequence alignment - Sequence alignment generation (structure-based) - Structure-based sequence alignment construction - beta12orEarlier - Sequence alignment (structure-based) - Structure-based sequence alignment generation - Align molecular sequences using sequence and structural information. - - - - - - - - - - Structure alignment - - - - - - - - - - Align (superimpose) molecular tertiary structures. - Structure alignment generation - Structure alignment construction - beta12orEarlier - Multiple structure alignment construction - Multiple structure alignment generation - - - - - - - - - - Sequence profile generation - - - - - - - - - - - - - - - - - - - - - Sequence profile construction - beta12orEarlier - Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. - - - - - - - - - - 3D profile generation - - - - - - - - - - - - - - - - - - - - - Structural profile generation - Generate some type of structural (3D) profile or template from a structure or structure alignment. - Structural profile construction - beta12orEarlier - - - - - - - - - - Profile-to-profile alignment - - - - - - - - - - - - - - - - - - - - Sequence profile alignment - beta12orEarlier - See also 'Sequence alignment comparison'. - Sequence profile alignment construction - Align sequence profiles (representing sequence alignments). - Sequence profile alignment generation - - - - - - - - - - 3D profile-to-3D profile alignment - - - - - - - - - - - - - - - beta12orEarlier - 3D profile alignment (multiple) - 3D profile alignment - Multiple 3D profile alignment construction - Structural profile alignment construction (multiple) - Structural profile alignment - Structural profile alignment generation - Structural profile alignment construction - Align structural (3D) profiles or templates (representing structures or structure alignments). - - - - - - - - - - Sequence-to-profile alignment - - - - - - - - - - - - - - - - - - - - Sequence-profile alignment construction - Sequence-profile alignment generation - beta12orEarlier - Align molecular sequence(s) to sequence profile(s). - Sequence-profile alignment - A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. - - - - - - - - - - Sequence-to-3D-profile alignment - - - - - - - - - - - - - - - beta12orEarlier - Sequence-3D profile alignment construction - Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). - Sequence-3D profile alignment generation - Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Sequence-3D profile alignment - - - - - - - - - - Protein threading - - - - - - - - - - - - - - - beta12orEarlier - Align molecular sequence to structure in 3D space (threading). - Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Sequence-structure alignment - - - - - - - - - - Protein fold recognition - - - - - - - - - - - beta12orEarlier - Protein domain prediction - Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. - Recognize (predict and identify) known protein structural domains or folds in protein sequence(s). - Protein fold prediction - - - - - - - - - - Metadata retrieval - - - - - - - - Data retrieval (documentation) - Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described. - Data retrieval (metadata) - beta12orEarlier - This includes documentation, general information and other metadata on entities such as databases, database entries and tools. - - - - - - - - - - Literature search - - - - - - - - - - - - - - beta12orEarlier - Query the biomedical and informatics literature. - - - - - - - - - - Text mining - - - - - - - - - - - - - - - - - - - - Text data mining - beta12orEarlier - Process and analyse text (typically the biomedical and informatics literature) to extract information from it. - - - - - - - - - - Virtual PCR - - - - - - - - beta12orEarlier - Perform in-silico (virtual) PCR. - - - - - - - - - - PCR primer design - - - - - - - - - - - - - - - - - - - - PCR primer prediction - Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. - Design or predict oligonucleotide primers for PCR and DNA amplification etc. - beta12orEarlier - - - - - - - - - - Microarray probe design - - - - - - - - - - - - - - - - - - - - - - - - - - - Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. - beta12orEarlier - Microarray probe prediction - - - - - - - - - - Sequence assembly - - - - - - - - - - - - - - - beta12orEarlier - For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. - Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence. - - - - - - - - - - Microarray data standardization and normalization - - - - - - - - - - - - - - - beta12orEarlier - Standardize or normalize microarray data. - This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. - - - - - - - - - - Sequencing-based expression profile data processing - - Process (read and / or write) SAGE, MPSS or SBS experimental data. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - Gene expression profile clustering - - - - - - - - - beta12orEarlier - Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles. - - - - - - - - - - Gene expression profiling - - - - - - - - - Expression profiling - Gene expression profile construction - Functional profiling - Generate a gene expression profile or pattern, for example from microarray data. - beta12orEarlier - Gene expression profile generation - - - - - - - - - - Gene expression profile comparison - - - - - - - - - beta12orEarlier - Compare gene expression profiles or patterns. - - - - - - - - - - Functional profiling - - true - beta12orEarlier - Interpret (in functional terms) and annotate gene expression data. - beta12orEarlier - - - - - - - - - - EST and cDNA sequence analysis - - Analyse EST or cDNA sequences. - For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Structural genomics target selection - - beta12orEarlier - Identify and select targets for protein structural determination. - beta12orEarlier - Methods will typically navigate a graph of protein families of known structure. - true - - - - - - - - - - Protein secondary structure assignment - - - - - - - - - - - - - - beta12orEarlier - Assign secondary structure from protein coordinate or experimental data. - - - - - - - - - - Protein structure assignment - - - - - - - - - - - - - - - beta12orEarlier - Assign a protein tertiary structure (3D coordinates) from raw experimental data. - - - - - - - - - - Protein model validation - - - - - - - - - - - - - - - - - - - - - Evaluate the quality or correctness a protein three-dimensional model. - Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. - WHATIF: CorrectedPDBasXML - Protein structure validation - WHATIF: UseFileDB - The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. - beta12orEarlier - - - - - - - - - - Molecular model refinement - - - Protein model refinement - WHATIF: CorrectedPDBasXML - beta12orEarlier - Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc. - - - - - - - - - - Phylogenetic tree generation - - - - - - - - - - - - - - - Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. - Phylogenetic tree construction - Construct a phylogenetic tree. - beta12orEarlier - - - - - - - - - - Phylogenetic tree analysis - - - - - - - - - - - - - - beta12orEarlier - Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions. - - - - - - - - - - Phylogenetic tree comparison - - - beta12orEarlier - Compare two or more phylogenetic trees. - For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. - - - - - - - - - - Phylogenetic tree editing - - - - - - - - - - - - - - - Edit a phylogenetic tree. - beta12orEarlier - - - - - - - - - - Phylogenetic footprinting / shadowing - - - - - - - - A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. - beta12orEarlier - Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing). - - - - - - - - - - Protein folding simulation - - beta12orEarlier - Simulate the folding of a protein. - - - - - - - - - - Protein folding pathway prediction - - - Predict the folding pathway(s) or non-native structural intermediates of a protein. - beta12orEarlier - - - - - - - - - - Protein SNP mapping - - - - - - - - - beta12orEarlier - Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). - - - - - - - - - - Protein modelling (mutation) - - - - - - - - - - - - - - - Methods might predict silent or pathological mutations. - Protein mutation modelling - Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function. - beta12orEarlier - - - - - - - - - - Immunogen design - - true - Design molecules that elicit an immune response (immunogens). - beta12orEarlier - beta12orEarlier - - - - - - - - - - Zinc finger prediction - - - - - - - - - - - - - - Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). - beta12orEarlier - - - - - - - - - - Enzyme kinetics calculation - - - - - - - - - - - - - - beta12orEarlier - Calculate Km, Vmax and derived data for an enzyme reaction. - - - - - - - - - - Formatting - - beta12orEarlier - Reformat a file of data (or equivalent entity in memory). - Format conversion - File formatting - Reformatting - File reformatting - File format conversion - - - - - - - - - - Format validation - - - Test and validate the format and content of a data file. - File format validation - beta12orEarlier - - - - - - - - - - Visualisation - - - - - - - - - - - - - - - - - - - - beta12orEarlier - Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. - Rendering - - - - - - - - - - Sequence database search - - - - - - - - - - - - - - - Search a sequence database by sequence comparison and retrieve similar sequences. - -sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. - beta12orEarlier - This excludes direct retrieval methods (e.g. the dbfetch program). - - - - - - - - - - Structure database search - - - - - - - - beta12orEarlier - Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data. - - - - - - - - - - Protein secondary database search - - 1.8 - beta12orEarlier - true - Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group. - - - - - - - - - - Motif database search - - beta12orEarlier - Screen a sequence against a motif or pattern database. - true - 1.8 - - - - - - - - - - Sequence profile database search - - true - beta12orEarlier - Search a database of sequence profiles with a query sequence. - 1.4 - - - - - - - - - - Transmembrane protein database search - - true - beta12orEarlier - Search a database of transmembrane proteins, for example for sequence or structural similarities. - beta12orEarlier - - - - - - - - - - Sequence retrieval (by code) - - Query a database and retrieve sequences with a given entry code or accession number. - true - 1.6 - beta12orEarlier - - - - - - - - - - Sequence retrieval (by keyword) - - true - Query a database and retrieve sequences containing a given keyword. - beta12orEarlier - 1.6 - - - - - - - - - - Sequence similarity search - - - Structure database search (by sequence) - Sequence database search (by sequence) - beta12orEarlier - Search a sequence database and retrieve sequences that are similar to a query sequence. - - - - - - - - - - Sequence database search (by motif or pattern) - - 1.8 - Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. - beta12orEarlier - true - - - - - - - - - - Sequence database search (by amino acid composition) - - true - Search a sequence database and retrieve sequences of a given amino acid composition. - 1.6 - beta12orEarlier - - - - - - - - - - Sequence database search (by property) - - Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property. - beta12orEarlier - - - - - - - - - - Sequence database search (by sequence using word-based methods) - - beta12orEarlier - Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. - 1.6 - true - Sequence similarity search (word-based methods) - Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method. - - - - - - - - - - Sequence database search (by sequence using profile-based methods) - - true - Sequence similarity search (profile-based methods) - Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query. - beta12orEarlier - This includes tools based on PSI-BLAST. - 1.6 - - - - - - - - - - Sequence database search (by sequence using local alignment-based methods) - - Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method. - 1.6 - beta12orEarlier - true - Sequence similarity search (local alignment-based methods) - This includes tools based on the Smith-Waterman algorithm or FASTA. - - - - - - - - - - Sequence database search (by sequence using global alignment-based methods) - - This includes tools based on the Needleman and Wunsch algorithm. - Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method. - 1.6 - Sequence similarity search (global alignment-based methods) - beta12orEarlier - true - - - - - - - - - - Sequence database search (by sequence for primer sequences) - - true - beta12orEarlier - Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences. - 1.6 - STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. - Sequence similarity search (primer sequences) - - - - - - - - - - Sequence database search (by molecular weight) - - Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry. - 1.6 - Protein fingerprinting - true - beta12orEarlier - Peptide mass fingerprinting - - - - - - - - - - Sequence database search (by isoelectric point) - - 1.6 - beta12orEarlier - Search sequence(s) or a sequence database for sequences of a given isoelectric point. - true - - - - - - - - - - Structure retrieval (by code) - - Query a tertiary structure database and retrieve entries with a given entry code or accession number. - 1.6 - beta12orEarlier - true - - - - - - - - - - Structure retrieval (by keyword) - - true - 1.6 - Query a tertiary structure database and retrieve entries containing a given keyword. - beta12orEarlier - - - - - - - - - - Structure database search (by sequence) - - beta12orEarlier - true - Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. - 1.8 - - - - - - - - - - Structural similarity search - - - - - - - - - beta12orEarlier - Search a database of molecular structure and retrieve structures that are similar to a query structure. - Structure database search (by structure) - Structure retrieval by structure - - - - - - - - - - Sequence annotation - - - - - - - - - - - - - - beta12orEarlier - Annotate a molecular sequence record with terms from a controlled vocabulary. - - - - - - - - - - Genome annotation - - beta12orEarlier - Annotate a genome sequence with terms from a controlled vocabulary. - - - - - - - - - - Nucleic acid sequence reverse and complement - - beta12orEarlier - Generate the reverse and / or complement of a nucleotide sequence. - - - - - - - - - - Random sequence generation - - Generate a random sequence, for example, with a specific character composition. - beta12orEarlier - - - - - - - - - - Nucleic acid restriction digest - - - - - - - - - beta12orEarlier - Generate digest fragments for a nucleotide sequence containing restriction sites. - - - - - - - - - - Protein sequence cleavage - - - - - - - - - - - - - - - beta12orEarlier - Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses. - - - - - - - - - - Sequence mutation and randomization - - beta12orEarlier - Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition. - - - - - - - - - - Sequence masking - - Mask characters in a molecular sequence (replacing those characters with a mask character). - For example, SNPs or repeats in a DNA sequence might be masked. - beta12orEarlier - - - - - - - - - - Sequence cutting - - Cut (remove) characters or a region from a molecular sequence. - beta12orEarlier - - - - - - - - - - Restriction site creation - - Create (or remove) restriction sites in sequences, for example using silent mutations. - beta12orEarlier - - - - - - - - - - DNA translation - - - - - - - - beta12orEarlier - Translate a DNA sequence into protein. - - - - - - - - - - DNA transcription - - - - - - - - beta12orEarlier - Transcribe a nucleotide sequence into mRNA sequence(s). - - - - - - - - - - Sequence composition calculation (nucleic acid) - - true - Calculate base frequency or word composition of a nucleotide sequence. - 1.8 - beta12orEarlier - - - - - - - - - - Sequence composition calculation (protein) - - 1.8 - Calculate amino acid frequency or word composition of a protein sequence. - beta12orEarlier - true - - - - - - - - - - Repeat sequence detection - - - beta12orEarlier - Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. - - - - - - - - - - Repeat sequence organisation analysis - - - beta12orEarlier - Analyse repeat sequence organization such as periodicity. - - - - - - - - - - Protein hydropathy calculation (from structure) - - - - Analyse the hydrophobic, hydrophilic or charge properties of a protein structure. - beta12orEarlier - - - - - - - - - - Protein solvent accessibility calculation - - - - - - - - - - - - - - beta12orEarlier - Calculate solvent accessible or buried surface areas in protein structures. - - - - - - - - - - Protein hydropathy cluster calculation - - - beta12orEarlier - Identify clusters of hydrophobic or charged residues in a protein structure. - - - - - - - - - - Protein dipole moment calculation - - - - - - - - beta12orEarlier - Calculate whether a protein structure has an unusually large net charge (dipole moment). - - - - - - - - - - Protein surface and interior calculation - - - - - - - - beta12orEarlier - Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc. - - - - - - - - - - Protein binding site prediction (from structure) - - - Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures. - beta12orEarlier - Ligand-binding and active site prediction (from structure) - Binding site prediction (from structure) - - - - - - - - - - Protein-nucleic acid binding site analysis - - - - - - - - Analyse RNA or DNA-binding sites in protein structure. - beta12orEarlier - - - - - - - - - - Protein peeling - - beta12orEarlier - Decompose a structure into compact or globular fragments (protein peeling). - - - - - - - - - - Protein distance matrix calculation - - - - - - - - beta12orEarlier - Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure. - - - - - - - - - - Protein contact map calculation - - - - - - - - beta12orEarlier - Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure. - - - - - - - - - - Protein residue cluster calculation - - - - - - - - Cluster of contacting residues might be key structural residues. - Calculate clusters of contacting residues in protein structures. - beta12orEarlier - - - - - - - - - - Hydrogen bond calculation - - - - - - - - WHATIF:ShowHydrogenBonds - WHATIF:HasHydrogenBonds - The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. - beta12orEarlier - WHATIF:ShowHydrogenBondsM - Identify potential hydrogen bonds between amino acids and other groups. - - - - - - - - - - Residue non-canonical interaction detection - - - beta12orEarlier - Calculate non-canonical atomic interactions in protein structures. - - - - - - - - - - Ramachandran plot calculation - - - - - - - - Calculate a Ramachandran plot of a protein structure. - beta12orEarlier - - - - - - - - - - Ramachandran plot validation - - - - - - - - - - - - - - beta12orEarlier - Validate a Ramachandran plot of a protein structure. - - - - - - - - - - Protein molecular weight calculation - - - - - - - - - - - - - - Calculate the molecular weight of a protein sequence or fragments. - beta12orEarlier - - - - - - - - - - Protein extinction coefficient calculation - - - - - - - - beta12orEarlier - Predict extinction coefficients or optical density of a protein sequence. - - - - - - - - - - Protein pH-dependent property calculation - - - - - - - - - - - - - - Calculate pH-dependent properties from pKa calculations of a protein sequence. - beta12orEarlier - - - - - - - - - - Protein hydropathy calculation (from sequence) - - - Hydropathy calculation on a protein sequence. - beta12orEarlier - - - - - - - - - - Protein titration curve plotting - - - - - - - - - beta12orEarlier - Plot a protein titration curve. - - - - - - - - - - Protein isoelectric point calculation - - - - - - - - beta12orEarlier - Calculate isoelectric point of a protein sequence. - - - - - - - - - - Protein hydrogen exchange rate calculation - - - - - - - - Estimate hydrogen exchange rate of a protein sequence. - beta12orEarlier - - - - - - - - - - Protein hydrophobic region calculation - - Calculate hydrophobic or hydrophilic / charged regions of a protein sequence. - beta12orEarlier - - - - - - - - - - Protein aliphatic index calculation - - - - - - - - beta12orEarlier - Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein. - - - - - - - - - - Protein hydrophobic moment plotting - - - - - - - - - beta12orEarlier - Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. - Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity. - - - - - - - - - - Protein globularity prediction - - - - - - - - Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc. - beta12orEarlier - - - - - - - - - - Protein solubility prediction - - - - - - - - Predict the solubility or atomic solvation energy of a protein sequence. - beta12orEarlier - - - - - - - - - - Protein crystallizability prediction - - - - - - - - beta12orEarlier - Predict crystallizability of a protein sequence. - - - - - - - - - - Protein signal peptide detection (eukaryotes) - - beta12orEarlier - Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins. - - - - - - - - - - Protein signal peptide detection (bacteria) - - Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins. - beta12orEarlier - - - - - - - - - - MHC peptide immunogenicity prediction - - Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc. - beta12orEarlier - - - - - - - - - - Protein feature prediction (from sequence) - - Methods typically involve scanning for known motifs, patterns and regular expressions. - beta12orEarlier - true - Sequence feature detection (protein) - 1.6 - Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure. - - - - - - - - - - Nucleic acid feature detection - - - - - - - - - - - - - - - Sequence feature detection (nucleic acid) - Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions. - Methods typically involve scanning for known motifs, patterns and regular expressions. - beta12orEarlier - Nucleic acid feature recognition - Nucleic acid feature prediction - - - - - - - - - - Epitope mapping - - - - - - - - - beta12orEarlier - Predict antigenic determinant sites (epitopes) in protein sequences. - Epitope mapping is commonly done during vaccine design. - - - - - - - - - - Protein post-translation modification site prediction - - - - - - - - Predict post-translation modification sites in protein sequences. - beta12orEarlier - Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. - - - - - - - - - - Protein signal peptide detection - - - - - - - - - beta12orEarlier - Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. - Detect or predict signal peptides and signal peptide cleavage sites in protein sequences. - - - - - - - - - - Protein binding site prediction (from sequence) - - - Binding site prediction (from sequence) - Predict catalytic residues, active sites or other ligand-binding sites in protein sequences. - Ligand-binding and active site prediction (from sequence) - Protein binding site detection - beta12orEarlier - - - - - - - - - - Protein-nucleic acid binding prediction - - beta12orEarlier - Predict RNA and DNA-binding binding sites in protein sequences. - - - - - - - - - - Protein folding site prediction - - - Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization. - beta12orEarlier - - - - - - - - - - Protein cleavage site prediction - - - - - - - - beta12orEarlier - Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. - - - - - - - - - - Epitope mapping (MHC Class I) - - 1.8 - true - beta12orEarlier - Predict epitopes that bind to MHC class I molecules. - - - - - - - - - - Epitope mapping (MHC Class II) - - Predict epitopes that bind to MHC class II molecules. - 1.8 - true - beta12orEarlier - - - - - - - - - - - Whole gene prediction - - beta12orEarlier - Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc. - - - - - - - - - - Gene component prediction - - Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. - beta12orEarlier - Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences. - - - - - - - - - - Transposon prediction - - beta12orEarlier - Detect or predict transposons, retrotransposons / retrotransposition signatures etc. - - - - - - - - - - PolyA signal detection - - Detect polyA signals in nucleotide sequences. - beta12orEarlier - - - - - - - - - - Quadruplex formation site detection - - - - - - - - - - - - - - beta12orEarlier - Quadruplex structure prediction - Detect quadruplex-forming motifs in nucleotide sequences. - Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. - - - - - - - - - - CpG island and isochore detection - - - - - - - - An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence. - beta12orEarlier - Find CpG rich regions in a nucleotide sequence or isochores in genome sequences. - CpG island and isochores rendering - CpG island and isochores detection - - - - - - - - - - Restriction site recognition - - - - - - - - beta12orEarlier - Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map. - - - - - - - - - - Nucleosome formation or exclusion sequence prediction - - beta12orEarlier - Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA. - - - - - - - - - - Splice site prediction - - - - - - - - beta12orEarlier - Identify, predict or analyse splice sites in nucleotide sequences. - Methods might require a pre-mRNA or genomic DNA sequence. - - - - - - - - - - Integrated gene prediction - - Predict whole gene structure using a combination of multiple methods to achieve better predictions. - beta12orEarlier - - - - - - - - - - Operon prediction - - Find operons (operators, promoters and genes) in bacteria genes. - beta12orEarlier - - - - - - - - - - Coding region prediction - - Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences. - ORF prediction - ORF finding - beta12orEarlier - - - - - - - - - - Selenocysteine insertion sequence (SECIS) prediction - - - - - - - - Predict selenocysteine insertion sequence (SECIS) in a DNA sequence. - SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. - beta12orEarlier - - - - - - - - - - Regulatory element prediction - - - - - - - - Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences. - Translational regulatory element prediction - Transcription regulatory element prediction - This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. - beta12orEarlier - - - - - - - - - - Translation initiation site prediction - - - - - - - - Predict translation initiation sites, possibly by searching a database of sites. - beta12orEarlier - - - - - - - - - - Promoter prediction - - Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences. - Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. - beta12orEarlier - - - - - - - - - - Transcription regulatory element prediction (DNA-cis) - - beta12orEarlier - Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. - Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences. - - - - - - - - - - Transcription regulatory element prediction (RNA-cis) - - Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. - Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences. - beta12orEarlier - - - - - - - - - - Transcription regulatory element prediction (trans) - - - - - - - - beta12orEarlier - Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. - Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets. - Functional RNA identification - - - - - - - - - - Matrix/scaffold attachment site prediction - - MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. - Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences. - beta12orEarlier - - - - - - - - - - Transcription factor binding site prediction - - beta12orEarlier - Identify or predict transcription factor binding sites in DNA sequences. - - - - - - - - - - Exonic splicing enhancer prediction - - - - - - - - An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA. - Identify or predict exonic splicing enhancers (ESE) in exons. - beta12orEarlier - - - - - - - - - - Sequence alignment validation - - - Evaluation might be purely sequence-based or use structural information. - Sequence alignment quality evaluation - Evaluate molecular sequence alignment accuracy. - beta12orEarlier - - - - - - - - - - Sequence alignment analysis (conservation) - - beta12orEarlier - Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence. - Residue conservation analysis - Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. - - - - - - - - - - Sequence alignment analysis (site correlation) - - - Analyse correlations between sites in a molecular sequence alignment. - This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. - beta12orEarlier - - - - - - - - - - Chimeric sequence detection - - beta12orEarlier - A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. - Detects chimeric sequences (chimeras) from a sequence alignment. - Sequence alignment analysis (chimeric sequence detection) - - - - - - - - - - Recombination detection - - Sequence alignment analysis (recombination detection) - beta12orEarlier - Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment. - Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. - - - - - - - - - - Indel detection - - beta12orEarlier - Sequence alignment analysis (indel detection) - Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. - Identify insertion, deletion and duplication events from a sequence alignment. - - - - - - - - - - Nucleosome formation potential prediction - - true - beta12orEarlier - Predict nucleosome formation potential of DNA sequences. - beta12orEarlier - - - - - - - - - - Nucleic acid thermodynamic property calculation - - - - - - - - Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy. - beta12orEarlier - - - - - - - - - - Nucleic acid melting profile plotting - - - - - - - - - Calculate and plot a DNA or DNA/RNA melting profile. - A melting profile is used to visualise and analyse partly melted DNA conformations. - beta12orEarlier - - - - - - - - - - Nucleic acid stitch profile plotting - - - - - - - - A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. - beta12orEarlier - Calculate and plot a DNA or DNA/RNA stitch profile. - - - - - - - - - - Nucleic acid melting curve plotting - - - - - - - - Calculate and plot a DNA or DNA/RNA melting curve. - beta12orEarlier - - - - - - - - - - Nucleic acid probability profile plotting - - - - - - - - beta12orEarlier - Calculate and plot a DNA or DNA/RNA probability profile. - - - - - - - - - - Nucleic acid temperature profile plotting - - - - - - - - Calculate and plot a DNA or DNA/RNA temperature profile. - beta12orEarlier - - - - - - - - - - Nucleic acid curvature calculation - - - - - - - - Calculate curvature and flexibility / stiffness of a nucleotide sequence. - beta12orEarlier - This includes properties such as. - - - - - - - - - - microRNA detection - - Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence. - beta12orEarlier - - - - - - - - - - tRNA gene prediction - - - - - - - - Identify or predict tRNA genes in genomic sequences (tRNA). - beta12orEarlier - - - - - - - - - - siRNA binding specificity prediction - - - - - - - - beta12orEarlier - Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences. - - - - - - - - - - Protein secondary structure prediction (integrated) - - Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions. - beta12orEarlier - - - - - - - - - - Protein secondary structure prediction (helices) - - beta12orEarlier - Predict helical secondary structure of protein sequences. - - - - - - - - - - Protein secondary structure prediction (turns) - - Predict turn structure (for example beta hairpin turns) of protein sequences. - beta12orEarlier - - - - - - - - - - Protein secondary structure prediction (coils) - - beta12orEarlier - Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences. - - - - - - - - - - Protein secondary structure prediction (disulfide bonds) - - beta12orEarlier - Predict cysteine bonding state and disulfide bond partners in protein sequences. - - - - - - - - - - GPCR prediction - - - beta12orEarlier - G protein-coupled receptor (GPCR) prediction - Predict G protein-coupled receptors (GPCR). - - - - - - - - - - GPCR analysis - - - - - - - - Analyse G-protein coupled receptor proteins (GPCRs). - beta12orEarlier - G protein-coupled receptor (GPCR) analysis - - - - - - - - - - Protein structure prediction - - - - - - - - - - - - - - - - - beta12orEarlier - Predict tertiary structure (backbone and side-chain conformation) of protein sequences. - - - - - - - - - - Nucleic acid structure prediction - - - - - - - - - - - - - - - - beta12orEarlier - Methods might identify thermodynamically stable or evolutionarily conserved structures. - Predict tertiary structure of DNA or RNA. - - - - - - - - - - Ab initio structure prediction - - Predict tertiary structure of protein sequence(s) without homologs of known structure. - de novo structure prediction - beta12orEarlier - - - - - - - - - - Protein modelling - - - - - - - - - - Comparative modelling - beta12orEarlier - Build a three-dimensional protein model based on known (for example homologs) structures. - The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. - Homology modelling - Homology structure modelling - Protein structure comparative modelling - - - - - - - - - - Molecular docking - - - - - - - - - - - - - - - - - - - - - Model the structure of a protein in complex with a small molecule or another macromolecule. - beta12orEarlier - This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. - Docking simulation - Protein docking - - - - - - - - - - Protein modelling (backbone) - - Model protein backbone conformation. - Methods might require a preliminary C(alpha) trace. - beta12orEarlier - - - - - - - - - - Protein modelling (side chains) - - beta12orEarlier - Methods might use a residue rotamer library. - Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc. - - - - - - - - - - Protein modelling (loops) - - beta12orEarlier - Model loop conformation in protein structures. - - - - - - - - - - Protein-ligand docking - - - - - - - - - - - - - - beta12orEarlier - Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. - Ligand-binding simulation - Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques. - Virtual ligand screening - - - - - - - - - - Structured RNA prediction and optimisation - - - - - - - - - - - - - - Nucleic acid folding family identification - RNA inverse folding - beta12orEarlier - Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection. - - - - - - - - - - SNP detection - - - - Find single nucleotide polymorphisms (SNPs) between sequences. - Single nucleotide polymorphism detection - beta12orEarlier - This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. - - - - - - - - - - Radiation Hybrid Mapping - - - - - - - - Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers. - beta12orEarlier - - - - - - - - - - Functional mapping - - beta12orEarlier - true - This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). - Map the genetic architecture of dynamic complex traits. - beta12orEarlier - - - - - - - - - - Haplotype mapping - - - - - - - - - Haplotype map generation - Haplotype inference - Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. - beta12orEarlier - Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). - Haplotype reconstruction - - - - - - - - - - Linkage disequilibrium calculation - - - - - - - - beta12orEarlier - Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes. - Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). - - - - - - - - - - Genetic code prediction - - - - - - - - - beta12orEarlier - Predict genetic code from analysis of codon usage data. - - - - - - - - - - Dotplot plotting - - - - - - - - - - beta12orEarlier - Draw a dotplot of sequence similarities identified from word-matching or character comparison. - - - - - - - - - - Pairwise sequence alignment - - - - - - - - Pairwise sequence alignment generation - Pairwise sequence alignment - Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Align exactly two molecular sequences. - Pairwise sequence alignment construction - beta12orEarlier - - - - - - - - - - Multiple sequence alignment - - Multiple sequence alignment construction - Align two or more molecular sequences. - This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. - Multiple sequence alignment - beta12orEarlier - Multiple sequence alignment generation - - - - - - - - - - Pairwise sequence alignment generation (local) - - beta12orEarlier - Local pairwise sequence alignment construction - Locally align exactly two molecular sequences. - Pairwise sequence alignment (local) - true - Local alignment methods identify regions of local similarity. - 1.6 - Pairwise sequence alignment construction (local) - - - - - - - - - - - Pairwise sequence alignment generation (global) - - Pairwise sequence alignment construction (global) - Global pairwise sequence alignment construction - 1.6 - true - Globally align exactly two molecular sequences. - beta12orEarlier - Global alignment methods identify similarity across the entire length of the sequences. - Pairwise sequence alignment (global) - - - - - - - - - - - Local sequence alignment - - Multiple sequence alignment (local) - Local multiple sequence alignment construction - beta12orEarlier - Local alignment methods identify regions of local similarity. - Multiple sequence alignment construction (local) - Sequence alignment generation (local) - Sequence alignment (local) - Locally align two or more molecular sequences. - - - - - - - - - - Global sequence alignment - - Global multiple sequence alignment construction - Multiple sequence alignment (global) - beta12orEarlier - Sequence alignment (global) - Multiple sequence alignment construction (global) - Globally align two or more molecular sequences. - Sequence alignment generation (global) - Global alignment methods identify similarity across the entire length of the sequences. - - - - - - - - - - Constrained sequence alignment - - beta12orEarlier - Align two or more molecular sequences with user-defined constraints. - Multiple sequence alignment construction (constrained) - Sequence alignment generation (constrained) - Multiple sequence alignment (constrained) - Sequence alignment (constrained) - Constrained multiple sequence alignment construction - - - - - - - - - - Consensus-based sequence alignment - - Consensus multiple sequence alignment construction - Sequence alignment (consensus) - beta12orEarlier - Align two or more molecular sequences using multiple methods to achieve higher quality. - Sequence alignment generation (consensus) - Multiple sequence alignment construction (consensus) - Multiple sequence alignment (consensus) - - - - - - - - - - Tree-based sequence alignment - - - - - - - - Sequence alignment generation (phylogenetic tree-based) - This is supposed to give a more biologically meaningful alignment than standard alignments. - beta12orEarlier - Phylogenetic tree-based multiple sequence alignment construction - Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. - Sequence alignment (phylogenetic tree-based) - Multiple sequence alignment construction (phylogenetic tree-based) - Multiple sequence alignment (phylogenetic tree-based) - - - - - - - - - - Secondary structure alignment generation - - beta12orEarlier - 1.6 - Secondary structure alignment construction - Secondary structure alignment - true - Align molecular secondary structure (represented as a 1D string). - - - - - - - - - - Protein secondary structure alignment generation - - - - - - - - - Protein secondary structure alignment construction - Align protein secondary structures. - beta12orEarlier - Secondary structure alignment (protein) - Protein secondary structure alignment - - - - - - - - - - RNA secondary structure alignment - - - - - - - - - - - - - - - RNA secondary structure alignment generation - RNA secondary structure alignment - Align RNA secondary structures. - RNA secondary structure alignment construction - Secondary structure alignment (RNA) - beta12orEarlier - - - - - - - - - - Pairwise structure alignment - - beta12orEarlier - Pairwise structure alignment generation - Pairwise structure alignment construction - Align (superimpose) exactly two molecular tertiary structures. - - - - - - - - - - Multiple structure alignment construction - - Align (superimpose) two or more molecular tertiary structures. - This includes methods that use an existing alignment. - 1.6 - true - Multiple structure alignment - beta12orEarlier - - - - - - - - - - Structure alignment (protein) - - beta13 - true - beta12orEarlier - Align protein tertiary structures. - - - - - - - - - - Structure alignment (RNA) - - beta13 - true - Align RNA tertiary structures. - beta12orEarlier - - - - - - - - - - Pairwise structure alignment generation (local) - - Locally align (superimpose) exactly two molecular tertiary structures. - Pairwise structure alignment (local) - Local alignment methods identify regions of local similarity, common substructures etc. - Pairwise structure alignment construction (local) - 1.6 - true - Local pairwise structure alignment construction - beta12orEarlier - - - - - - - - - - - Pairwise structure alignment generation (global) - - Global pairwise structure alignment construction - Global alignment methods identify similarity across the entire structures. - true - beta12orEarlier - 1.6 - Pairwise structure alignment construction (global) - Globally align (superimpose) exactly two molecular tertiary structures. - Pairwise structure alignment (global) - - - - - - - - - - - Local structure alignment - - Local multiple structure alignment construction - Local alignment methods identify regions of local similarity, common substructures etc. - Structure alignment construction (local) - beta12orEarlier - Locally align (superimpose) two or more molecular tertiary structures. - Multiple structure alignment construction (local) - Multiple structure alignment (local) - Structure alignment generation (local) - - - - - - - - - - Global structure alignment - - Structure alignment construction (global) - Multiple structure alignment (global) - Structure alignment generation (global) - Multiple structure alignment construction (global) - beta12orEarlier - Global alignment methods identify similarity across the entire structures. - Global multiple structure alignment construction - Globally align (superimpose) two or more molecular tertiary structures. - - - - - - - - - - Profile-to-profile alignment (pairwise) - - Sequence alignment generation (pairwise profile) - Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Pairwise sequence profile alignment construction - Sequence profile alignment construction (pairwise) - Sequence profile alignment (pairwise) - beta12orEarlier - Align exactly two molecular profiles. - Sequence profile alignment generation (pairwise) - - - - - - - - - - Sequence alignment generation (multiple profile) - - Align two or more molecular profiles. - 1.6 - true - Sequence profile alignment generation (multiple) - beta12orEarlier - Sequence profile alignment (multiple) - Sequence profile alignment construction (multiple) - Multiple sequence profile alignment construction - - - - - - - - - - 3D profile-to-3D profile alignment (pairwise) - - Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Pairwise structural (3D) profile alignment construction - Structural (3D) profile alignment (pairwise) - Structural profile alignment construction (pairwise) - Align exactly two molecular Structural (3D) profiles. - beta12orEarlier - Structural profile alignment generation (pairwise) - - - - - - - - - - Structural profile alignment generation (multiple) - - true - Structural profile alignment construction (multiple) - Align two or more molecular 3D profiles. - Multiple structural (3D) profile alignment construction - beta12orEarlier - Structural (3D) profile alignment (multiple) - 1.6 - - - - - - - - - - Data retrieval (tool metadata) - - Data retrieval (tool annotation) - 1.6 - Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function. - beta12orEarlier - true - Tool information retrieval - - - - - - - - - - Data retrieval (database metadata) - - beta12orEarlier - true - Data retrieval (database annotation) - Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword. - Database information retrieval - 1.6 - - - - - - - - - - PCR primer design (for large scale sequencing) - - - - - - - - Predict primers for large scale sequencing. - beta12orEarlier - - - - - - - - - - PCR primer design (for genotyping polymorphisms) - - beta12orEarlier - Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs). - - - - - - - - - - PCR primer design (for gene transcription profiling) - - - - - - - - Predict primers for gene transcription profiling. - beta12orEarlier - - - - - - - - - - PCR primer design (for conserved primers) - - Predict primers that are conserved across multiple genomes or species. - beta12orEarlier - - - - - - - - - - PCR primer design (based on gene structure) - - - - - - - - Predict primers based on gene structure, promoters, exon-exon junctions etc. - beta12orEarlier - - - - - - - - - - PCR primer design (for methylation PCRs) - - beta12orEarlier - Predict primers for methylation PCRs. - - - - - - - - - - Sequence assembly (mapping assembly) - - Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome. - beta12orEarlier - The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. - - - - - - - - - - Sequence assembly (de-novo assembly) - - Sequence assembly by combining fragments without the aid of a reference sequence or genome. - De-novo assemblers are much slower and more memory intensive than mapping assemblers. - beta12orEarlier - - - - - - - - - - Sequence assembly (genome assembly) - - Sequence assembly capable on a very large scale such as assembly of whole genomes. - beta12orEarlier - - - - - - - - - - Sequence assembly (EST assembly) - - beta12orEarlier - Sequence assembly for EST sequences (transcribed mRNA). - Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. - - - - - - - - - - Tag mapping - - - - - - - - - Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. - Tag to gene assignment - Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts. - beta12orEarlier - - - - - - - - - - SAGE data processing - - beta12orEarlier - Serial analysis of gene expression data processing - beta12orEarlier - Process (read and / or write) serial analysis of gene expression (SAGE) data. - true - - - - - - - - - - MPSS data processing - - beta12orEarlier - Process (read and / or write) massively parallel signature sequencing (MPSS) data. - true - Massively parallel signature sequencing data processing - beta12orEarlier - - - - - - - - - - SBS data processing - - beta12orEarlier - Sequencing by synthesis data processing - beta12orEarlier - Process (read and / or write) sequencing by synthesis (SBS) data. - true - - - - - - - - - - Heat map generation - - - - - - - - - beta12orEarlier - The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. - Heat map construction - Generate a heat map of gene expression from microarray data. - - - - - - - - - - Gene expression profile analysis - - true - Functional profiling - beta12orEarlier - Analyse one or more gene expression profiles, typically to interpret them in functional terms. - 1.6 - - - - - - - - - - Gene expression profile pathway mapping - - - - - - - - - - beta12orEarlier - Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway. - - - - - - - - - - Protein secondary structure assignment (from coordinate data) - - - beta12orEarlier - Assign secondary structure from protein coordinate data. - - - - - - - - - - Protein secondary structure assignment (from CD data) - - - - - - - - Assign secondary structure from circular dichroism (CD) spectroscopic data. - beta12orEarlier - - - - - - - - - - Protein structure assignment (from X-ray crystallographic data) - - true - 1.7 - Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data. - beta12orEarlier - - - - - - - - - - Protein structure assignment (from NMR data) - - beta12orEarlier - Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. - true - 1.7 - - - - - - - - - - Phylogenetic tree generation (data centric) - - Phylogenetic tree construction (data centric) - beta12orEarlier - Construct a phylogenetic tree from a specific type of data. - - - - - - - - - - Phylogenetic tree generation (method centric) - - Phylogenetic tree construction (method centric) - Construct a phylogenetic tree using a specific method. - beta12orEarlier - - - - - - - - - - Phylogenetic tree generation (from molecular sequences) - - - Phylogenetic tree construction from molecular sequences. - beta12orEarlier - Phylogenetic tree construction (from molecular sequences) - Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. - - - - - - - - - - Phylogenetic tree generation (from continuous quantitative characters) - - - - - - - - Phylogenetic tree construction (from continuous quantitative characters) - beta12orEarlier - Phylogenetic tree construction from continuous quantitative character data. - - - - - - - - - - Phylogenetic tree generation (from gene frequencies) - - - - - - - - - - - - - - Phylogenetic tree construction (from gene frequencies) - Phylogenetic tree construction from gene frequency data. - beta12orEarlier - - - - - - - - - - Phylogenetic tree construction (from polymorphism data) - - - - - - - - Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data. - Phylogenetic tree generation (from polymorphism data) - beta12orEarlier - - - - - - - - - - Phylogenetic species tree construction - - Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison. - Phylogenetic species tree generation - beta12orEarlier - - - - - - - - - - Phylogenetic tree generation (parsimony methods) - - Phylogenetic tree construction (parsimony methods) - Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment. - This includes evolutionary parsimony (invariants) methods. - beta12orEarlier - - - - - - - - - - Phylogenetic tree generation (minimum distance methods) - - This includes neighbor joining (NJ) clustering method. - beta12orEarlier - Phylogenetic tree construction (minimum distance methods) - Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances. - - - - - - - - - - Phylogenetic tree generation (maximum likelihood and Bayesian methods) - - Phylogenetic tree construction (maximum likelihood and Bayesian methods) - Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution. - Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. - beta12orEarlier - - - - - - - - - - Phylogenetic tree generation (quartet methods) - - beta12orEarlier - Phylogenetic tree construction (quartet methods) - Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely. - - - - - - - - - - Phylogenetic tree generation (AI methods) - - Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms. - Phylogenetic tree construction (AI methods) - beta12orEarlier - - - - - - - - - - DNA substitution modelling - - - - - - - - - - - - - - - Sequence alignment analysis (phylogenetic modelling) - beta12orEarlier - Identify a plausible model of DNA substitution that explains a DNA sequence alignment. - - - - - - - - - - Phylogenetic tree analysis (shape) - - Phylogenetic tree topology analysis - Analyse the shape (topology) of a phylogenetic tree. - beta12orEarlier - - - - - - - - - - Phylogenetic tree bootstrapping - - - Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree. - beta12orEarlier - - - - - - - - - - Phylogenetic tree analysis (gene family prediction) - - - - - - - - - - - - - - Predict families of genes and gene function based on their position in a phylogenetic tree. - beta12orEarlier - - - - - - - - - - Phylogenetic tree analysis (natural selection) - - beta12orEarlier - Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait. - Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive). - - - - - - - - - - Phylogenetic tree generation (consensus) - - - Compare two or more phylogenetic trees to produce a consensus tree. - Methods typically test for topological similarity between trees using for example a congruence index. - beta12orEarlier - Phylogenetic tree construction (consensus) - - - - - - - - - - Phylogenetic sub/super tree detection - - beta12orEarlier - Compare two or more phylogenetic trees to detect subtrees or supertrees. - - - - - - - - - - Phylogenetic tree distances calculation - - - - - - - - beta12orEarlier - Compare two or more phylogenetic trees to calculate distances between trees. - - - - - - - - - - Phylogenetic tree annotation - - beta12orEarlier - http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation - Annotate a phylogenetic tree with terms from a controlled vocabulary. - - - - - - - - - - Immunogenicity prediction - - - - - - - - - - - - - - - - - - - - beta12orEarlier - Peptide immunogen prediction - Predict and optimise peptide ligands that elicit an immunological response. - - - - - - - - - - DNA vaccine design - - - - - - - - - - - - - - - beta12orEarlier - Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. - - - - - - - - - - Sequence formatting - - - - - - - - - - - - - - beta12orEarlier - Reformat (a file or other report of) molecular sequence(s). - Sequence file format conversion - - - - - - - - - - Sequence alignment formatting - - - - - - - - - - - - - - Reformat (a file or other report of) molecular sequence alignment(s). - beta12orEarlier - - - - - - - - - - Codon usage table formatting - - - - - - - - - - - - - - - Reformat a codon usage table. - beta12orEarlier - - - - - - - - - - Sequence visualisation - - - - - - - - - - - - - - - beta12orEarlier - Visualise, format or render a molecular sequence, possibly with sequence features or properties shown. - Sequence rendering - - - - - - - - - - Sequence alignment visualisation - - - - - - - - - - - - - - - Sequence alignment rendering - Visualise, format or print a molecular sequence alignment. - beta12orEarlier - - - - - - - - - - Sequence cluster visualisation - - - - - - - - - - - - - - Sequence cluster rendering - beta12orEarlier - Visualise, format or render sequence clusters. - - - - - - - - - - Phylogenetic tree visualisation - - - - - - - - - Render or visualise a phylogenetic tree. - Phylogenetic tree rendering - beta12orEarlier - - - - - - - - - - RNA secondary structure visualisation - - - - - - - - - RNA secondary structure rendering - Visualise RNA secondary structure, knots, pseudoknots etc. - beta12orEarlier - - - - - - - - - - Protein secondary structure rendering - Protein secondary structure visualisation - - - - - - - - Render and visualise protein secondary structure. - beta12orEarlier - - - - - - - - - - Structure visualisation - - - - - - - - - - - - - - - Structure rendering - Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation. - beta12orEarlier - - - - - - - - - - Microarray data rendering - - - - - - - - - - Visualise microarray data. - beta12orEarlier - - - - - - - - - - Protein interaction network rendering - Protein interaction network visualisation - - - - - - - - - beta12orEarlier - Identify and analyse networks of protein interactions. - - - - - - - - - - Map drawing - - - - - - - - beta12orEarlier - DNA map drawing - Map rendering - Draw or visualise a DNA map. - - - - - - - - - - Sequence motif rendering - - Render a sequence with motifs. - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - Restriction map drawing - - - - - - - - - Draw or visualise restriction maps in DNA sequences. - beta12orEarlier - - - - - - - - - - DNA linear map rendering - - beta12orEarlier - beta12orEarlier - true - Draw a linear maps of DNA. - - - - - - - - - - Plasmid map drawing - - beta12orEarlier - DNA circular map rendering - Draw a circular maps of DNA, for example a plasmid map. - - - - - - - - - - Operon drawing - - - - - - - - Visualise operon structure etc. - beta12orEarlier - Operon rendering - - - - - - - - - - Nucleic acid folding family identification - - true - beta12orEarlier - Identify folding families of related RNAs. - beta12orEarlier - - - - - - - - - - Nucleic acid folding energy calculation - - beta12orEarlier - Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants. - - - - - - - - - - Annotation retrieval - - beta12orEarlier - Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. - Retrieve existing annotation (or documentation), typically annotation on a database entity. - beta12orEarlier - true - - - - - - - - - - Protein function prediction - - - - - - - - - beta12orEarlier - Predict general functional properties of a protein. - For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. - - - - - - - - - - Protein function comparison - - - - - - - - - Compare the functional properties of two or more proteins. - beta12orEarlier - - - - - - - - - - Sequence submission - - Submit a molecular sequence to a database. - beta12orEarlier - 1.6 - true - - - - - - - - - - Gene regulatory network analysis - - - - - - - - beta12orEarlier - Analyse a known network of gene regulation. - - - - - - - - - - - Loading - - - - - - - - Data loading - WHATIF:UploadPDB - Prepare or load a user-specified data file so that it is available for use. - beta12orEarlier - - - - - - - - - - Sequence retrieval - - This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. - Data retrieval (sequences) - 1.6 - Query a sequence data resource (typically a database) and retrieve sequences and / or annotation. - beta12orEarlier - true - - - - - - - - - - Structure retrieval - - true - WHATIF:EchoPDB - beta12orEarlier - WHATIF:DownloadPDB - This includes direct retrieval methods but not those that perform calculations on the sequence or structure. - Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation. - 1.6 - - - - - - - - - - Surface rendering - - - beta12orEarlier - WHATIF:GetSurfaceDots - Calculate the positions of dots that are homogeneously distributed over the surface of a molecule. - A dot has three coordinates (x,y,z) and (typically) a color. - - - - - - - - - - Protein atom surface calculation (accessible) - - beta12orEarlier - WHATIF:AtomAccessibilitySolventPlus - WHATIF:AtomAccessibilitySolvent - Calculate the solvent accessibility ('accessible surface') for each atom in a structure. - Waters are not considered. - - - - - - - - - - Protein atom surface calculation (accessible molecular) - - beta12orEarlier - Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. - Waters are not considered. - WHATIF:AtomAccessibilityMolecular - WHATIF:AtomAccessibilityMolecularPlus - - - - - - - - - - Protein residue surface calculation (accessible) - - WHATIF:ResidueAccessibilitySolvent - beta12orEarlier - Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - Calculate the solvent accessibility ('accessible surface') for each residue in a structure. - - - - - - - - - - Protein residue surface calculation (vacuum accessible) - - Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. - WHATIF:ResidueAccessibilityVacuum - beta12orEarlier - - - - - - - - - - Protein residue surface calculation (accessible molecular) - - Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. - WHATIF:ResidueAccessibilityMolecular - Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - beta12orEarlier - - - - - - - - - - Protein residue surface calculation (vacuum molecular) - - Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - beta12orEarlier - Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. - WHATIF:ResidueAccessibilityVacuumMolecular - - - - - - - - - - Protein surface calculation (accessible molecular) - - WHATIF:TotAccessibilityMolecular - beta12orEarlier - Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. - - - - - - - - - - Protein surface calculation (accessible) - - WHATIF:TotAccessibilitySolvent - Calculate the solvent accessibility ('accessible surface') for a structure as a whole. - beta12orEarlier - - - - - - - - - - Backbone torsion angle calculation - - beta12orEarlier - WHATIF:ResidueTorsionsBB - Calculate for each residue in a protein structure all its backbone torsion angles. - - - - - - - - - - Full torsion angle calculation - - beta12orEarlier - Calculate for each residue in a protein structure all its torsion angles. - WHATIF:ResidueTorsions - - - - - - - - - - Cysteine torsion angle calculation - - beta12orEarlier - Calculate for each cysteine (bridge) all its torsion angles. - WHATIF:CysteineTorsions - - - - - - - - - - Tau angle calculation - - WHATIF:ShowTauAngle - beta12orEarlier - Tau is the backbone angle N-Calpha-C (angle over the C-alpha). - For each amino acid in a protein structure calculate the backbone angle tau. - - - - - - - - - - Cysteine bridge detection - - WHATIF:ShowCysteineBridge - Detect cysteine bridges (from coordinate data) in a protein structure. - beta12orEarlier - - - - - - - - - - Free cysteine detection - - beta12orEarlier - A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. - Detect free cysteines in a protein structure. - WHATIF:ShowCysteineFree - - - - - - - - - - Metal-bound cysteine detection - - beta12orEarlier - WHATIF:ShowCysteineMetal - Detect cysteines that are bound to metal in a protein structure. - - - - - - - - - - Residue contact calculation (residue-nucleic acid) - - - - beta12orEarlier - WHATIF:ShowProteiNucleicContacts - Calculate protein residue contacts with nucleic acids in a structure. - WHATIF:HasNucleicContacts - - - - - - - - - - Residue contact calculation (residue-metal) - - - WHATIF:HasMetalContacts - beta12orEarlier - Calculate protein residue contacts with metal in a structure. - WHATIF:HasMetalContactsPlus - - - - - - - - - - Residue contact calculation (residue-negative ion) - - Calculate ion contacts in a structure (all ions for all side chain atoms). - WHATIF:HasNegativeIonContactsPlus - beta12orEarlier - WHATIF:HasNegativeIonContacts - - - - - - - - - - Residue bump detection - - WHATIF:ShowBumps - beta12orEarlier - Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance. - - - - - - - - - - Residue symmetry contact calculation - - Calculate the number of symmetry contacts made by residues in a protein structure. - WHATIF:SymmetryContact - A symmetry contact is a contact between two atoms in different asymmetric unit. - beta12orEarlier - - - - - - - - - - Residue contact calculation (residue-ligand) - - - beta12orEarlier - Calculate contacts between residues and ligands in a protein structure. - WHATIF:ShowDrugContactsShort - WHATIF:ShowLigandContacts - WHATIF:ShowDrugContacts - - - - - - - - - - Salt bridge calculation - - Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. - WHATIF:HasSaltBridgePlus - WHATIF:ShowSaltBridges - beta12orEarlier - WHATIF:HasSaltBridge - WHATIF:ShowSaltBridgesH - Calculate (and possibly score) salt bridges in a protein structure. - - - - - - - - - - Rotamer likelihood prediction - - WHATIF:ShowLikelyRotamers - WHATIF:ShowLikelyRotamers500 - Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure. - WHATIF:ShowLikelyRotamers800 - WHATIF:ShowLikelyRotamers600 - WHATIF:ShowLikelyRotamers900 - Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. - WHATIF:ShowLikelyRotamers700 - WHATIF:ShowLikelyRotamers400 - WHATIF:ShowLikelyRotamers300 - WHATIF:ShowLikelyRotamers200 - WHATIF:ShowLikelyRotamers100 - beta12orEarlier - - - - - - - - - - Proline mutation value calculation - - Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein. - WHATIF:ProlineMutationValue - beta12orEarlier - - - - - - - - - - Residue packing validation - - beta12orEarlier - Identify poorly packed residues in protein structures. - WHATIF: PackingQuality - - - - - - - - - - Dihedral angle validation - - WHATIF: ImproperQualitySum - Identify for each residue in a protein structure any improper dihedral (phi/psi) angles. - beta12orEarlier - WHATIF: ImproperQualityMax - - - - - - - - - - PDB file sequence retrieval - - Extract a molecular sequence from a PDB file. - beta12orEarlier - WHATIF: PDB_sequence - true - beta12orEarlier - - - - - - - - - - HET group detection - - Identify HET groups in PDB files. - WHATIF: HETGroupNames - beta12orEarlier - A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. - - - - - - - - - - DSSP secondary structure assignment - - Determine for residue the DSSP determined secondary structure in three-state (HSC). - beta12orEarlier - WHATIF: ResidueDSSP - beta12orEarlier - true - - - - - - - - - - Structure formatting - - Reformat (a file or other report of) tertiary structure data. - beta12orEarlier - WHATIF: PDBasXML - - - - - - - - - - Protein cysteine and disulfide bond assignment - - - - - - - - Assign cysteine bonding state and disulfide bond partners in protein structures. - beta12orEarlier - - - - - - - - - - Residue validation - - Identify poor quality amino acid positions in protein structures. - beta12orEarlier - WHATIF: UseResidueDB - The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). - - - - - - - - - - Structure retrieval (water) - - beta12orEarlier - 1.6 - WHATIF:MovedWaterPDB - true - Query a tertiary structure database and retrieve water molecules. - - - - - - - - - - siRNA duplex prediction - - - - - - - - beta12orEarlier - Identify or predict siRNA duplexes in RNA. - - - - - - - - - - Sequence alignment refinement - - - Refine an existing sequence alignment. - beta12orEarlier - - - - - - - - - - Listfile processing - - 1.6 - Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). - true - beta12orEarlier - - - - - - - - - - Sequence file editing - - - beta12orEarlier - Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, creation of subset or a new file of sequences. - - - - - - - - - - Sequence alignment file processing - - beta12orEarlier - Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences. - 1.6 - true - - - - - - - - - - Small molecule data processing - - beta13 - true - beta12orEarlier - Process (read and / or write) physicochemical property data for small molecules. - - - - - - - - - - Data retrieval (ontology annotation) - - beta13 - Ontology information retrieval - true - Search and retrieve documentation on a bioinformatics ontology. - beta12orEarlier - - - - - - - - - - Data retrieval (ontology concept) - - Query an ontology and retrieve concepts or relations. - true - beta13 - beta12orEarlier - Ontology retrieval - - - - - - - - - - Representative sequence identification - - - - - - - - Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences. - beta12orEarlier - - - - - - - - - - Structure file processing - - Perform basic (non-analytical) operations on a file of molecular tertiary structural data. - 1.6 - beta12orEarlier - true - - - - - - - - - - Data retrieval (sequence profile) - - Query a profile data resource and retrieve one or more profile(s) and / or associated annotation. - true - This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. - beta13 - beta12orEarlier - - - - - - - - - - Statistical calculation - - Statistical analysis - Perform a statistical data operation of some type, e.g. calibration or validation. - beta12orEarlier - true - - - - - - - - - - 3D-1D scoring matrix generation - - - - - - - - - - - - - - - - beta12orEarlier - 3D-1D scoring matrix construction - A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. - Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. - - - - - - - - - - Transmembrane protein visualisation - - - - - - - - - Visualise transmembrane proteins, typically the transmembrane regions within a sequence. - beta12orEarlier - Transmembrane protein rendering - - - - - - - - - - Demonstration - - beta12orEarlier - true - An operation performing purely illustrative (pedagogical) purposes. - beta13 - - - - - - - - - Data retrieval (pathway or network) - - beta12orEarlier - true - Query a biological pathways database and retrieve annotation on one or more pathways. - beta13 - - - - - - - - - - Data retrieval (identifier) - - beta12orEarlier - Query a database and retrieve one or more data identifiers. - beta13 - true - - - - - - - - - - Nucleic acid density plotting - - - beta12orEarlier - Calculate a density plot (of base composition) for a nucleotide sequence. - - - - - - - - - - Sequence analysis - - - - - - - - Analyse one or more known molecular sequences. - beta12orEarlier - Sequence analysis (general) - - - - - - - - - - Sequence motif processing - - true - 1.6 - Process (read and / or write) molecular sequence motifs. - beta12orEarlier - - - - - - - - - - Protein interaction data processing - - 1.6 - Process (read and / or write) protein interaction data. - true - beta12orEarlier - - - - - - - - - - Protein structure analysis - - - - - - - - - - - - - - - Structure analysis (protein) - beta12orEarlier - Analyse protein tertiary structural data. - - - - - - - - - - Annotation processing - - true - beta12orEarlier - beta12orEarlier - Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity. - - - - - - - - - - Sequence feature analysis - - beta12orEarlier - true - Analyse features in molecular sequences. - beta12orEarlier - - - - - - - - - - Utility operation - - - - - - - - Basic (non-analytical) operations of some data, either a file or equivalent entity in memory. - File processing - beta12orEarlier - Report handling - File handling - Data file processing - - - - - - - - - - Gene expression analysis - - Analyse gene expression and regulation data. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Structural profile processing - - beta12orEarlier - 1.6 - Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. - 3D profile processing - true - - - - - - - - - - Data index processing - - Database index processing - true - Process (read and / or write) an index of (typically a file of) biological data. - 1.6 - beta12orEarlier - - - - - - - - - - Sequence profile processing - - true - beta12orEarlier - Process (read and / or write) some type of sequence profile. - 1.6 - - - - - - - - - - Protein function analysis - - - - - - - - This is a broad concept and is used a placeholder for other, more specific concepts. - beta12orEarlier - Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report. - - - - - - - - - - Protein folding analysis - - - - - - - - - - - - - - - This is a broad concept and is used a placeholder for other, more specific concepts. - Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report. - Protein folding modelling - beta12orEarlier - - - - - - - - - - Protein secondary structure analysis - - - - - - - - - - - - - - Analyse known protein secondary structure data. - beta12orEarlier - Secondary structure analysis (protein) - - - - - - - - - - Physicochemical property data processing - - beta13 - true - Process (read and / or write) data on the physicochemical property of a molecule. - beta12orEarlier - - - - - - - - - - Primer and probe design - - - - - - - - - Primer and probe prediction - beta12orEarlier - Predict oligonucleotide primers or probes. - - - - - - - - - - Operation (typed) - - Computation - Calculation - Processing - Process (read and / or write) data of a specific type, for example applying analytical methods. - beta12orEarlier - - - - - - - - - - Database search - - - - - - - - beta12orEarlier - Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. - Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query. - - - - - - - - - - Data retrieval - - - - - - - - Information retrieval - beta12orEarlier - Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords. - - - - - - - - - - Prediction and recognition - - beta12orEarlier - Recognition - Prediction - Predict, recognise, detect or identify some properties of a biomolecule. - Detection - - - - - - - - - - Comparison - - beta12orEarlier - Compare two or more things to identify similarities. - - - - - - - - - - Optimisation and refinement - - beta12orEarlier - Refine or optimise some data model. - - - - - - - - - - Modelling and simulation - - - - - - - - beta12orEarlier - Model or simulate some biological entity or system. - - - - - - - - - - Data handling - - true - beta12orEarlier - Perform basic operations on some data or a database. - beta12orEarlier - - - - - - - - - - Validation - - beta12orEarlier - Validation and standardisation - Validate some data. - - - - - - - - - - Mapping - - This is a broad concept and is used a placeholder for other, more specific concepts. - Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts. - beta12orEarlier - - - - - - - - - - Design - - beta12orEarlier - Design a biological entity (typically a molecular sequence or structure) with specific properties. - true - - - - - - - - - - Microarray data processing - - beta12orEarlier - Process (read and / or write) microarray data. - beta12orEarlier - true - - - - - - - - - - Codon usage table processing - - Process (read and / or write) a codon usage table. - beta12orEarlier - - - - - - - - - - Data retrieval (codon usage table) - - Retrieve a codon usage table and / or associated annotation. - beta12orEarlier - true - beta13 - - - - - - - - - - Gene expression profile processing - - 1.6 - Process (read and / or write) a gene expression profile. - true - beta12orEarlier - - - - - - - - - - Functional enrichment - - - - - - - - - beta12orEarlier - Gene expression profile annotation - The Gene Ontology (GO) is invariably used, the input is a set of Gene IDs and the output of the analysis is typically a ranked list of GO terms, each associated with a p-value. - Analyse a set of genes (genes corresponding to an expression profile, or any other set) with respect to concepts from an ontology of gene functions. - GO term enrichment - - - - - - - - - - Gene regulatory network prediction - - - - - - - - - - - - - - - Predict a network of gene regulation. - beta12orEarlier - - - - - - - - - - Pathway or network processing - - - - - - - - Generate, analyse or handle a biological pathway or network. - beta12orEarlier - - - - - - - - - - RNA secondary structure analysis - - - - - - - - beta12orEarlier - Process (read and / or write) RNA secondary structure data. - - - - - - - - - - Structure processing (RNA) - - Process (read and / or write) RNA tertiary structure data. - beta12orEarlier - beta13 - true - - - - - - - - - - RNA structure prediction - - - - - - - - beta12orEarlier - Predict RNA tertiary structure. - - - - - - - - - - DNA structure prediction - - - - - - - - Predict DNA tertiary structure. - beta12orEarlier - - - - - - - - - - Phylogenetic tree processing - - - - - - - - beta12orEarlier - Process (read and / or write) a phylogenetic tree. - - - - - - - - - - Protein secondary structure processing - - Process (read and / or write) protein secondary structure data. - 1.6 - true - beta12orEarlier - - - - - - - - - - Protein interaction network processing - - true - beta12orEarlier - Process (read and / or write) a network of protein interactions. - 1.6 - - - - - - - - - - Sequence processing - - Sequence processing (general) - Process (read and / or write) one or more molecular sequences and associated annotation. - true - beta12orEarlier - 1.6 - - - - - - - - - - Sequence processing (protein) - - Process (read and / or write) a protein sequence and associated annotation. - beta12orEarlier - true - 1.6 - - - - - - - - - - Sequence processing (nucleic acid) - - 1.6 - true - beta12orEarlier - Process (read and / or write) a nucleotide sequence and associated annotation. - - - - - - - - - - Sequence comparison - - - - - - - - - - - - - - - - - - - - - Compare two or more molecular sequences. - beta12orEarlier - - - - - - - - - - Sequence cluster processing - - Process (read and / or write) a sequence cluster. - true - beta12orEarlier - 1.6 - - - - - - - - - - Feature table processing - - Process (read and / or write) a sequence feature table. - 1.6 - true - beta12orEarlier - - - - - - - - - - Gene prediction - - - - - - - - - - - - - - Gene and gene component prediction - beta12orEarlier - Detect, predict and identify genes or components of genes in DNA sequences. - Gene finding - - - - - - - - - - GPCR classification - - - - - - - - - beta12orEarlier - G protein-coupled receptor (GPCR) classification - Classify G-protein coupled receptors (GPCRs) into families and subfamilies. - - - - - - - - - - GPCR coupling selectivity prediction - - - - - - - - - - Predict G-protein coupled receptor (GPCR) coupling selectivity. - beta12orEarlier - - - - - - - - - - Structure processing (protein) - - true - 1.6 - beta12orEarlier - Process (read and / or write) a protein tertiary structure. - - - - - - - - - - Protein atom surface calculation - - Waters are not considered. - Calculate the solvent accessibility for each atom in a structure. - beta12orEarlier - - - - - - - - - - Protein residue surface calculation - - beta12orEarlier - Calculate the solvent accessibility for each residue in a structure. - - - - - - - - - - Protein surface calculation - - beta12orEarlier - Calculate the solvent accessibility of a structure as a whole. - - - - - - - - - - Sequence alignment processing - - beta12orEarlier - true - Process (read and / or write) a molecular sequence alignment. - 1.6 - - - - - - - - - - Protein-protein interaction prediction - - - - - - - - - - - - - - Identify or predict protein-protein interactions, interfaces, binding sites etc. - beta12orEarlier - - - - - - - - - - Structure processing - - true - 1.6 - Process (read and / or write) a molecular tertiary structure. - beta12orEarlier - - - - - - - - - - Map annotation - - Annotate a DNA map of some type with terms from a controlled vocabulary. - true - beta12orEarlier - 1.6 - - - - - - - - - - Data retrieval (protein annotation) - - Retrieve information on a protein. - beta13 - true - Protein information retrieval - beta12orEarlier - - - - - - - - - - Data retrieval (phylogenetic tree) - - beta12orEarlier - beta13 - Retrieve a phylogenetic tree from a data resource. - true - - - - - - - - - - Data retrieval (protein interaction annotation) - - Retrieve information on a protein interaction. - true - beta13 - beta12orEarlier - - - - - - - - - - Data retrieval (protein family annotation) - - beta12orEarlier - Protein family information retrieval - beta13 - Retrieve information on a protein family. - true - - - - - - - - - - Data retrieval (RNA family annotation) - - true - Retrieve information on an RNA family. - RNA family information retrieval - beta12orEarlier - beta13 - - - - - - - - - - Data retrieval (gene annotation) - - beta12orEarlier - Gene information retrieval - Retrieve information on a specific gene. - true - beta13 - - - - - - - - - - Data retrieval (genotype and phenotype annotation) - - Retrieve information on a specific genotype or phenotype. - Genotype and phenotype information retrieval - beta12orEarlier - beta13 - true - - - - - - - - - - Protein architecture comparison - - - Compare the architecture of two or more protein structures. - beta12orEarlier - - - - - - - - - - Protein architecture recognition - - - - beta12orEarlier - Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces. - Identify the architecture of a protein structure. - - - - - - - - - - Molecular dynamics simulation - - - - - - - - - - - - - - - - - - - - - - Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. - beta12orEarlier - - - - - - - - - - Nucleic acid sequence analysis - - - - - - - - - - - - - - - Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). - beta12orEarlier - Sequence analysis (nucleic acid) - - - - - - - - - - Protein sequence analysis - - - - - - - - - Analyse a protein sequence (using methods that are only applicable to protein sequences). - Sequence analysis (protein) - beta12orEarlier - - - - - - - - - - Structure analysis - - - - - - - - beta12orEarlier - Analyse known molecular tertiary structures. - - - - - - - - - - Nucleic acid structure analysis - - - - - - - - - - - - - - - Analyse nucleic acid tertiary structural data. - beta12orEarlier - - - - - - - - - - Secondary structure processing - - 1.6 - Process (read and / or write) a molecular secondary structure. - true - beta12orEarlier - - - - - - - - - - Structure comparison - - - - - - - - - beta12orEarlier - Compare two or more molecular tertiary structures. - - - - - - - - - - Helical wheel drawing - - - - - - - - Helical wheel rendering - beta12orEarlier - Render a helical wheel representation of protein secondary structure. - - - - - - - - - - Topology diagram drawing - - - - - - - - Topology diagram rendering - beta12orEarlier - Render a topology diagram of protein secondary structure. - - - - - - - - - - Protein structure comparison - - - - - - - - - - beta12orEarlier - Structure comparison (protein) - Methods might identify structural neighbors, find structural similarities or define a structural core. - Compare protein tertiary structures. - - - - - - - - - - Protein secondary structure comparison - - - - Compare protein secondary structures. - beta12orEarlier - Secondary structure comparison (protein) - Protein secondary structure - - - - - - - - - - Protein subcellular localization prediction - - - - - - - - - The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. - Predict the subcellular localization of a protein sequence. - Protein targeting prediction - beta12orEarlier - - - - - - - - - - Residue contact calculation (residue-residue) - - beta12orEarlier - Calculate contacts between residues in a protein structure. - - - - - - - - - - Hydrogen bond calculation (inter-residue) - - - Identify potential hydrogen bonds between amino acid residues. - beta12orEarlier - - - - - - - - - - Protein interaction prediction - - - - - - - - - - - - - - - Predict the interactions of proteins with other molecules. - beta12orEarlier - - - - - - - - - - Codon usage data processing - - beta12orEarlier - beta13 - Process (read and / or write) codon usage data. - true - - - - - - - - - - Gene expression data analysis - - - - - - - - beta12orEarlier - Gene expression profile analysis - Gene expression (microarray) data processing - Microarray data processing - Gene expression data processing - Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms. - - - - - - - - - - Gene regulatory network processing - - 1.6 - beta12orEarlier - Process (read and / or write) a network of gene regulation. - true - - - - - - - - - Pathway or network analysis - - - - - - - - Analyse a known biological pathway or network. - Pathway analysis - Network analysis - beta12orEarlier - - - - - - - - - - Sequencing-based expression profile data analysis - - Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - Splicing model analysis - - - - - - - - - - Analyse, characterize and model alternative splicing events from comparing multiple nucleic acid sequences. - Splicing analysis - beta12orEarlier - - - - - - - - - - Microarray raw data analysis - - beta12orEarlier - beta12orEarlier - true - Analyse raw microarray data. - - - - - - - - - - Nucleic acid analysis - - - - - - - - Process (read and / or write) nucleic acid sequence or structural data. - Nucleic acid data processing - beta12orEarlier - - - - - - - - - - Protein analysis - - - - - - - - beta12orEarlier - Protein data processing - Process (read and / or write) protein sequence or structural data. - - - - - - - - - - Sequence data processing - - beta12orEarlier - Process (read and / or write) molecular sequence data. - beta13 - true - - - - - - - - - Structural data processing - - Process (read and / or write) molecular structural data. - beta13 - true - beta12orEarlier - - - - - - - - - - Text processing - - true - beta12orEarlier - Process (read and / or write) text. - 1.6 - - - - - - - - - - Protein sequence alignment analysis - - - - - - - - - - Analyse a protein sequence alignment, typically to detect features or make predictions. - beta12orEarlier - Sequence alignment analysis (protein) - - - - - - - - - - Nucleic acid sequence alignment analysis - - - - - - - - - - beta12orEarlier - Sequence alignment analysis (nucleic acid) - Analyse a protein sequence alignment, typically to detect features or make predictions. - - - - - - - - - - Nucleic acid sequence comparison - - - - Sequence comparison (nucleic acid) - Compare two or more nucleic acid sequences. - beta12orEarlier - - - - - - - - - - Protein sequence comparison - - - - beta12orEarlier - Sequence comparison (protein) - Compare two or more protein sequences. - - - - - - - - - - DNA back-translation - - - - - - - - beta12orEarlier - Back-translate a protein sequence into DNA. - - - - - - - - - - Sequence editing (nucleic acid) - - 1.8 - true - Edit or change a nucleic acid sequence, either randomly or specifically. - beta12orEarlier - - - - - - - - - - Sequence editing (protein) - - Edit or change a protein sequence, either randomly or specifically. - beta12orEarlier - true - 1.8 - - - - - - - - - - Sequence generation (nucleic acid) - - Generate a nucleic acid sequence by some means. - beta12orEarlier - - - - - - - - - - Sequence generation (protein) - - - Generate a protein sequence by some means. - beta12orEarlier - - - - - - - - - - Nucleic acid sequence visualisation - - Visualise, format or render a nucleic acid sequence. - true - Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. - 1.8 - beta12orEarlier - - - - - - - - - - Protein sequence visualisation - - true - beta12orEarlier - Visualise, format or render a protein sequence. - 1.8 - Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. - - - - - - - - - - Nucleic acid structure comparison - - - - Compare nucleic acid tertiary structures. - beta12orEarlier - Structure comparison (nucleic acid) - - - - - - - - - - Structure processing (nucleic acid) - - 1.6 - beta12orEarlier - true - Process (read and / or write) nucleic acid tertiary structure data. - - - - - - - - - - DNA mapping - - - - - - - - - - - - - - - - - - - - beta12orEarlier - Generate a map of a DNA sequence annotated with positional or non-positional features of some type. - - - - - - - - - - Map data processing - - DNA map data processing - Process (read and / or write) a DNA map of some type. - beta12orEarlier - true - 1.6 - - - - - - - - - - Protein hydropathy calculation - - - - - - - - - - - - - - beta12orEarlier - Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information). - - - - - - - - - - Protein binding site prediction - - - - - - - - Ligand-binding and active site prediction - beta12orEarlier - Binding site prediction - Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures. - - - - - - - - - - Sequence tagged site (STS) mapping - - - - - - - - beta12orEarlier - Sequence mapping - An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences. - Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS). - - - - - - - - - - Alignment - - - - - - - - - Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits. - Alignment - Alignment generation - beta12orEarlier - Alignment construction - - - - - - - - - - Protein fragment weight comparison - - - beta12orEarlier - Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data. - - - - - - - - - - Protein property comparison - - - - - - - - Compare the physicochemical properties of two or more proteins (or reference data). - beta12orEarlier - - - - - - - - - - Secondary structure comparison - - - - - - - - Compare two or more molecular secondary structures. - beta12orEarlier - - - - - - - - - - Hopp and Woods plotting - - - beta12orEarlier - Generate a Hopp and Woods plot of antigenicity of a protein. - - - - - - - - - - Microarray cluster textual view generation - - beta12orEarlier - Visualise gene clusters with gene names. - - - - - - - - - - Microarray wave graph plotting - - Microarray wave graph rendering - Microarray cluster temporal graph rendering - beta12orEarlier - This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades. - Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis. - - - - - - - - - - Microarray dendrograph plotting - - Microarray dendrograph rendering - Generate a dendrograph of raw, preprocessed or clustered microarray data. - beta12orEarlier - Microarray checks view rendering - Microarray view rendering - - - - - - - - - - Microarray proximity map plotting - - beta12orEarlier - Microarray distance map rendering - Generate a plot of distances (distance matrix) between genes. - Microarray proximity map rendering - - - - - - - - - - Microarray tree or dendrogram rendering - - Microarray 2-way dendrogram rendering - beta12orEarlier - Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression. - Microarray matrix tree plot rendering - - - - - - - - - - Microarray principal component plotting - - beta12orEarlier - Microarray principal component rendering - Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values. - - - - - - - - - - Microarray scatter plot plotting - - Generate a scatter plot of microarray data, typically after principal component analysis. - beta12orEarlier - Microarray scatter plot rendering - - - - - - - - - - Whole microarray graph plotting - - Visualise gene expression data where each band (or line graph) corresponds to a sample. - beta12orEarlier - Whole microarray graph rendering - - - - - - - - - - Microarray tree-map rendering - - beta12orEarlier - Visualise gene expression data after hierarchical clustering for representing hierarchical relationships. - - - - - - - - - - Microarray Box-Whisker plot plotting - - beta12orEarlier - Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles. - - - - - - - - - - Physical mapping - - - - - - - - - - - - - - beta12orEarlier - Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. - - - - - - - - - - Analysis - - Apply analytical methods to existing data of a specific type. - For non-analytical operations, see the 'Processing' branch. - beta12orEarlier - - - - - - - - - - - Alignment analysis - - Process or analyse an alignment of molecular sequences or structures. - true - beta12orEarlier - 1.8 - - - - - - - - - - Article analysis - - - - - - - - - - - - - - - - - - - - Analyse a body of scientific text (typically a full text article from a scientific journal.) - beta12orEarlier - Article analysis - - - - - - - - - - Molecular interaction analysis - - Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact. - beta12orEarlier - beta13 - true - - - - - - - - - Protein interaction analysis - - - - - - - - - - - - - - beta12orEarlier - Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions. - - - - - - - - - - Residue contact calculation - - Calculate contacts between residues and some other group in a protein structure. - beta12orEarlier - - - - - - - - - - Alignment processing - - true - Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data. - 1.6 - beta12orEarlier - - - - - - - - - - - Structure alignment processing - - Process (read and / or write) a molecular tertiary (3D) structure alignment. - 1.6 - beta12orEarlier - true - - - - - - - - - - Codon usage bias calculation - - - - - - - - Calculate codon usage bias. - beta12orEarlier - - - - - - - - - - Codon usage bias plotting - - - - - - - - - beta12orEarlier - Generate a codon usage bias plot. - - - - - - - - - - Codon usage fraction calculation - - - - - - - - Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc. - beta12orEarlier - - - - - - - - - - Classification - - beta12orEarlier - Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category. - - - - - - - - - - Molecular interaction data processing - - beta13 - true - beta12orEarlier - Process (read and / or write) molecular interaction data. - - - - - - - - - Sequence classification - - - beta12orEarlier - Assign molecular sequence(s) to a group or category. - - - - - - - - - - Structure classification - - - Assign molecular structure(s) to a group or category. - beta12orEarlier - - - - - - - - - - Protein comparison - - Compare two or more proteins (or some aspect) to identify similarities. - beta12orEarlier - - - - - - - - - - Nucleic acid comparison - - beta12orEarlier - Compare two or more nucleic acids to identify similarities. - - - - - - - - - - Prediction and recognition (protein) - - beta12orEarlier - Predict, recognise, detect or identify some properties of proteins. - - - - - - - - - - Prediction and recognition (nucleic acid) - - beta12orEarlier - Predict, recognise, detect or identify some properties of nucleic acids. - - - - - - - - - - Structure editing - - - - - - - - beta13 - Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically. - - - - - - - - - - Sequence alignment editing - - Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically. - beta13 - - - - - - - - - - Pathway or network visualisation - - - - - - - - - Render (visualise) a biological pathway or network. - Pathway or network rendering - beta13 - - - - - - - - - - Protein function prediction (from sequence) - - beta13 - true - Predict general (non-positional) functional properties of a protein from analysing its sequence. - For functional properties that are positional, use 'Protein site detection' instead. - 1.6 - - - - - - - - - - Protein sequence feature detection - - - - Protein site recognition - Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions. - Protein site prediction - Sequence profile database search - Protein site detection - Protein secondary database search - Sequence feature detection (protein) - beta13 - - - - - - - - - - Protein property calculation (from sequence) - - - beta13 - Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. - - - - - - - - - - Protein feature prediction (from structure) - - beta13 - 1.6 - true - Predict, recognise and identify positional features in proteins from analysing protein structure. - - - - - - - - - - Protein feature detection - - - - - - - - - - - - - - - Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group. - - Predict, recognise and identify positional features in proteins from analysing protein sequences or structures. - beta13 - Protein feature recognition - Protein feature prediction - - - - - - - - - - Database search (by sequence) - - Sequence screening - true - 1.6 - Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries. - beta13 - - - - - - - - - - Protein interaction network prediction - - - - - - - - - - - - - - beta13 - Predict a network of protein interactions. - - - - - - - - - - Nucleic acid design - - - beta13 - Design (or predict) nucleic acid sequences with specific chemical or physical properties. - - - - - - - - - - Editing - - beta13 - Edit a data entity, either randomly or specifically. - - - - - - - - - - Sequence assembly validation - - - - - - - - - - - - - - - - - - - - - 1.1 - Evaluate a DNA sequence assembly, typically for purposes of quality control. - - - - - - - - - - Genome alignment - - Align two or more (tpyically huge) molecular sequences that represent genomes. - Genome alignment construction - 1.1 - Genome alignment - - - - - - - - - - Localized reassembly - - Reconstruction of a sequence assembly in a localised area. - 1.1 - - - - - - - - - - Sequence assembly visualisation - - Assembly rendering - Sequence assembly rendering - Render and visualise a DNA sequence assembly. - 1.1 - Assembly visualisation - - - - - - - - - - Base-calling - - - - - - - - Phred base calling - 1.1 - Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. - Base calling - Phred base-calling - - - - - - - - - - Bisulfite mapping - - 1.1 - Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected. - The mapping of methylation sites in a DNA (genome) sequence. - Bisulfite sequence alignment - Bisulfite sequence mapping - - - - - - - - - - Sequence contamination filtering - - - - - - - - beta12orEarlier - Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced. - - - - - - - - - - Trim ends - - 1.1 - Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. - For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. - - - - - - - - - - Trim vector - - Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. - 1.1 - - - - - - - - - - Trim to reference - - 1.1 - Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. - - - - - - - - - - Sequence trimming - - 1.1 - Cut (remove) the end from a molecular sequence. - - - - - - - - - - Genome feature comparison - - Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on. - Compare the features of two genome sequences. - 1.1 - - - - - - - - - - Sequencing error detection - - - - - - - - Short read error correction - Short-read error correction - beta12orEarlier - Detect errors in DNA sequences generated from sequencing projects). - - - - - - - - - - Genotyping - - 1.1 - Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. - Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence. - - - - - - - - - - Genetic variation analysis - - - 1.1 - Sequence variation analysis - Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. - Genetic variation annotation - Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. - - - - - - - - - - Read mapping - - - Short oligonucleotide alignment - Oligonucleotide mapping - Oligonucleotide alignment generation - Short read mapping - Oligonucleotide alignment construction - The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. - Oligonucleotide alignment - Read alignment - 1.1 - Short read alignment - Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. - Short sequence read mapping - - - - - - - - - - Split read mapping - - A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation. - 1.1 - - - - - - - - - - DNA barcoding - - Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. - 1.1 - Sample barcoding - - - - - - - - - - SNP calling - - Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism. - Operations usually score confidence in the prediction or some other statistical measure of evidence. - 1.1 - - - - - - - - - - Mutation detection - - Polymorphism detection - Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware. - 1.1 - - - - - - - - - - Chromatogram visualisation - - Visualise, format or render an image of a Chromatogram. - Chromatogram viewing - 1.1 - - - - - - - - - - Methylation analysis - - 1.1 - Determine cytosine methylation states in nucleic acid sequences. - - - - - - - - - - Methylation calling - - - 1.1 - Determine cytosine methylation status of specific positions in a nucleic acid sequences. - - - - - - - - - - Methylation level analysis (global) - - 1.1 - Global methylation analysis - Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay. - - - - - - - - - - Methylation level analysis (gene-specific) - - Gene-specific methylation analysis - Many different techniques are available for this. - Measure the level of methyl cytosines in specific genes. - 1.1 - - - - - - - - - - Genome visualisation - - 1.1 - Genome visualization - Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence. - Genome rendering - Genome visualisation - Genome viewing - Genome browsing - - - - - - - - - - Genome comparison - - Compare the sequence or features of two or more genomes, for example, to find matching regions. - 1.1 - Genomic region matching - - - - - - - - - - Genome indexing - - - - - - - - Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. - Generate an index of a genome sequence. - 1.1 - - - - - - - - - - Genome indexing (Burrows-Wheeler) - - The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. - Generate an index of a genome sequence using the Burrows-Wheeler algorithm. - 1.1 - - - - - - - - - - Genome indexing (suffix arrays) - - 1.1 - Generate an index of a genome sequence using a suffix arrays algorithm. - suffix arrays - A suffix array consists of the lexicographically sorted list of suffixes of a genome. - - - - - - - - - - Spectral analysis - - Spectral analysis - 1.1 - Spectrum analysis - Analyse a spectrum from a mass spectrometry (or other) experiment. - Mass spectrum analysis - - - - - - - - - - Peak detection - - - - - - - - 1.1 - Peak finding - Peak assignment - Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment. - - - - - - - - - - Scaffolding - - - - - - - - - Scaffold construction - Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps. - 1.1 - Scaffold may be positioned along a chromosome physical map to create a "golden path". - Scaffold generation - - - - - - - - - - Scaffold gap completion - - Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences. - Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. - 1.1 - - - - - - - - - - Sequencing quality control - - - Raw sequence data quality control. - Analyse raw sequence data from a sequencing pipeline and identify problems. - Sequencing QC - 1.1 - - - - - - - - - - Read pre-processing - - - Sequence read pre-processing - This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. - Pre-process sequence reads to ensure (or improve) quality and reliability. - 1.1 - - - - - - - - - - Species frequency estimation - - - - - - - - Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples. - 1.1 - - - - - - - - - - Peak calling - - Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). - Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. - Protein binding peak detection - 1.1 - - - - - - - - - - Differential expression analysis - - Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups. - Differentially expressed gene identification - Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. - 1.1 - - - - - - - - - - Gene set testing - - 1.1 - Gene sets can be defined beforehand by biological function, chromosome locations and so on. - Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc. - - - - - - - - - - Variant classification - - - Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins. - 1.1 - Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) - - - - - - - - - - Variant prioritization - - Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. - Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. - 1.1 - - - - - - - - - - Variant calling - - Variant mapping - 1.1 - Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence. - Methods often utilise a database of aligned reads. - - - - - - - - - - Structural variation discovery - - Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s). - 1.1 - Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. - - - - - - - - - - Exome analysis - - 1.1 - Targeted exome capture - Exome sequencing is considered a cheap alternative to whole genome sequencing. - Exome sequence analysis - Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome. - - - - - - - - - - Read depth analysis - - 1.1 - Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications. - - - - - - - - - - Gene expression QTL analysis - - - - - - - - expression quantitative trait loci profiling - 1.1 - eQTL profiling - Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes. - expression QTL profiling - - - - - - - - - - Copy number estimation - - Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number). - Transcript copy number estimation - 1.1 - Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors. - - - - - - - - - - Primer removal - - 1.2 - Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). - - - - - - - - - - Transcriptome assembly - - - - - - - - - - - - - - Infer a transcriptome sequence by analysis of short sequence reads. - 1.2 - - - - - - - - - - Transcriptome assembly (de novo) - - de novo transcriptome assembly - true - 1.6 - 1.2 - Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other. - - - - - - - - - - Transcriptome assembly (mapping) - - Infer a transcriptome sequence by mapping short reads to a reference genome. - 1.6 - 1.2 - true - - - - - - - - - - Sequence coordinate conversion - - - - - - - - - - - - - - 1.3 - Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc. - - - - - - - - - - Document similarity calculation - - Calculate similarity between 2 or more documents. - 1.3 - - - - - - - - - - Document clustering - - - Cluster (group) documents on the basis of their calculated similarity. - 1.3 - - - - - - - - - - Named entity recognition - - - Entity identification - Entity chunking - Entity extraction - Recognise named entities (text tokens) within documents. - 1.3 - - - - - - - - - - ID mapping - - - Identifier mapping - The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence. - 1.3 - Accession mapping - Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration. - - - - - - - - - - Anonymisation - - Process data in such a way that makes it hard to trace to the person which the data concerns. - 1.3 - Data anonymisation - - - - - - - - - - ID retrieval - - - - - - - - id retrieval - Data retrieval (accession) - Data retrieval (ID) - Identifier retrieval - Data retrieval (id) - Accession retrieval - Search for and retrieve a data identifier of some kind, e.g. a database entry accession. - 1.3 - - - - - - - - - - Sequence checksum generation - - - - - - - - - - - - - - Generate a checksum of a molecular sequence. - 1.4 - - - - - - - - - - Bibliography generation - - - - - - - - Bibliography construction - Construct a bibliography from the scientific literature. - 1.4 - - - - - - - - - - Protein quaternary structure prediction - - 1.4 - Predict the structure of a multi-subunit protein and particularly how the subunits fit together. - - - - - - - - - - Protein surface analysis - - 1.4 - Analyse the surface properties of proteins. - - - - - - - - - - Ontology comparison - - 1.4 - Compare two or more ontologies, e.g. identify differences. - - - - - - - - - - Ontology comparison - - 1.4 - Compare two or more ontologies, e.g. identify differences. - 1.9 - - - - - - - - - - Format detection - - - - - - - - - - - - - - Recognition of which format the given data is in. - 1.4 - Format identification - Format recognition - 'Format recognition' is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology. - Format inference - - - - - - The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs. - - - - - - - - - - - Splitting - - File splitting - Split a file containing multiple data items into many files, each containing one item - 1.4 - - - - - - - - - - Generation - - Construction - beta12orEarlier - For non-analytical operations, see the 'Processing' branch. - Construct some data entity. - - - - - - - - - - Nucleic acid sequence feature detection - - - Nucleic acid site prediction - Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions. - Nucleic acid site recognition - 1.6 - Nucleic acid site detection - - - - - - - - - - Deposition - - Deposit some data in a database or some other type of repository or software system. - 1.6 - Database submission - Submission - Data submission - Data deposition - Database deposition - For non-analytical operations, see the 'Processing' branch. - - - - - - - - - - Clustering - - 1.6 - Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters). - - - - - - - - - - Assembly - - 1.6 - Construct some entity (typically a molecule sequence) from component pieces. - - - - - - - - - - Conversion - - 1.6 - Non-analytical data conversion. - - - - - - - - - - Standardization and normalization - - 1.6 - Standardize or normalize data. - - - - - - - - - - Aggregation - - Combine multiple files or data items into a single file or object. - 1.6 - - - - - - - - - - Article comparison - - Compare two or more scientific articles. - 1.6 - - - - - - - - - - Calculation - - Mathemetical determination of the value of something, typically a properly of a molecule. - 1.6 - - - - - - - - - - Pathway or network prediction - - - 1.6 - Predict a molecular pathway or network. - - - - - - - - - - Genome assembly - - 1.6 - The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. - - - - - - - - - - Plotting - - Generate a graph, or other visual representation, of data, showing the relationship between two or more variables. - 1.6 - - - - - - - - - - Image analysis - - - - - - - - 1.7 - The analysis of a image (typically a digital image) of some type in order to extract information from it. - Image processing - - - - - - - - - - - Diffraction data analysis - - 1.7 - Analysis of data from a diffraction experiment. - - - - - - - - - - Cell migration analysis - - - - - - - - 1.7 - Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression. - - - - - - - - - - Diffraction data reduction - - 1.7 - Processing of diffraction data into a corrected, ordered, and simplified form. - - - - - - - - - - Neurite measurement - - - - - - - - Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images. - 1.7 - - - - - - - - - - Diffraction data integration - - 1.7 - Diffraction summation integration - Diffraction profile fitting - The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment. - - - - - - - - - - Phasing - - Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods. - 1.7 - - - - - - - - - - Molecular replacement - - 1.7 - A technique used to construct an atomic model of an unknown structure from diffraction data, based upon an atomic model of a known structure, either a related protein or the same protein from a different crystal form. - The technique solves the phase problem, i.e. retrieve information concern phases of the structure. - - - - - - - - - - Rigid body refinement - - 1.7 - Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data. - A method used to refine a structure by moving the whole molecule or parts of it as a rigid unit, rather than moving individual atoms. - - - - - - - - - - Single particle analysis - - - - - - - - - An image processing technique that combines and analyze multiple images of a particulate sample, in order to produce an image with clearer features that are more easily interpreted. - 1.7 - Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM). - - - - - - - - - - Single particle alignment and classification - - - Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle. - 1.7 - A micrograph can include particles in multiple different orientations and/or conformations. Particles are compared and organised into sets based on their similarity. Typically iterations of classification and alignment and are performed to optimise the final image; average images produced by classification are used as a reference image for subsequent alignment of the whole image set. - - - - - - - - - - Functional clustering - - - - - - - - 1.7 - Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype. - Functional sequence clustering - - - - - - - - - - Taxonomic classification - - 1.7 - Classifiication of molecular sequences by assignment to some taxonomic hierarchy. - - - - - - - - - - Virulence prediction - - - - - - - - - Pathogenicity prediction - The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences. - 1.7 - - - - - - - - - - Gene expression correlation analysis - - - 1.7 - Gene co-expression network analysis - Analyse the correlation patterns among genes across across a variety of experiments, microarray samples etc. - - - - - - - - - - - Correlation - - - - - - - - 1.7 - Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data. - - - - - - - - - - RNA structure covariance model generation - - - - - - - - - Compute the covariance model for (a family of) RNA secondary structures. - 1.7 - - - - - - - - - - RNA secondary structure prediction (shape-based) - - RNA shape prediction - Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds. - 1.7 - - - - - - - - - - Nucleic acid alignment folding prediction (alignment-based) - - 1.7 - Prediction of nucleic-acid folding using sequence alignments as a source of data. - - - - - - - - - - k-mer counting - - Count k-mers (substrings of length k) in DNA sequence data. - 1.7 - k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads. - - - - - - - - - - Phylogenetic tree reconstruction - - - - - - - - Reconstructing the inner node labels of a phylogenetic tree from its leafes. - Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one. - 1.7 - - - - - - - - - - Probabilistic data generation - - Generate some data from a choosen probibalistic model, possibly to evaluate algorithms. - 1.7 - - - - - - - - - - Probabilistic sequence generation - - - 1.7 - Generate sequences from some probabilistic model, e.g. a model that simulates evolution. - - - - - - - - - - Antimicrobial resistance prediction - - - - - - - - - 1.7 - Identify or predict causes for antibiotic resistance from molecular sequence analysis. - - - - - - - - - - Enrichment - - - - - - - - - A relevant ontology will be used. The input is typically a set of identifiers or other data, and the output of the analysis is typically a ranked list of ontology terms, each associated with a p-value. - Term enrichment - 1.8 - Analyse a dataset with respect to concepts from an ontology. - - - - - - - - - - Chemical class enrichment - - - - - - - - - 1.8 - Analyse a dataset with respect to concepts from an ontology of chemical structure. - - - - - - - - - - Incident curve plotting - - 1.8 - Plot an incident curve such as a survival curve, death curve, mortality curve. - - - - - - - - - - Variant pattern analysis - - Methods often utilise a database of aligned reads. - Identify and map patterns of genomic variations. - 1.8 - - - - - - - - - - Mathematical modelling - - Model some biological system using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. - beta12orEarlier - - - - - - - - - - Microscope image visualisation - - - - - - - - Visualise images resulting from various types of microscopy. - 1.9 - Microscopy image visualisation - - - - - - - - - - Image annotation - - 1.9 - Annotate an image of some sort, typically with terms from a controlled vocabulary. - - - - - - - - - - Imputation - - Data imputation - Replace missing data with substituted values, usually by using some statistical or other mathematical approach. - true - 1.9 - - - - - - - - - - Ontology visualisation - - 1.9 - Visualise, format or render data from an ontology, typically a tree of terms. - Ontology browsing - - - - - - - - - - Maximum occurence analysis - - A method for making numerical assessments about the maximum percent of time that a conformer of a flexible macromolecule can exist and still be compatible with the experimental data. - beta12orEarlier - - - - - - - - - - Database comparison - - - 1.9 - Data model comparison - Compare the models or schemas used by two or more databases, or any other general comparison of databases rather than a detailed comparison of the entries themselves. - Schema comparison - - - - - - - - - - Network simulation - - - - - - - - Simulate the bevaviour of a biological pathway or network. - Pathway simulation - Network topology simulation - 1.9 - - - - - - - - - - RNA-seq read count analysis - - Analyze read counts from RNA-seq experiments. - 1.9 - - - - - - - - - - Chemical redundancy removal - - 1.9 - Identify and remove redudancy from a set of small molecule structures. - - - - - - - - - - RNA-seq time series data analysis - - 1.9 - Analyze time series data from an RNA-seq experiment. - - - - - - - - - - Simulated gene expression data generation - - 1.9 - Simulate gene expression data, e.g. for purposes of benchmarking. - - - - - - - - - - Topic - - http://purl.org/biotop/biotop.owl#Quality - http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research - http://www.onto-med.de/ontologies/gfo.owl#Category - http://www.ifomis.org/bfo/1.1/snap#Quality - http://www.onto-med.de/ontologies/gfo.owl#Perpetuant - A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality - beta12orEarlier - http://www.ifomis.org/bfo/1.1/snap#Continuant - sumo:FieldOfStudy - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method - - - - - - - - - - Nucleic acids - - The processing and analysis of nucleic acid sequence, structural and other data. - Nucleic acid bioinformatics - Nucleic acid analysis - Nucleic acid informatics - http://purl.bioontology.org/ontology/MSH/D017423 - Nucleic acid properties - Nucleic acid physicochemistry - http://purl.bioontology.org/ontology/MSH/D017422 - beta12orEarlier - - - - - - - - - - Proteins - - Protein bioinformatics - Protein informatics - Protein databases - Protein analysis - http://purl.bioontology.org/ontology/MSH/D020539 - Archival, processing and analysis of protein data, typically molecular sequence and structural data. - beta12orEarlier - - - - - - - - - - Metabolites - - Metabolite structures - This concept excludes macromolecules such as proteins and nucleic acids. - The structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. - beta12orEarlier - - - - - - - - - - Sequence analysis - - beta12orEarlier - Sequence databases - Sequences - http://purl.bioontology.org/ontology/MSH/D017421 - The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles. - - - - - - - - - - - Structure analysis - - Computational structural biology - The curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. - http://purl.bioontology.org/ontology/MSH/D015394 - Structure analysis - Structural bioinformatics - Structure databases - This includes related concepts such as structural properties, alignments and structural motifs. - Structure data resources - beta12orEarlier - - - - - - - - - - - Structure prediction - - beta12orEarlier - The prediction of molecular (secondary or tertiary) structure. - - - - - - - - - - Alignment - - beta12orEarlier - true - The alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). - beta12orEarlier - - - - - - - - - - - Phylogeny - - Phylogeny reconstruction - Phylogenetic stratigraphy - beta12orEarlier - Phylogenetic dating - Phylogenetic clocks - http://purl.bioontology.org/ontology/MSH/D010802 - The study of evolutionary relationships amongst organisms. - Phylogenetic simulation - This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc. - - - - - - - - - - - Functional genomics - - - beta12orEarlier - The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. - - - - - - - - - - - Ontology and terminology - - Terminology - beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D002965 - Applied ontology - Ontology - The conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource. - Ontologies - - - - - - - - - - - Information retrieval - - beta12orEarlier - Data retrieval - The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information. - This includes, for example, search, query and retrieval of molecular sequences and associated data. - Data search - VT 1.3.3 Information retrieval - Data query - - - - - - - - - - Bioinformatics - - This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation. - VT 1.5.6 Bioinformatics - The archival, curation, processing and analysis of complex biological data. - http://purl.bioontology.org/ontology/MSH/D016247 - beta12orEarlier - - - - - - - - - - - Data visualisation - - Data rendering - Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data. - VT 1.2.5 Computer graphics - beta12orEarlier - Computer graphics - - - - - - - - - - Nucleic acid thermodynamics - - true - The study of the thermodynamic properties of a nucleic acid. - 1.3 - - - - - - - - - - Nucleic acid structure analysis - - Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc. - DNA melting - Nucleic acid denaturation - RNA alignment - The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. - RNA structure alignment - beta12orEarlier - Nucleic acid structure - Nucleic acid thermodynamics - RNA structure - - - - - - - - - - RNA - - beta12orEarlier - RNA sequences and structures. - - - - - - - - - - Nucleic acid restriction - - 1.3 - beta12orEarlier - Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids. - true - - - - - - - - - - Mapping - - Genetic linkage - Linkage - Linkage mapping - Synteny - DNA mapping - beta12orEarlier - The mapping of complete (typically nucleotide) sequences. - This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. - - - - - - - - - - Genetic codes and codon usage - - beta12orEarlier - true - 1.3 - Codon usage analysis - The study of codon usage in nucleotide sequence(s), genetic codes and so on. - - - - - - - - - - Protein expression - - Translation - The translation of mRNA into protein and subsequent protein processing in the cell. - beta12orEarlier - - - - - - - - - - - Gene finding - - 1.3 - This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. - Gene discovery - Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences. - beta12orEarlier - Gene prediction - true - - - - - - - - - - Transcription - - 1.3 - The transcription of DNA into mRNA. - beta12orEarlier - true - - - - - - - - - - Promoters - - true - beta12orEarlier - Promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). - beta13 - - - - - - - - - - Nucleic acid folding - - beta12orEarlier - The folding (in 3D space) of nucleic acid molecules. - true - beta12orEarlier - - - - - - - - - - Gene structure - - - This includes the study of promoters, coding regions etc. - beta12orEarlier - Gene features - Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. - - - - - - - - - - - Proteomics - - beta12orEarlier - Protein and peptide identification, especially in the study of whole proteomes of organisms. - Protein and peptide identification - Peptide identification - Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues. - http://purl.bioontology.org/ontology/MSH/D040901 - Protein expression - - - - - - - - - - - Structural genomics - - - beta12orEarlier - The elucidation of the three dimensional structure for all (available) proteins in a given organism. - - - - - - - - - - - Protein properties - - The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein. - Protein hydropathy - Protein physicochemistry - beta12orEarlier - - - - - - - - - - Protein interactions - - - Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. - Protein-nucleic acid interactions - Protein-RNA interaction - This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. - Protein-protein interactions - Protein-ligand interactions - beta12orEarlier - Protein-DNA interaction - - - - - - - - - - Protein folding, stability and design - - Protein folding - Protein stability - beta12orEarlier - Protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. - Protein residue interactions - Protein design - Rational protein design - - - - - - - - - - Two-dimensional gel electrophoresis - - Two-dimensional gel electrophoresis image and related data. - beta13 - beta12orEarlier - true - - - - - - - - - - Mass spectrometry - - beta12orEarlier - An analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. - - - - - - - - - - - Protein microarrays - - Protein microarray data. - true - beta12orEarlier - beta13 - - - - - - - - - - Protein hydropathy - - beta12orEarlier - true - The study of the hydrophobic, hydrophilic and charge properties of a protein. - 1.3 - - - - - - - - - - Protein targeting and localization - - Protein targeting - Protein sorting - The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. - Protein localization - beta12orEarlier - - - - - - - - - - Protein cleavage sites and proteolysis - - true - beta12orEarlier - 1.3 - Enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. - - - - - - - - - - Protein structure comparison - - The comparison of two or more protein structures. - beta12orEarlier - true - Use this concept for methods that are exclusively for protein structure. - beta12orEarlier - - - - - - - - - - - Protein residue interactions - - The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. - Protein residue interactions - true - 1.3 - beta12orEarlier - - - - - - - - - - Protein-protein interactions - - Protein interaction networks - true - Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc. - beta12orEarlier - 1.3 - - - - - - - - - - Protein-ligand interactions - - beta12orEarlier - true - 1.3 - Protein-ligand (small molecule) interactions. - - - - - - - - - - Protein-nucleic acid interactions - - beta12orEarlier - 1.3 - Protein-DNA/RNA interactions. - true - - - - - - - - - - Protein design - - 1.3 - beta12orEarlier - The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. - true - - - - - - - - - - G protein-coupled receptors (GPCR) - - G-protein coupled receptors (GPCRs). - true - beta12orEarlier - beta12orEarlier - - - - - - - - - - Carbohydrates - - beta12orEarlier - Carbohydrates, typically including structural information. - - - - - - - - - - Lipids - - beta12orEarlier - Lipids and their structures. - - - - - - - - - - Small molecules - - Small molecules of biological significance, typically archival, curation, processing and analysis of structural information. - Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. - CHEBI:23367 - beta12orEarlier - - - - - - - - - - Sequence editing - - beta12orEarlier - true - beta12orEarlier - Edit, convert or otherwise change a molecular sequence, either randomly or specifically. - - - - - - - - - - - Sequence composition, complexity and repeats - - Sequence complexity - Repeat sequences - The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences. - beta12orEarlier - Sequence repeats - Low complexity sequences - Sequence composition - - - - - - - - - - Sequence motifs - - beta12orEarlier - Motifs - true - 1.3 - Conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. - - - - - - - - - - Sequence comparison - - The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. - beta12orEarlier - The comparison of two or more molecular sequences, for example sequence alignment and clustering. - - - - - - - - - - Sequence sites, features and motifs - - Sequence features - The archival, detection, prediction and analysis of -positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. - Functional sites - Sequence motifs - Sequence profiles - Sequence sites - HMMs - beta12orEarlier - - - - - - - - - - Sequence database search - - beta12orEarlier - Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence). - beta12orEarlier - true - The query is a sequence-based entity such as another sequence, a motif or profile. - - - - - - - - - - Sequence clustering - - This includes systems that generate, process and analyse sequence clusters. - beta12orEarlier - true - 1.7 - The comparison and grouping together of molecular sequences on the basis of their similarities. - Sequence clusters - - - - - - - - - - Protein structural motifs and surfaces - - - This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc. - Protein structural features - Structural motifs - Protein 3D motifs - beta12orEarlier - Protein structural motifs - Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. - Protein surfaces - - - - - - - - - - Structural (3D) profiles - - The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment. - true - beta12orEarlier - 1.3 - Structural profiles - - - - - - - - - - Protein structure prediction - - - beta12orEarlier - The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. - - - - - - - - - - Nucleic acid structure prediction - - - The folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. - DNA structure prediction - Nucleic acid design - RNA structure prediction - beta12orEarlier - Nucleic acid folding - - - - - - - - - - Ab initio structure prediction - - 1.7 - The prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates. - true - beta12orEarlier - - - - - - - - - - Homology modelling - - 1.4 - The modelling of the three-dimensional structure of a protein using known sequence and structural data. - true - beta12orEarlier - - - - - - - - - - Molecular dynamics - - This includes resources concerning flexibility and motion in protein and other molecular structures. - Protein dynamics - Molecular flexibility - Molecular motions - beta12orEarlier - The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. - - - - - - - - - - Molecular docking - - beta12orEarlier - The modelling the structure of proteins in complex with small molecules or other macromolecules. - - - - - - - - - - Protein secondary structure prediction - - beta12orEarlier - 1.3 - The prediction of secondary or supersecondary structure of protein sequences. - true - - - - - - - - - - - Protein tertiary structure prediction - - 1.3 - true - The prediction of tertiary structure of protein sequences. - beta12orEarlier - - - - - - - - - - - Protein fold recognition - - For example threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). - The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). - beta12orEarlier - - - - - - - - - - Sequence alignment - - This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. - beta12orEarlier - 1.7 - The alignment of molecular sequences or sequence profiles (representing sequence alignments). - true - - - - - - - - - - Structure alignment - - The superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). - This includes the generation, storage, analysis, rendering etc. of structure alignments. - true - 1.7 - beta12orEarlier - - - - - - - - - - Threading - - Sequence-structure alignment - 1.3 - beta12orEarlier - The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). - true - - - - - - - - - - Sequence profiles and HMMs - - true - Sequence profiles; typically a positional, numerical matrix representing a sequence alignment. - beta12orEarlier - 1.3 - Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. - - - - - - - - - - Phylogeny reconstruction - - The reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. - 1.3 - true - Currently too specific for the topic sub-ontology (but might be unobsoleted). - beta12orEarlier - - - - - - - - - - Phylogenomics - - - beta12orEarlier - The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. - - - - - - - - - - - Virtual PCR - - beta13 - Polymerase chain reaction - beta12orEarlier - Simulated polymerase chain reaction (PCR). - PCR - true - - - - - - - - - - Sequence assembly - - Assembly - The assembly of fragments of a DNA sequence to reconstruct the original sequence. - beta12orEarlier - This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. - - - - - - - - - - Genetic variation - - - http://purl.bioontology.org/ontology/MSH/D014644 - Stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. - DNA variation - Mutation - Polymorphism - beta12orEarlier - - - - - - - - - - Microarrays - - true - http://purl.bioontology.org/ontology/MSH/D046228 - Microarrays, for example, to process microarray data or design probes and experiments. - 1.3 - DNA microarrays - beta12orEarlier - - - - - - - - - - Pharmacology - - Computational pharmacology - beta12orEarlier - Pharmacoinformatics - The study of drugs and their effects or responses in living systems. - VT 3.1.7 Pharmacology and pharmacy - - - - - - - - - - - Gene expression - - This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on. - Gene expression profiling - Expression profiling - beta12orEarlier - http://edamontology.org/topic_0197 - Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc. - http://purl.bioontology.org/ontology/MSH/D015870 - Gene expression analysis - DNA microarrays - The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. - Codon usage - - - - - - - - - - - Gene regulation - - beta12orEarlier - The regulation of gene expression. - - - - - - - - - - Pharmacogenomics - - - beta12orEarlier - The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. - - - - - - - - - - - Medicinal chemistry - - - VT 3.1.4 Medicinal chemistry - The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes. - This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. - Drug design - beta12orEarlier - - - - - - - - - - - Fish - - beta12orEarlier - true - 1.3 - Information on a specific fish genome including molecular sequences, genes and annotation. - - - - - - - - - - Flies - - 1.3 - true - beta12orEarlier - Information on a specific fly genome including molecular sequences, genes and annotation. - - - - - - - - - - Mice or rats - - Information on a specific mouse or rat genome including molecular sequences, genes and annotation. - The resource may be specific to a group of mice / rats or all mice / rats. - beta12orEarlier - - - - - - - - - - Worms - - true - 1.3 - beta12orEarlier - Information on a specific worm genome including molecular sequences, genes and annotation. - - - - - - - - - - Literature analysis - - beta12orEarlier - 1.3 - The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query. - true - - - - - - - - - - Data mining - - beta12orEarlier - Text data mining - The analysis of the biomedical and informatics literature. - Literature analysis - Text mining - Literature mining - - - - - - - - - - - Data deposition, annotation and curation - - Deposition and curation of database accessions, including annotation, typically with terms from a controlled vocabulary. - Database curation - beta12orEarlier - - - - - - - - - - - Document, record and content management - - Document management - File management - This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. - Content management - The management and manipulation of digital documents, including database records, files and reports. - VT 1.3.6 Multimedia, hypermedia - Record management - beta12orEarlier - - - - - - - - - - Sequence annotation - - beta12orEarlier - beta12orEarlier - true - Annotation of a molecular sequence. - - - - - - - - - - Genome annotation - - Annotation of a genome. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - - NMR - - - ROESY - NOESY - Nuclear Overhauser Effect Spectroscopy - An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. - HOESY - beta12orEarlier - Heteronuclear Overhauser Effect Spectroscopy - Nuclear magnetic resonance spectroscopy - Spectroscopy - NMR spectroscopy - Rotational Frame Nuclear Overhauser Effect Spectroscopy - - - - - - - - - - - Sequence classification - - beta12orEarlier - The classification of molecular sequences based on some measure of their similarity. - Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. - - - - - - - - - - Protein classification - - 1.3 - true - beta12orEarlier - primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc. - - - - - - - - - - Sequence motif or profile - - beta12orEarlier - true - Sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type. - This includes comparison, discovery, recognition etc. of sequence motifs. - beta12orEarlier - - - - - - - - - - - Protein modifications - - GO:0006464 - Protein chemical modifications, e.g. post-translational modifications. - Protein post-translational modification - MOD:00000 - EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) - beta12orEarlier - - - - - - - - - - Molecular interactions, pathways and networks - - Biological networks - Network or pathway analysis - beta13 - Molecular interactions - Biological models - Molecular interactions, biological pathways, networks and other models. - Biological pathways - http://edamontology.org/topic_3076 - - - - - - - - - - - Informatics - - The study and practice of information processing and use of computer information systems. - VT 1.3.99 Other - Knowledge management - VT 1.3.4 Information management - beta12orEarlier - Information management - VT 1.3.5 Knowledge management - VT 1.3.3 Information retrieval - VT 1.3 Information sciences - Information science - - - - - - - - - Literature data resources - - Data resources for the biological or biomedical literature, either a primary source of literature or some derivative. - true - 1.3 - beta12orEarlier - - - - - - - - - - Laboratory information management - - Laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. - beta12orEarlier - Laboratory resources - - - - - - - - - - - - Cell and tissue culture - - Tissue culture - 1.3 - true - General cell culture or data on a specific cell lines. - Cell culture - beta12orEarlier - - - - - - - - - - Ecology - - The ecological and environmental sciences and especially the application of information technology (ecoinformatics). - http://purl.bioontology.org/ontology/MSH/D004777 - Ecological informatics - VT 1.5.15 Ecology - Computational ecology - beta12orEarlier - Ecoinformatics - Environmental science - - - - - - - - - - - Electron microscopy - - - SEM - Scanning electron microscopy - TEM - The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light. - - Transmission electron microscopy - beta12orEarlier - Electron crystallography - Electron diffraction experiment - Single particle electron microscopy - - - - - - - - - - - Cell cycle - - beta13 - beta12orEarlier - true - The cell cycle including key genes and proteins. - - - - - - - - - - Peptides and amino acids - - beta12orEarlier - The physicochemical, biochemical or structural properties of amino acids or peptides. - Amino acids - Peptides - - - - - - - - - - Organelles - - Cell membrane - Cytoplasm - Organelle genes and proteins - Smooth endoplasmic reticulum - beta12orEarlier - Lysosome - Centriole - Ribosome - Nucleus - true - A specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). - Mitochondria - Golgi apparatus - Rough endoplasmic reticulum - 1.3 - - - - - - - - - - Ribosomes - - beta12orEarlier - Ribosomes, typically of ribosome-related genes and proteins. - Ribosome genes and proteins - 1.3 - true - - - - - - - - - - Scents - - A database about scents. - beta12orEarlier - beta13 - true - - - - - - - - - - Drugs and target structures - - - Drug structures - beta12orEarlier - The structures of drugs, drug target, their interactions and binding affinities. - Target structures - - - - - - - - - - - Model organisms - - This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism. - beta12orEarlier - A specific organism, or group of organisms, used to study a particular aspect of biology. - Organisms - - - - - - - - - - - Genomics - - http://purl.bioontology.org/ontology/MSH/D023281 - beta12orEarlier - Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. - - - - - - - - - - - Gene families - - Particular gene(s), gene family or other gene group or system and their encoded proteins. - beta12orEarlier - Gene family - Gene system - Genes, gene family or system - Gene and protein families - - - - - - - - - - - Chromosomes - - beta12orEarlier - Study of chromosomes. - - - - - - - - - - Genotype and phenotype - - Genotype and phenotype resources - The study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. - Genotyping - Phenotyping - beta12orEarlier - - - - - - - - - - - Gene expression and microarray - - true - beta12orEarlier - beta12orEarlier - Gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc. - - - - - - - - - - - Sequence design - - Probes - This includes the design of primers for PCR and DNA amplification or the design of molecular probes. - http://purl.bioontology.org/ontology/MSH/D015335 - Gene design - Molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR). - Probe design - in silico cloning - Primer design - Primers - beta12orEarlier - - - - - - - - - - Pathology - - Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. - beta12orEarlier - Diseases - VT 3.1.6 Pathology - - - - - - - - - - - Specific protein resources - - 1.3 - A particular protein, protein family or other group of proteins. - true - Specific protein - beta12orEarlier - - - - - - - - - - Taxonomy - - beta12orEarlier - VT 1.5.25 Taxonomy - Organism classification, identification and naming. - - - - - - - - - - Protein sequence analysis - - beta12orEarlier - Archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. - 1.8 - true - - - - - - - - - - Nucleic acid sequence analysis - - beta12orEarlier - 1.8 - true - The archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. - - - - - - - - - - - Repeat sequences - - true - The repetitive nature of molecular sequences. - beta12orEarlier - 1.3 - - - - - - - - - - Low complexity sequences - - true - The (character) complexity of molecular sequences, particularly regions of low complexity. - 1.3 - beta12orEarlier - - - - - - - - - - Proteome - - A specific proteome including protein sequences and annotation. - beta12orEarlier - beta13 - true - - - - - - - - - - DNA - - DNA analysis - beta12orEarlier - DNA sequences and structure, including processes such as methylation and replication. - The DNA sequences might be coding or non-coding sequences. - - - - - - - - - - Coding RNA - - EST - cDNA - mRNA - This includes expressed sequence tag (EST) or complementary DNA (cDNA) sequences. - Protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames - beta12orEarlier - - - - - - - - - - Functional, regulatory and non-coding RNA - - - ncRNA - Non-coding RNA - Functional RNA - Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). - Regulatory RNA - Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA). - beta12orEarlier - - - - - - - - - - rRNA - - 1.3 - One or more ribosomal RNA (rRNA) sequences. - true - - - - - - - - - - tRNA - - 1.3 - true - One or more transfer RNA (tRNA) sequences. - - - - - - - - - - Protein secondary structure - - true - beta12orEarlier - 1.8 - Protein secondary structure or secondary structure alignments. - This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. - - - - - - - - - - RNA structure - - 1.3 - RNA secondary or tertiary structure and alignments. - beta12orEarlier - true - - - - - - - - - - Protein tertiary structure - - 1.8 - true - Protein tertiary structures. - beta12orEarlier - - - - - - - - - - Nucleic acid classification - - Classification of nucleic acid sequences and structures. - 1.3 - true - beta12orEarlier - - - - - - - - - - Protein families - - beta12orEarlier - Protein sequence classification - Protein secondary databases - A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. - Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group. - - - - - - - - - - - Protein domains and folds - - beta12orEarlier - Protein folds - Protein tertiary structural domains and folds. - Protein domains - - - - - - - - - - Nucleic acid sequence alignment - - beta12orEarlier - true - 1.3 - Nucleotide sequence alignments. - - - - - - - - - - Protein sequence alignment - - 1.3 - Protein sequence alignments. - beta12orEarlier - true - A sequence profile typically represents a sequence alignment. - - - - - - - - - - Nucleic acid sites and features - - beta12orEarlier - 1.3 - true - The archival, detection, prediction and analysis of -positional features such as functional sites in nucleotide sequences. - - - - - - - - - - - Protein sites and features - - beta12orEarlier - The detection, identification and analysis of positional features in proteins, such as functional sites. - 1.3 - true - - - - - - - - - - - Transcription factors and regulatory sites - - - - Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators. - Proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. - Transcriptional regulatory sites - TFBS - Transcription factors - beta12orEarlier - Transcription factor binding sites - - - - - - - - - - Phosphorylation sites - - 1.0 - Protein phosphorylation and phosphorylation sites in protein sequences. - true - beta12orEarlier - - - - - - - - - - - Metabolic pathways - - beta12orEarlier - Metabolic pathways. - - - - - - - - - - Signaling pathways - - Signaling pathways. - Signal transduction pathways - beta12orEarlier - - - - - - - - - - Protein and peptide identification - - 1.3 - beta12orEarlier - true - - - - - - - - - - Workflows - - Biological or biomedical analytical workflows or pipelines. - beta12orEarlier - true - 1.0 - - - - - - - - - Data types and objects - - Structuring data into basic types and (computational) objects. - beta12orEarlier - 1.0 - true - - - - - - - - - - Theoretical biology - - 1.3 - true - - - - - - - - - - Mitochondria - - beta12orEarlier - true - Mitochondria, typically of mitochondrial genes and proteins. - 1.3 - - - - - - - - - - Plants - - The resource may be specific to a plant, a group of plants or all plants. - Plant science - Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. - Plant biology - Botany - VT 1.5.22 Plant science - Plant - VT 1.5.10 Botany - beta12orEarlier - - - - - - - - - - Viruses - - Virology - VT 1.5.28 Virology - beta12orEarlier - Viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. - The resource may be specific to a virus, a group of viruses or all viruses. - - - - - - - - - - Fungi - - Mycology - beta12orEarlier - The resource may be specific to a fungus, a group of fungi or all fungi. - Yeast - VT 1.5.21 Mycology - Fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. - - - - - - - - - - Pathogens - - Pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. - beta12orEarlier - The resource may be specific to a pathogen, a group of pathogens or all pathogens. - - - - - - - - - - Arabidopsis - - beta12orEarlier - Arabidopsis-specific data. - 1.3 - true - - - - - - - - - - Rice - - Rice-specific data. - true - 1.3 - beta12orEarlier - - - - - - - - - - Genetic mapping and linkage - - Linkage mapping - beta12orEarlier - 1.3 - true - Genetic linkage - Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. - - - - - - - - - - Comparative genomics - - The study (typically comparison) of the sequence, structure or function of multiple genomes. - beta12orEarlier - - - - - - - - - - - Mobile genetic elements - - - Transposons - beta12orEarlier - Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. - - - - - - - - - - Human disease - - Human diseases, typically describing the genes, mutations and proteins implicated in disease. - beta13 - true - beta12orEarlier - - - - - - - - - - Immunology - - VT 3.1.3 Immunology - Immunoinformatics - http://purl.bioontology.org/ontology/MSH/D007120 - http://purl.bioontology.org/ontology/MSH/D007125 - beta12orEarlier - Computational immunology - The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. - - - - - - - - - - - Membrane and lipoproteins - - Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. - beta12orEarlier - Membrane proteins - Lipoproteins - Transmembrane proteins - - - - - - - - - - Enzymes - - Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. - beta12orEarlier - Enzymology - - - - - - - - - - Primers - - PCR primers and hybridization oligos in a nucleic acid sequence. - Nucleic acid features (primers) - beta12orEarlier - Primer binding sites - - - - - - - - - - - PolyA signal or sites - - beta12orEarlier - Nucleic acid features (PolyA signal or site) - PolyA signal - A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. - PolyA site - Regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. - - - - - - - - - - - CpG island and isochores - - beta12orEarlier - Nucleic acid features (CpG island and isochore) - CpG rich regions (isochores) in a nucleotide sequence. - - - - - - - - - - - Restriction sites - - Restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. - Nucleic acid features (restriction sites) - beta12orEarlier - Nucleic acid restriction sites (report) - - - - - - - - - - - Splice sites - - - Nucleic acid features (splice sites) - Nucleic acid report (RNA splicing) - beta12orEarlier - Splice sites in a nucleotide sequence or alternative RNA splicing events. - Nucleic acid report (RNA splice model) - - - - - - - - - - - Matrix/scaffold attachment sites - - Nucleic acid features (matrix/scaffold attachment sites) - beta12orEarlier - Matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. - - - - - - - - - - - Operon - - Gene features (operon) - beta12orEarlier - Nucleic acid features (operon) - The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. - Operons (operators, promoters and genes) from a bacterial genome. - - - - - - - - - - - Promoters - - Whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. - beta12orEarlier - Nucleic acid features (promoters) - - - - - - - - - - - Structural biology - - Structural assignment - Structure determination - This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. - 1.3 - This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy. Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen. - The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. - VT 1.5.24 Structural biology - Structural determination - - - - - - - - - - - Protein membrane regions - - - 1.8 - Protein features (membrane regions) - This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. - Intramembrane regions - Trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. - Protein transmembrane regions - Transmembrane regions - - - - - - - - - - - Structure comparison - - This might involve comparison of secondary or tertiary (3D) structural information. - The comparison of two or more molecular structures, for example structure alignment and clustering. - beta12orEarlier - - - - - - - - - - - Function analysis - - Protein function prediction - The study of gene and protein function including the prediction of functional properties of a protein. - Protein function analysis - beta12orEarlier - - - - - - - - - - - Prokaryotes and archae - - The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. - VT 1.5.2 Bacteriology - Bacteriology - beta12orEarlier - Specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation. - - - - - - - - - - Protein databases - - true - 1.3 - Protein data resources. - beta12orEarlier - Protein data resources - - - - - - - - - - Structure determination - - Experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. - beta12orEarlier - true - 1.3 - - - - - - - - - - Cell biology - - beta12orEarlier - VT 1.5.11 Cell biology - Cells, such as key genes and proteins involved in the cell cycle. - - - - - - - - - - Classification - - beta13 - beta12orEarlier - Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships. - true - - - - - - - - - - Lipoproteins - - true - 1.3 - beta12orEarlier - Lipoproteins (protein-lipid assemblies). - - - - - - - - - - Phylogeny visualisation - - true - Visualise a phylogeny, for example, render a phylogenetic tree. - beta12orEarlier - beta12orEarlier - - - - - - - - - - Cheminformatics - - The application of information technology to chemistry in biological research environment. - Chemical informatics - beta12orEarlier - Chemoinformatics - - - - - - - - - - - Systems biology - - http://en.wikipedia.org/wiki/Systems_biology - This includes databases of models and methods to construct or analyse a model. - Biological models - http://purl.bioontology.org/ontology/MSH/D049490 - beta12orEarlier - Biological modelling - Biological system modelling - The holistic modelling and analysis of complex biological systems and the interactions therein. - - - - - - - - - - - Statistics and probability - - Biostatistics - The application of statistical methods to biological problems. - http://en.wikipedia.org/wiki/Biostatistics - beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D056808 - - - - - - - - - - - Structure database search - - The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. - beta12orEarlier - Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure). - beta12orEarlier - true - - - - - - - - - - Molecular modelling - - Homology modeling - Comparative modeling - Comparative modelling - beta12orEarlier - Homology modelling - Molecular modeling - The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. - - - - - - - - - - Protein function prediction - - 1.2 - beta12orEarlier - true - The prediction of functional properties of a protein. - - - - - - - - - - SNP - - Single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. - beta12orEarlier - Single nucleotide polymorphism - A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. - - - - - - - - - - Transmembrane protein prediction - - Predict transmembrane domains and topology in protein sequences. - beta12orEarlier - beta12orEarlier - true - - - - - - - - - - - Nucleic acid structure comparison - - The comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. - beta12orEarlier - true - beta12orEarlier - Use this concept for methods that are exclusively for nucleic acid structures. - - - - - - - - - - - Exons - - Gene features (exon) - beta12orEarlier - Exons in a nucleotide sequences. - - - - - - - - - - - Gene transcription features - - GC signals (report) - CAAT signals (report) - -35 signals (report) - Gene transcriptional features - This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. - Enhancers (report) - Terminators (report) - Transcription of DNA into RNA including the regulation of transcription. - Ribosome binding sites (report) - -10 signals (report) - beta12orEarlier - TATA signals (report) - Attenuators (report) - - - - - - - - - - - DNA mutation - - - Mutation annotation - beta12orEarlier - DNA mutation. - Nucleic acid features (mutation) - - - - - - - - - - - Oncology - - beta12orEarlier - VT 3.2.16 Oncology - Cancer - The study of cancer, for example, genes and proteins implicated in cancer. - Cancer biology - - - - - - - - - - - Toxins and targets - - - Toxins - Targets - beta12orEarlier - Structural and associated data for toxic chemical substances. - - - - - - - - - - - Introns - - Gene features (intron) - Nucleic acid features (intron) - Introns in a nucleotide sequences. - beta12orEarlier - - - - - - - - - - - Tool topic - - beta12orEarlier - A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool. - true - beta12orEarlier - - - - - - - - - - Study topic - - A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding. - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - Nomenclature - - true - 1.3 - beta12orEarlier - Biological nomenclature (naming), symbols and terminology. - - - - - - - - - - Disease genes and proteins - - 1.3 - true - beta12orEarlier - The genes, gene variations and proteins involved in one or more specific diseases. - - - - - - - - - - Protein structure analysis - - Protein structure - Protein secondary or tertiary structural data and/or associated annotation. - http://edamontology.org/topic_3040 - beta12orEarlier - - - - - - - - - - - Humans - - beta12orEarlier - true - The human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general. - - - - - - - - - - Gene resources - - Gene resource - beta12orEarlier - 1.3 - Informatics resource (typically a database) primarily focussed on genes. - Gene database - true - - - - - - - - - - Yeast - - beta12orEarlier - Yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation. - true - 1.3 - - - - - - - - - - Eukaryotes - - Eukaryote - Eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation. - The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. - beta12orEarlier - - - - - - - - - - Invertebrates - - The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. - beta12orEarlier - Invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation. - - - - - - - - - - Vertebrates - - The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. - Vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. - beta12orEarlier - - - - - - - - - - Unicellular eukaryotes - - Unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation. - beta12orEarlier - The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. - - - - - - - - - - Protein structure alignment - - Protein secondary or tertiary structure alignments. - beta12orEarlier - true - 1.3 - - - - - - - - - - X-ray diffraction - - - The study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample. - beta12orEarlier - X-ray microscopy - Crystallography - X-ray crystallography - - - - - - - - - - - Ontologies, nomenclature and classification - - true - Conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics. - 1.3 - http://purl.bioontology.org/ontology/MSH/D002965 - beta12orEarlier - - - - - - - - - - Immunoproteins, genes and antigens - - - Immunopeptides - Immunity-related genes, proteins and their ligands. - Antigens - This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." - beta12orEarlier - Immunoproteins - Immunogenes - - - - - - - - - - - Molecules - - CHEBI:23367 - beta12orEarlier - beta12orEarlier - Specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. - true - - - - - - - - - - Toxicology - - - Toxins and the adverse effects of these chemical substances on living organisms. - VT 3.1.9 Toxicology - Toxicoinformatics - Toxicology - beta12orEarlier - Computational toxicology - - - - - - - - - - - High-throughput sequencing - - Next-generation sequencing - beta13 - true - beta12orEarlier - Parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously. - - - - - - - - - - Structural clustering - - The comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters. - 1.7 - Structure classification - true - beta12orEarlier - - - - - - - - - - Gene regulatory networks - - - Gene regulatory networks. - beta12orEarlier - - - - - - - - - - Disease (specific) - - Informatics resources dedicated to one or more specific diseases (not diseases in general). - beta12orEarlier - true - beta12orEarlier - - - - - - - - - - VNTR - - Nucleic acid features (VNTR) - Variable number of tandem repeat polymorphism - Variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. - beta12orEarlier - VNTR annotation - VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. - - - - - - - - - - - Microsatellites - - beta12orEarlier - Nucleic acid features (microsatellite) - A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. - Microsatellite annotation - Microsatellite polymorphism in a DNA sequence. - - - - - - - - - - - RFLP - - Restriction fragment length polymorphisms (RFLP) in a DNA sequence. - An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. - RFLP annotation - beta12orEarlier - Nucleic acid features (RFLP) - - - - - - - - - - - DNA polymorphism - - - Nucleic acid features (polymorphism) - DNA polymorphism. - Polymorphism annotation - beta12orEarlier - - - - - - - - - - - Nucleic acid design - - Topic for the design of nucleic acid sequences with specific conformations. - 1.3 - beta12orEarlier - true - - - - - - - - - - Primer or probe design - - 1.3 - true - beta13 - The design of primers for PCR and DNA amplification or the design of molecular probes. - - - - - - - - - - Structure databases - - beta13 - true - 1.2 - Structure data resources - Molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. - - - - - - - - - - Nucleic acid structure - - true - beta13 - Nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation. - 1.2 - - - - - - - - - - Sequence databases - - Molecular sequence data resources, including sequence sites, alignments, motifs and profiles. - true - beta13 - Sequence data resources - Sequence data - Sequence data resource - 1.3 - - - - - - - - - - Nucleic acid sequences - - Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. - beta13 - 1.3 - true - Nucleotide sequences - - - - - - - - - - Protein sequences - - Protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles. - beta13 - 1.3 - true - - - - - - - - - - Protein interaction networks - - 1.3 - true - - - - - - - - - - Molecular biology - - VT 1.5.4 Biochemistry and molecular biology - beta13 - The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. - - - - - - - - - - - Mammals - - true - beta13 - 1.3 - Mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. - - - - - - - - - - Biodiversity - - The degree of variation of life forms within a given ecosystem, biome or an entire planet. - beta13 - VT 1.5.5 Biodiversity conservation - http://purl.bioontology.org/ontology/MSH/D044822 - - - - - - - - - - - Sequence clusters and classification - - This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. - The comparison, grouping together and classification of macromolecules on the basis of sequence similarity. - Sequence families - 1.3 - true - Sequence clusters - beta13 - - - - - - - - - - Genetics - - http://purl.bioontology.org/ontology/MSH/D005823 - The study of genes, genetic variation and heredity in living organisms. - beta13 - Heredity - - - - - - - - - - - Quantitative genetics - - beta13 - The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). - - - - - - - - - - Population genetics - - The distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. - beta13 - - - - - - - - - - - Regulatory RNA - - 1.3 - Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). - true - beta13 - - - - - - - - - - Documentation and help - - The documentation of resources such as tools, services and databases and how to get help. - Help - beta13 - Documentation - - - - - - - - - - - Genetic organisation - - The structural and functional organisation of genes and other genetic elements. - 1.3 - beta13 - true - - - - - - - - - - Medical informatics - - Health informatics - Clinical informatics - Biomedical informatics - Translational medicine - The application of information technology to health, disease and biomedicine. - Healthcare informatics - beta13 - Health and disease - Molecular medicine - - - - - - - - - - - Developmental biology - - VT 1.5.14 Developmental biology - beta13 - How organisms grow and develop. - - - - - - - - - - - Embryology - - beta13 - The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. - - - - - - - - - - - Anatomy - - VT 3.1.1 Anatomy and morphology - beta13 - The form and function of the structures of living organisms. - - - - - - - - - - - Literature and reference - - Literature search - beta13 - The scientific literature, reference information and documentation. - Literature sources - http://purl.bioontology.org/ontology/MSH/D011642 - - - - - - - - - - - Biology - - VT 1.5.8 Biology - beta13 - VT 1.5 Biological sciences - VT 1.5.23 Reproductive biology - Cryobiology - Biological rhythms - A particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on. - VT 1.5.7 Biological rhythm - Biological science - Aerobiology - VT 1.5.99 Other - Chronobiology - VT 1.5.13 Cryobiology - - VT 1.5.1 Aerobiology - VT 1.5.3 Behavioural biology - Reproductive biology - Behavioural biology - - - - - - - - - - - Data management - - The development and use of architectures, policies, practices and procedures for management of data. - beta13 - Data handling - http://purl.bioontology.org/ontology/MSH/D030541 - VT 1.3.1 Data management - - - - - - - - - - - Sequence feature detection - - 1.3 - true - beta13 - The detection of the positional features, such as functional and other key sites, in molecular sequences. - http://purl.bioontology.org/ontology/MSH/D058977 - - - - - - - - - - Nucleic acid feature detection - - The detection of positional features such as functional sites in nucleotide sequences. - true - beta13 - 1.3 - - - - - - - - - - Protein feature detection - - The detection, identification and analysis of positional protein sequence features, such as functional sites. - beta13 - 1.3 - true - - - - - - - - - - Biological system modelling - - 1.2 - true - beta13 - Topic for modelling biological systems in mathematical terms. - - - - - - - - - - Data acquisition - - The acquisition of data, typically measurements of physical systems using any type of sampling system, or by another other means. - beta13 - - - - - - - - - - Genes and proteins resources - - 1.3 - Gene family - beta13 - Gene and protein families - Specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. - true - - - - - - - - - - Protein topological domains - - - Topological domains such as cytoplasmic regions in a protein. - Protein features (topological domains) - 1.8 - - - - - - - - - - - Protein variants - - protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. - beta13 - - - - - - - - - - - Expression signals - - - beta13 - Nucleic acid features (expression signal) - Regions within a nucleic acid sequence containing a signal that alters a biological function. - - - - - - - - - - - DNA binding sites - - - This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). - beta13 - Nucleic acid features (binding) - Nucleic acids binding to some other molecule. - - - - - - - - - - - Nucleic acid repeats - - beta13 - This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. - Repetitive elements within a nucleic acid sequence. - - - - - - - - - - - DNA replication and recombination - - DNA replication or recombination. - This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. - Nucleosome exclusion sequences - Nucleic acid features (replication and recombination) - beta13 - - - - - - - - - - - Signal or transit peptide - - beta13 - Nucleic acid features (signal or transit peptide) - A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. - Coding sequences for a signal or transit peptide. - - - - - - - - - - - Sequence tagged sites - - Nucleic acid features (STS) - beta13 - Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. - Sequence tagged sites (STS) in nucleic acid sequences. - - - - - - - - - - - Sequencing - - http://purl.bioontology.org/ontology/MSH/D059014 - 1.1 - NGS - Next generation sequencing - The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. - Next gen sequencing - - - - - - - - - - - ChIP-seq - - true - 1.3 - Chip sequencing - Chip seq - 1.1 - The analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. - Chip-sequencing - - - - - - - - - - RNA-Seq - - Small RNA-seq - Whole transcriptome shotgun sequencing - RNA-seq - 1.1 - 1.3 - A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. - Small RNA-Seq - WTSS - This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. - true - - - - - - - - - - DNA methylation - - true - DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. - 1.3 - http://purl.bioontology.org/ontology/MSH/D019175 - 1.1 - - - - - - - - - - Metabolomics - - The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism. - http://purl.bioontology.org/ontology/MSH/D055432 - 1.1 - - - - - - - - - - - Epigenomics - - - Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. - 1.1 - http://purl.bioontology.org/ontology/MSH/D057890 - The study of the epigenetic modifications of a whole cell, tissue, organism etc. - - - - - - - - - - - Metagenomics - - - http://purl.bioontology.org/ontology/MSH/D056186 - Ecogenomics - Community genomics - Environmental genomics - 1.1 - The study of genetic material recovered from environmental samples, and associated environmental data. - - - - - - - - - - - Structural variation - - - 1.1 - Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. - Genomic structural variation - - - - - - - - - - DNA packaging - - beta12orEarlier - DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. - http://purl.bioontology.org/ontology/MSH/D042003 - - - - - - - - - - DNA-Seq - - 1.1 - A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements. - 1.3 - DNA-seq - true - - - - - - - - - - RNA-Seq alignment - - true - 1.3 - RNA-seq alignment - The alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. - beta12orEarlier - - - - - - - - - - ChIP-on-chip - - true - 1.3 - 1.1 - Experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. - ChIP-chip - - - - - - - - - - Data security - - 1.3 - Data privacy - The protection of data, such as patient health data, from damage or unwanted access from unauthorized users. - - - - - - - - - - Sample collections - - samples - biobanking - 1.3 - biosamples - Biological samples and specimens. - Specimen collections - - - - - - - - - - - Biochemistry - - - VT 1.5.4 Biochemistry and molecular biology - Chemical biology - 1.3 - Biological chemistry - Chemical substances and physico-chemical processes and that occur within living organisms. - - - - - - - - - - - Phylogenetics - - - The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). - 1.3 - http://purl.bioontology.org/ontology/MSH/D010802 - - - - - - - - - - Epigenetics - - Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. - DNA methylation - This includes sub-topics such as histone modification and DNA methylation. - http://purl.bioontology.org/ontology/MSH/D019175 - Histone modification - 1.3 - - - - - - - - - - - Biotechnology - - 1.3 - The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. - - - - - - - - - - - Phenomics - - - Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. - 1.3 - - - - - - - - - - - Evolutionary biology - - VT 1.5.16 Evolutionary biology - 1.3 - The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. - - - - - - - - - - - Physiology - - The functions of living organisms and their constituent parts. - 1.3 - VT 3.1.8 Physiology - - - - - - - - - - - Microbiology - - The biology of microorganisms. - 1.3 - VT 1.5.20 Microbiology - - - - - - - - - - - Parasitology - - 1.3 - The biology of parasites. - - - - - - - - - - - Medicine - - General medicine - Research in support of healing by diagnosis, treatment, and prevention of disease. - 1.3 - VT 3.1 Basic medicine - VT 3.2.9 General and internal medicine - Experimental medicine - Biomedical research - Clinical medicine - VT 3.2 Clinical medicine - Internal medicine - - - - - - - - - - - Neurobiology - - Neuroscience - 1.3 - The study of the nervous system and brain; its anatomy, physiology and function. - VT 3.1.5 Neuroscience - - - - - - - - - - - Public health and epidemiology - - VT 3.3.1 Epidemiology - Topic concerning the the patterns, cause, and effect of disease within populations. - 1.3 - Public health - Epidemiology - - - - - - - - - - - Biophysics - - - 1.3 - VT 1.5.9 Biophysics - The use of physics to study biological system. - - - - - - - - - - - Computational biology - - - VT 1.5.19 Mathematical biology - VT 1.5.12 Computational biology - This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology). - Mathematical biology - VT 1.5.26 Theoretical biology - Theoretical biology - 1.3 - The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. - Biomathematics - - - - - - - - - - - Transcriptomics - - - The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. - Transcriptome - 1.3 - - - - - - - - - - - Chemistry - - VT 1.7.10 Polymer science - VT 1.7.7 Mathematical chemistry - VT 1.7.3 Colloid chemistry - 1.3 - Mathematical chemistry - Physical chemistry - VT 1.7.9 Physical chemistry - Polymer science - Chemical science - Organic chemistry - VT 1.7.6 Inorganic and nuclear chemistry - VT 1.7 Chemical sciences - VT 1.7.5 Electrochemistry - Inorganic chemistry - VT 1.7.2 Chemistry - Nuclear chemistry - VT 1.7.8 Organic chemistry - The composition and properties of matter, reactions, and the use of reactions to create new substances. - - - - - - - - - - - Mathematics - - The study of numbers (quantity) and other topics including structure, space, and change. - VT:1.1 Mathematics - Maths - VT 1.1.99 Other - 1.3 - - - - - - - - - - - Computer science - - 1.3 - VT 1.2 Computer sciences - VT 1.2.99 Other - The theory and practical use of computer systems. - - - - - - - - - - - Physics - - The study of matter, space and time, and related concepts such as energy and force. - 1.3 - - - - - - - - - - - RNA splicing - - - RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons. - This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. - 1.3 - - - - - - - - - - Molecular genetics - - 1.3 - The structure and function of genes at a molecular level. - - - - - - - - - - - Respiratory medicine - - VT 3.2.25 Respiratory systems - Pulmonology - The study of respiratory system. - Pulmonary medicine - Respiratory disease - 1.3 - Pulmonary disorders - - - - - - - - - - - Metabolic disease - - The study of metabolic diseases. - 1.4 - 1.3 - true - - - - - - - - - - Infectious disease - - Transmissable disease - VT 3.3.4 Infectious diseases - Communicable disease - The branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions). - 1.3 - - - - - - - - - - - Rare diseases - - 1.3 - The study of rare diseases. - - - - - - - - - - - Computational chemistry - - - 1.3 - VT 1.7.4 Computational chemistry - Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. - - - - - - - - - - - Neurology - - Neurological disorders - 1.3 - The branch of medicine that deals with the anatomy, functions and disorders of the nervous system. - - - - - - - - - - - Cardiology - - Cardiovascular disease - VT 3.2.4 Cardiac and Cardiovascular systems - 1.3 - Cardiovascular medicine - Heart disease - VT 3.2.22 Peripheral vascular disease - The diseases and abnormalities of the heart and circulatory system. - - - - - - - - - - - Drug discovery - - - The discovery and design of drugs or potential drug compounds. - This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. - 1.3 - - - - - - - - - - - Biobank - - biobanking - 1.3 - Repositories of biological samples, typically human, for basic biological and clinical research. - Tissue collection - - - - - - - - - - - Mouse clinic - - 1.3 - Laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. - - - - - - - - - - - Microbial collection - - Collections of microbial cells including bacteria, yeasts and moulds. - 1.3 - - - - - - - - - - - Cell culture collection - - 1.3 - Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells. - - - - - - - - - - - Clone library - - 1.3 - Collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. - - - - - - - - - - - Translational medicine - - 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. - 1.3 - - - - - - - - - - - Compound libraries and screening - - Translational medicine - Chemical library - Collections of chemicals, typically for use in high-throughput screening experiments. - Compound library - Chemical screening - 1.3 - - - - - - - - - - - Biomedical science - - - Topic concerning biological science that is (typically) performed in the context of medicine. - VT 3.3 Health sciences - Health science - 1.3 - - - - - - - - - - - Data identity and mapping - - Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases. - 1.3 - - - - - - - - - - - Sequence search - - 1.3 - Sequence database search - The search and retrieval from a database on the basis of molecular sequence similarity. - - - - - - - - - - Biomarkers - - Diagnostic markers - 1.4 - Objective indicators of biological state often used to assess health, and determinate treatment. - - - - - - - - - - Laboratory techniques - - The procedures used to conduct an experiment. - Lab techniques - 1.4 - - - - - - - - - - - Data architecture, analysis and design - - The development of policies, models and standards that cover data acquisitioin, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data. - Data analysis - Data design - 1.4 - Data architecture - - - - - - - - - - - Data integration and warehousing - - The combination and integration of data from different sources, for example into a central repository or warehouse, to provide users with a unified view of these data. - - - Data integration - 1.4 - Data warehousing - - - - - - - - - - - Biomaterials - - Any matter, surface or construct that interacts with a biological system. - Diagnostic markers - 1.4 - - - - - - - - - - - Chemical biology - - - 1.4 - The use of synthetic chemistry to study and manipulate biological systems. - - - - - - - - - - - Analytical chemistry - - 1.4 - The study of the separation, identification, and quantification of the chemical components of natural and artificial materials. - VT 1.7.1 Analytical chemistry - - - - - - - - - - - Synthetic chemistry - - Synthetic organic chemistry - The use of chemistry to create new compounds. - 1.4 - - - - - - - - - - - Software engineering - - VT 1.2.1 Algorithms - Programming languages - VT 1.2.7 Data structures - Software development - Software engineering - Computer programming - 1.4 - 1.2.12 Programming languages - The process that leads from an original formulation of a computing problem to executable programs. - Data structures - Algorithms - VT 1.2.14 Software engineering - - - - - - - - - - - Drug development - - 1.4 - Medicine development - The process of bringing a new drug to market once a lead compounds has been identified through drug discovery. - Drug development science - Medicines development - - - - - - - - - - - Drug formulation and delivery - - The process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. - Drug delivery - Drug formulation - 1.4 - - - - - - - - - - - Pharmacokinetics and pharmacodynamics - - Pharmacodynamics - Pharmacokinetics - Drug distribution - 1.4 - Drug excretion - The study of how a drug interacts with the body. - Drug absorption - ADME - Drug metabolism - Drug metabolism - - - - - - - - - - - Medicines research and development - Medicine research and development - - The discovery, development and approval of medicines. - Health care research - Drug discovery and development - 1.4 - Health care science - - - - - - - - - - - Safety sciences - - 1.4 - Drug safety - The safety (or lack) of drugs and other medical interventions. - - - - - - - - - - - Pharmacovigilence - - 1.4 - Pharmacovigilence concerns safety once a drug has gone to market. - The detection, assesment, understanding and prevention of adverse effects of medicines. - - - - - - - - - - - Preclinical and clinical studies - - The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities. - Preclinical studies - 1.4 - Clinical studies - - - - - - - - - - - Imaging - - This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure. - Microscopy imaging - 1.4 - Microscopy - Diffraction experiment - The visual representation of an object. - - - - - - - - - - - Biological imaging - - The use of imaging techniques to understand biology. - 1.4 - - - - - - - - - - - Medical imaging - - VT 3.2.24 Radiology - The use of imaging techniques for clinical purposes for medical research. - 1.4 - Radiology - VT 3.2.14 Nuclear medicine - Nuclear medicine - VT 3.2.13 Medical imaging - - - - - - - - - - - Light microscopy - - The use of optical instruments to magnify the image of an object. - 1.4 - - - - - - - - - - - Laboratory animal science - - 1.4 - The use of animals and alternatives in experimental research. - - - - - - - - - - - Marine biology - - 1.4 - VT 1.5.18 Marine and Freshwater biology - The study of organisms in the ocean or brackish waters. - - - - - - - - - - - Molecular medicine - - The identification of molecular and genetic causes of disease and the development of interventions to correct them. - 1.4 - - - - - - - - - - - Nutritional science - - 1.4 - VT 3.3.7 Nutrition and Dietetics - Dietetics - The study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices. - Nutrition science - - - - - - - - - - - Omics - - The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. - 1.4 - - - - - - - - - - - Quality affairs - - The processes that need to be in place to ensure the quality of products for human or animal use. - Good clinical practice - Good manufacturing practice - Quality assurance - Good laboratory practice - 1.4 - - - - - - - - - - - Regulatory affairs - - The protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines. - 1.4 - - - - - - - - - - - Regnerative medicine - - Stem cell research - Biomedical approaches to clinical interventions that involve the use of stem cells. - 1.4 - - - - - - - - - - - Systems medicine - - 1.4 - An interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life. - - - - - - - - - - - Veterinary medicine - - 1.4 - Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals. - - - - - - - - - - - Bioengineering - - 1.4 - The application of biological concepts and methods to the analytical and synthetic methodologies of engineering. - Diagnostic markers - - - - - - - - - - - Geriatric medicine - - The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. - VT 3.2.10 Geriatrics and gerontology - Ageing - Aging - Gerontology - 1.4 - Geriatrics - - - - - - - - - - - Allergy, clinical immunology and immunotherapeutics. - - VT 3.2.1 Allergy - Health issues related to the immune system and their prevention, diagnosis and mangement. - 1.4 - Immune disorders - Clinical immunology - Immunomodulators - Allergy - Immunotherapeutics - - - - - - - - - - - Pain medicine - - Ageing - 1.4 - Algiatry - The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain. - - - - - - - - - - - Anaesthesiology - - Anaesthetics - Anaesthesia and anaesthetics. - 1.4 - VT 3.2.2 Anaesthesiology - - - - - - - - - - - Critical care medicine - - Acute medicine - Geriatrics - VT 3.2.5 Critical care/Emergency medicine - Emergency medicine - 1.4 - The multidisciplinary that cares for patients with acute, life-threatening illness or injury. - - - - - - - - - - - Dermatology - - The branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails. - Dermatological disorders - 1.4 - VT 3.2.7 Dermatology and venereal diseases - - - - - - - - - - - Dentistry - - 1.4 - The study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures. - - - - - - - - - - - Ear, nose and throat medicine - - Otolaryngology - 1.4 - The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat. - Otorhinolaryngology - Head and neck disorders - VT 3.2.20 Otorhinolaryngology - Audiovestibular medicine - - - - - - - - - - - Endocrinology and metabolism - - 1.4 - Metabolic disorders - Metabolism - Endocrinology - The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism. - Endocrine disorders - - - - - - - - - - - Haematology - - VT 3.2.11 Hematology - The branch of medicine that deals with the blood, blood-forming organs and blood diseases. - Haematological disorders - 1.4 - Blood disorders - - - - - - - - - - - Gastroenterology - - The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum. - Gastrointestinal disorders - VT 3.2.8 Gastroenterology and hepatology - 1.4 - - - - - - - - - - - Gender medicine - - The study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management. - 1.4 - - - - - - - - - - - Gynaecology and obstetrics - - VT 3.2.15 Obstetrics and gynaecology - 1.4 - Gynaecology - The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. - Gynaecological disorders - Obstetrics - - - - - - - - - - - Hepatic and biliary medicine - - Hepatobiliary medicine - Liver disorders - 1.4 - The branch of medicine that deals with the liver, gallbladder, bile ducts and bile. - - - - - - - - - - - Infectious tropical disease - - The branch of medicine that deals with the infectious diseases of the tropics. - 1.4 - - - - - - - - - - - Trauma medicine - - 1.4 - The branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident. - - - - - - - - - - - Medical toxicology - - The branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents. - 1.4 - - - - - - - - - - - Musculoskeletal medicine - - The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine. - VT 3.2.26 Rheumatology - VT 3.2.19 Orthopaedics - Musculoskeletal disorders - Orthopaedics - Rheumatology - 1.4 - - - - - - - - - - - Opthalmology - - Eye disoders - VT 3.2.18 Optometry - 1.4 - Optometry - VT 3.2.17 Ophthalmology - Audiovestibular medicine - The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles. - - - - - - - - - - - Paediatrics - - 1.4 - The branch of medicine that deals with the medical care of infants, children and adolescents. - VT 3.2.21 Paediatrics - Child health - - - - - - - - - - - Psychiatry - - The branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour. - 1.4 - Psychiatric disorders - VT 3.2.23 Psychiatry - Mental health - - - - - - - - - - - Reproductive health - - Reproductive disorders - Audiovestibular medicine - VT 3.2.3 Andrology - Andrology - 1.4 - Family planning - The health of the reproductive processes, functions and systems at all stages of life. - Fertility medicine - - - - - - - - - - - Surgery - - Transplantation - VT 3.2.28 Transplantation - The use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance. - 1.4 - - - - - - - - - - - Urology and nephrology - - The branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney. - VT 3.2.29 Urology and nephrology - 1.4 - Urology - Kidney disease - Urological disorders - Nephrology - - - - - - - - - - - Complementary medicine - - Medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health. - VT 3.2.12 Integrative and Complementary medicine - Holistic medicine - 1.4 - Alternative medicine - Integrative medicine - - - - - - - - - - - MRI - - Nuclear magnetic resonance imaging - 1.7 - MRT - Magnetic resonance tomography - Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. - NMRI - Magnetic resonance imaging - - - - - - - - - - - Neutron diffraction - - - The study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure. - Neutron microscopy - Elastic neutron scattering - 1.7 - Neutron diffraction experiment - - - - - - - - - - Tomography - - X-ray tomography - Imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram). - Electron tomography - 1.7 - - - - - - - - - - Data mining - - 1.7 - VT 1.3.2 Data mining - The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. - KDD - Knowledge discovery in databases - - - - - - - - - - Machine learning - - A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an ouput, rather than relying on explicitly encoded information only. - Artificial Intelligence - 1.7 - VT 1.2.2 Artificial Intelligence (expert systems, machine learning, robotics) - - - - - - - - - - Database management - - 1.8 - Data maintenance - Databases - Database administration - The general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. - - This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature. - Biological databases - - - - - - - - - - Animals - - 1.8 - Animal biology - Animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation. - Zoology - Animal - VT 1.5.29 Zoology - The resource may be specific to a plant, a group of plants or all plants. - Metazoa - - - - - - - - - - Protein sites, features and motifs - - Protein sequence features - Protein functional sites - 1.8 - The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. - - - - - - - - - - Nucleic acid sites, features and motifs - - Nucleic acid sequence features - 1.8 - Nucleic acid functional sites - The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. - - - - - - - - - - Gene transcript features - - - Nucleic acid features (mRNA features) - Features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. - mRNA features - This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). - 1.8 - - - - - - - - - - Protein-ligand interactions - - 1.8 - Protein-ligand (small molecule) interaction(s). - - - - - - - - - - Protein-drug interactions - - 1.8 - Protein-drug interaction(s). - - - - - - - - - - Genotyping experiment - - 1.8 - Genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. - - - - - - - - - - GWAS study - - 1.8 - Genome-wide association study experiments. - Genome-wide association study - - - - - - - - - - Microarray experiment - - 1.8 - This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. - Microarray experiments including conditions, protocol, sample:data relationships etc. - - - - - - - - - - PCR experiment - - 1.8 - PCR experiments, e.g. quantitative real-time PCR. - - - - - - - - - - Proteomics experiment - - Proteomics experiments. - 1.8 - - - - - - - - - - 2D PAGE experiment - - Two-dimensional gel electrophoresis experiments, gels or spots in a gel. - 1.8 - - - - - - - - - - Northern blot experiment - - Northern Blot experiments. - 1.8 - - - - - - - - - - RNAi experiment - - 1.8 - RNAi experiments. - - - - - - - - - - Simulation experiment - - 1.8 - Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. - - - - - - - - - - Protein-nucleic acid interactions - - 1.8 - Protein-DNA/RNA interaction(s). - - - - - - - - - - Protein-protein interactions - - Domain-domain interactions - Protein-protein interaction(s), including interactions between protein domains. - 1.8 - Protein interaction networks - - - - - - - - - - Cellular process pathways - - 1.8 - Cellular process pathways. - - - - - - - - - - Disease pathways - - Disease pathways, typically of human disease. - Pathway or network (disease) - 1.8 - - - - - - - - - - Environmental information processing pathways - - Environmental information processing pathways. - 1.8 - Pathway or network (environmental information processing) - - - - - - - - - - Genetic information processing pathways - - Pathway or network (genetic information processing) - 1.8 - Genetic information processing pathways. - - - - - - - - - - Protein super-secondary structure - - Super-secondary structure of protein sequence(s). - Protein features (super-secondary) - 1.8 - Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. - - - - - - - - - - Protein active sites - - Enzyme active site - 1.8 - Protein features (active sites) - Catalytic residues (active site) of an enzyme. - - - - - - - - - - Protein binding sites - - Ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. - 1.8 - Protein features (binding sites) - - - - - - - - - - Protein-nucleic acid binding sites - - RNA and DNA-binding proteins and binding sites in protein sequences. - 1.8 - Protein features (nucleic acid binding sites) - - - - - - - - - - Protein cleavage sites - - Cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. - Protein features (cleavage sites) - 1.8 - - - - - - - - - - Protein chemical modifications - - Chemical modification of a protein. - Protein features (chemical modifications) - MOD:00000 - 1.8 - GO:0006464 - - - - - - - - - - Protein disordered structure - - Disordered structure in a protein. - 1.8 - Protein features (disordered structure) - - - - - - - - - - Protein domains - - - The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. - Structural domains or 3D folds in a protein or polypeptide chain. - 1.8 - Protein structural domains - Protein features (domains) - - - - - - - - - - Protein key folding sites - - - Protein features (key folding sites) - 1.8 - Key residues involved in protein folding. - - - - - - - - - - Protein post-translational modifications - - Protein features (post-translation modifications) - Post-translation modifications - Post-translation modifications in a protein sequence, typically describing the specific sites involved. - 1.8 - - - - - - - - - - Protein secondary structure - - - The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). - Secondary structure (predicted or real) of a protein. - Protein features (secondary structure) - 1.8 - - - - - - - - - - Protein sequence repeats - - 1.8 - Protein features (repeats) - Short repetitive subsequences (repeat sequences) in a protein sequence. - Protein repeats - - - - - - - - - - Protein signal peptides - - Protein features (signal peptides) - Signal peptides or signal peptide cleavage sites in protein sequences. - 1.8 - - - - - - - - - - Applied mathematics - - VT 1.1.1 Applied mathematics - The application of mathematics to specific problems in science, typically by the formulation and analysis of mathematical models. - 1.10 - - - - - - - - - - Pure mathematics - - VT 1.1.1 Pure mathematics - The study of abstract mathematical concepts. - 1.10 - - - - - - - - - - Data governance - - Data handling - http://purl.bioontology.org/ontology/MSH/D030541 - The control of data entry and maintenance to ensure the data meets defined standards, qualities or constraints. - 1.10 - Data stewardship - - - - - - - - - - Data quality management - - http://purl.bioontology.org/ontology/MSH/D030541 - 1.10 - Data quality - Data integrity - Data clean-up - Data enrichment - The quality, integrity, cleaning up and enrichment of data. - - - - - - - - - - Freshwater biology - - 1.10 - VT 1.5.18 Marine and Freshwater biology - The study of organisms in freshwater ecosystems. - - - - - - - - - - - Human genetics - - The study of inheritatnce in human beings. - VT 3.1.2 Human genetics - 1.10 - - - - - - - - - - - Tropical medicine - - 1.10 - Health problems that are prevalent in tropical and subtropical regions. - VT 3.3.14 Tropical medicine - - - - - - - - - - - Medical biotechnology - - 1.10 - VT 3.4.1 Biomedical devices - VT 3.4.2 Health-related biotechnology - VT 3.4 Medical biotechnology - VT 3.3.14 Tropical medicine - Pharmaceutical biotechnology - Biotechnology applied to the medical sciences and the development of medicines. - - - - - - - - - - - Personalized medicine - - 1.10 - Health problems that are prevalent in tropical and subtropical regions. - Molecular diagnostics - VT 3.4.5 Molecular diagnostics - - - - - - - - - - - Obsolete concept (EDAM) - - - 1.2 - Needed for conversion to the OBO format. - An obsolete concept (redefined in EDAM). - true - - - - - - - - - - - - - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/action.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/action.cwl deleted file mode 100644 index 29a6418a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/action.cwl +++ /dev/null @@ -1,10 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -inputs: - initial_file: File - out_file_name: string -outputs: - processed_file: stdout -stdout: $(inputs.out_file_name) -arguments: [echo, $(inputs.initial_file.basename)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/args.py b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/args.py deleted file mode 100755 index 1baf6a09..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/args.py +++ /dev/null @@ -1,7 +0,0 @@ -#!/usr/bin/env python -import sys -import json -import os -args = [os.path.basename(a) for a in sys.argv[1:]] -with open("cwl.output.json", "w") as f: - json.dump({"args": args}, f) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/bar.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/bar.cwl deleted file mode 100644 index 6fa2a718..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/bar.cwl +++ /dev/null @@ -1,10 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in1: int -baseCommand: [echo] -outputs: - out1: - type: string - outputBinding: - outputEval: bar $(inputs.in1) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/capture_kit.yml b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/capture_kit.yml deleted file mode 100644 index 4323dd90..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/capture_kit.yml +++ /dev/null @@ -1,5 +0,0 @@ -- name: capture_kit - type: record - fields: - - name: bait - type: string diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/cat-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/cat-tool.cwl deleted file mode 100644 index ca2687fe..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/cat-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 - -inputs: - file1: File - -outputs: - output: - type: File - outputBinding: { glob: output } - -baseCommand: [cat] - -stdin: $(inputs.file1.path) -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/cat.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/cat.cwl deleted file mode 100644 index 9425e565..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/cat.cwl +++ /dev/null @@ -1,12 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in1: int - in2: int - in3: int -baseCommand: [echo] -outputs: - out1: - type: string - outputBinding: - outputEval: $(inputs.in1)$(inputs.in2)$(inputs.in3) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/check.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/check.cwl deleted file mode 100644 index da8b5c9f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/check.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - p: File - checkname: string -outputs: [] -arguments: - - sh - - "-c" - - | - name=`basename $(inputs.p.path)` - ls -l $(inputs.p.path) - if test $name = $(inputs.checkname) ; then - echo success - else - echo expected basename to be $(inputs.checkname) but was $name - exit 1 - fi diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/count-lines1-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/count-lines1-wf-noET.cwl deleted file mode 100755 index b48f06bc..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/count-lines1-wf-noET.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: - type: File - -outputs: - wc_output: - type: File - outputSource: step1/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: file1 - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/count-lines1-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/count-lines1-wf.cwl deleted file mode 100755 index bb4adbb6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/count-lines1-wf.cwl +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: - type: File - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: file1 - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/dcterms.rdf b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/dcterms.rdf deleted file mode 100644 index 3873ac54..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/dcterms.rdf +++ /dev/null @@ -1,1077 +0,0 @@ - - - - - - - - - -]> - - -DCMI Metadata Terms - other - -2012-06-14 - - -Title -A name given to the resource. - -2008-01-14 -2010-10-11 - - - - - - -Creator -An entity primarily responsible for making the resource. -Examples of a Creator include a person, an organization, or a service. - -2008-01-14 -2010-10-11 - - - - - - - - -Subject -The topic of the resource. -Typically, the subject will be represented using keywords, key phrases, or classification codes. Recommended best practice is to use a controlled vocabulary. - -2008-01-14 -2012-06-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - -Description -An account of the resource. -Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource. - -2008-01-14 -2008-01-14 - - - - - -Publisher -An entity responsible for making the resource available. -Examples of a Publisher include a person, an organization, or a service. - -2008-01-14 -2010-10-11 - - - - - - -Contributor -An entity responsible for making contributions to the resource. -Examples of a Contributor include a person, an organization, or a service. - -2008-01-14 -2010-10-11 - - - - - - -Date -A point or period of time associated with an event in the lifecycle of the resource. -Date may be used to express temporal information at any level of granularity. Recommended best practice is to use an encoding scheme, such as the W3CDTF profile of ISO 8601 [W3CDTF]. - -2008-01-14 -2008-01-14 - - - - - - -Type -The nature or genre of the resource. -Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMITYPE]. To describe the file format, physical medium, or dimensions of the resource, use the Format element. - -2008-01-14 -2008-01-14 - - - - - - -Format -The file format, physical medium, or dimensions of the resource. -Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME]. - -2008-01-14 -2008-01-14 - - - - - - -Identifier -An unambiguous reference to the resource within a given context. -Recommended best practice is to identify the resource by means of a string conforming to a formal identification system. - -2008-01-14 -2008-01-14 - - - - - - -Source -A related resource from which the described resource is derived. -The described resource may be derived from the related resource in whole or in part. Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system. - -2008-01-14 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -Language -A language of the resource. -Recommended best practice is to use a controlled vocabulary such as RFC 4646 [RFC4646]. - -2008-01-14 -2008-01-14 - - - - - - -Relation -A related resource. -Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system. - -2008-01-14 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - -Coverage -The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant. -Spatial topic and spatial applicability may be a named place or a location specified by its geographic coordinates. Temporal topic may be a named period, date, or date range. A jurisdiction may be a named administrative entity or a geographic place to which the resource applies. Recommended best practice is to use a controlled vocabulary such as the Thesaurus of Geographic Names [TGN]. Where appropriate, named places or time periods can be used in preference to numeric identifiers such as sets of coordinates or date ranges. - -2008-01-14 -2008-01-14 - - - - - - -Rights -Information about rights held in and over the resource. -Typically, rights information includes a statement about various property rights associated with the resource, including intellectual property rights. - -2008-01-14 -2008-01-14 - - - - - - -Audience -A class of entity for whom the resource is intended or useful. - -2001-05-21 -2008-01-14 - - - - - -Alternative Title -An alternative name for the resource. -The distinction between titles and alternative titles is application-specific. - -2000-07-11 -2010-10-11 - - - - - - - -Table Of Contents -A list of subunits of the resource. - -2000-07-11 -2008-01-14 - - - - - - -Abstract -A summary of the resource. - -2000-07-11 -2008-01-14 - - - - - - -Date Created -Date of creation of the resource. - -2000-07-11 -2008-01-14 - - - - - - - -Date Valid -Date (often a range) of validity of a resource. - -2000-07-11 -2008-01-14 - - - - - - - -Date Available -Date (often a range) that the resource became or will become available. - -2000-07-11 -2008-01-14 - - - - - - - -Date Issued -Date of formal issuance (e.g., publication) of the resource. - -2000-07-11 -2008-01-14 - - - - - - - -Date Modified -Date on which the resource was changed. - -2000-07-11 -2008-01-14 - - - - - - - -Extent -The size or duration of the resource. - -2000-07-11 -2008-01-14 - - - - - - - -Medium -The material or physical carrier of the resource. - -2000-07-11 -2008-01-14 - - - - - - - - -Is Version Of -A related resource of which the described resource is a version, edition, or adaptation. -Changes in version imply substantive changes in content rather than differences in format. - -2000-07-11 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -Has Version -A related resource that is a version, edition, or adaptation of the described resource. - -2000-07-11 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -Is Replaced By -A related resource that supplants, displaces, or supersedes the described resource. - -2000-07-11 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -Replaces -A related resource that is supplanted, displaced, or superseded by the described resource. - -2000-07-11 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -Is Required By -A related resource that requires the described resource to support its function, delivery, or coherence. - -2000-07-11 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -Requires -A related resource that is required by the described resource to support its function, delivery, or coherence. - -2000-07-11 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -Is Part Of -A related resource in which the described resource is physically or logically included. - -2000-07-11 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -Has Part -A related resource that is included either physically or logically in the described resource. - -2000-07-11 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -Is Referenced By -A related resource that references, cites, or otherwise points to the described resource. - -2000-07-11 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -References -A related resource that is referenced, cited, or otherwise pointed to by the described resource. - -2000-07-11 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -Is Format Of -A related resource that is substantially the same as the described resource, but in another format. - -2000-07-11 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -Has Format -A related resource that is substantially the same as the pre-existing described resource, but in another format. - -2000-07-11 -2008-01-14 - - -This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration. - - - - -Conforms To -An established standard to which the described resource conforms. - -2001-05-21 -2008-01-14 - - - - - - - -Spatial Coverage -Spatial characteristics of the resource. - -2000-07-11 -2008-01-14 - - - - - - - -Temporal Coverage -Temporal characteristics of the resource. - -2000-07-11 -2008-01-14 - - - - - - - -Mediator -An entity that mediates access to the resource and for whom the resource is intended or useful. -In an educational context, a mediator might be a parent, teacher, teaching assistant, or care-giver. - -2001-05-21 -2008-01-14 - - - - - - -Date Accepted -Date of acceptance of the resource. -Examples of resources to which a Date Accepted may be relevant are a thesis (accepted by a university department) or an article (accepted by a journal). - -2002-07-13 -2008-01-14 - - - - - - - -Date Copyrighted -Date of copyright. - -2002-07-13 -2008-01-14 - - - - - - - -Date Submitted -Date of submission of the resource. -Examples of resources to which a Date Submitted may be relevant are a thesis (submitted to a university department) or an article (submitted to a journal). - -2002-07-13 -2008-01-14 - - - - - - - -Audience Education Level -A class of entity, defined in terms of progression through an educational or training context, for which the described resource is intended. - -2002-07-13 -2008-01-14 - - - - - - -Access Rights -Information about who can access the resource or an indication of its security status. -Access Rights may include information regarding access or restrictions based on privacy, security, or other policies. - -2003-02-15 -2008-01-14 - - - - - - - -Bibliographic Citation -A bibliographic reference for the resource. -Recommended practice is to include sufficient bibliographic detail to identify the resource as unambiguously as possible. - -2003-02-15 -2008-01-14 - - - - - - - - -License -A legal document giving official permission to do something with the resource. - -2004-06-14 -2008-01-14 - - - - - - - -Rights Holder -A person or organization owning or managing rights over the resource. - -2004-06-14 -2008-01-14 - - - - - -Provenance -A statement of any changes in ownership and custody of the resource since its creation that are significant for its authenticity, integrity, and interpretation. -The statement may include a description of any changes successive custodians made to the resource. - -2004-09-20 -2008-01-14 - - - - - -Instructional Method -A process, used to engender knowledge, attitudes and skills, that the described resource is designed to support. -Instructional Method will typically include ways of presenting instructional materials or conducting instructional activities, patterns of learner-to-learner and learner-to-instructor interactions, and mechanisms by which group and individual levels of learning are measured. Instructional methods include all aspects of the instruction and learning processes from planning and implementation through evaluation and feedback. - -2005-06-13 -2008-01-14 - - - - - -Accrual Method -The method by which items are added to a collection. - -2005-06-13 -2010-10-11 - - - - - - -Accrual Periodicity -The frequency with which items are added to a collection. - -2005-06-13 -2010-10-11 - - - - - - -Accrual Policy -The policy governing the addition of items to a collection. - -2005-06-13 -2010-10-11 - - - - - - -Agent -A resource that acts or has the power to act. -Examples of Agent include person, organization, and software agent. - -2008-01-14 - - - - - -Agent Class -A group of agents. -Examples of Agent Class include groups seen as classes, such as students, women, charities, lecturers. - -2008-01-14 -2012-06-14 - - - - - -Bibliographic Resource -A book, article, or other documentary resource. - -2008-01-14 - - - - -File Format -A digital resource format. -Examples include the formats defined by the list of Internet Media Types. - -2008-01-14 - - - - - -Frequency -A rate at which something recurs. - -2008-01-14 - - - - -Jurisdiction -The extent or range of judicial, law enforcement, or other authority. - -2008-01-14 - - - - - -License Document -A legal document giving official permission to do something with a Resource. - -2008-01-14 - - - - - -Linguistic System -A system of signs, symbols, sounds, gestures, or rules used in communication. -Examples include written, spoken, sign, and computer languages. - -2008-01-14 - - - - -Location -A spatial region or named place. - -2008-01-14 - - - - - -Location, Period, or Jurisdiction -A location, period of time, or jurisdiction. - -2008-01-14 - - - - -Media Type -A file format or physical medium. - -2008-01-14 - - - - - -Media Type or Extent -A media type or extent. - -2008-01-14 - - - - -Method of Instruction -A process that is used to engender knowledge, attitudes, and skills. - -2008-01-14 - - - - -Method of Accrual -A method by which resources are added to a collection. - -2008-01-14 - - - - -Period of Time -An interval of time that is named or defined by its start and end dates. - -2008-01-14 - - - - - -Physical Medium -A physical material or carrier. -Examples include paper, canvas, or DVD. - -2008-01-14 - - - - - -Physical Resource -A material thing. - -2008-01-14 - - - - -Policy -A plan or course of action by an authority, intended to influence and determine decisions, actions, and other matters. - -2008-01-14 - - - - -Provenance Statement -A statement of any changes in ownership and custody of a resource since its creation that are significant for its authenticity, integrity, and interpretation. - -2008-01-14 - - - - -Rights Statement -A statement about the intellectual property rights (IPR) held in or over a Resource, a legal document giving official permission to do something with a resource, or a statement about access rights. - -2008-01-14 - - - - -Size or Duration -A dimension or extent, or a time taken to play or execute. -Examples include a number of pages, a specification of length, width, and breadth, or a period in hours, minutes, and seconds. - -2008-01-14 - - - - - -Standard -A basis for comparison; a reference point against which other things can be evaluated. - -2008-01-14 - - - - -ISO 639-2 -The three-letter alphabetic codes listed in ISO639-2 for the representation of names of languages. - -2000-07-11 -2008-01-14 - - - - - -RFC 1766 -The set of tags, constructed according to RFC 1766, for the identification of languages. - -2000-07-11 -2008-01-14 - - - - - -URI -The set of identifiers constructed according to the generic syntax for Uniform Resource Identifiers as specified by the Internet Engineering Task Force. - -2000-07-11 -2008-01-14 - - - - - -DCMI Point -The set of points in space defined by their geographic coordinates according to the DCMI Point Encoding Scheme. - -2000-07-11 -2008-01-14 - - - - - -ISO 3166 -The set of codes listed in ISO 3166-1 for the representation of names of countries. - -2000-07-11 -2008-01-14 - - - - - -DCMI Box -The set of regions in space defined by their geographic coordinates according to the DCMI Box Encoding Scheme. - -2000-07-11 -2008-01-14 - - - - - -DCMI Period -The set of time intervals defined by their limits according to the DCMI Period Encoding Scheme. - -2000-07-11 -2008-01-14 - - - - - -W3C-DTF -The set of dates and times constructed according to the W3C Date and Time Formats Specification. - -2000-07-11 -2008-01-14 - - - - - -RFC 3066 -The set of tags constructed according to RFC 3066 for the identification of languages. -RFC 3066 has been obsoleted by RFC 4646. - -2002-07-13 -2008-01-14 - - - - - -RFC 5646 -The set of tags constructed according to RFC 5646 for the identification of languages. -RFC 5646 obsoletes RFC 4646. - -2010-10-11 - - - - - -RFC 4646 -The set of tags constructed according to RFC 4646 for the identification of languages. -RFC 4646 obsoletes RFC 3066. - -2008-01-14 - - - - - -ISO 639-3 -The set of three-letter codes listed in ISO 639-3 for the representation of names of languages. - -2008-01-14 - - - - - -LCSH -The set of labeled concepts specified by the Library of Congress Subject Headings. - -2000-07-11 -2008-01-14 - - - - -MeSH -The set of labeled concepts specified by the Medical Subject Headings. - -2000-07-11 -2008-01-14 - - - - - -DDC -The set of conceptual resources specified by the Dewey Decimal Classification. - -2000-07-11 -2008-01-14 - - - - - -LCC -The set of conceptual resources specified by the Library of Congress Classification. - -2000-07-11 -2008-01-14 - - - - - -UDC -The set of conceptual resources specified by the Universal Decimal Classification. - -2000-07-11 -2008-01-14 - - - - - -DCMI Type Vocabulary -The set of classes specified by the DCMI Type Vocabulary, used to categorize the nature or genre of the resource. - -2000-07-11 -2012-06-14 - - - - - -IMT -The set of media types specified by the Internet Assigned Numbers Authority. - -2000-07-11 -2008-01-14 - - - - - -TGN -The set of places specified by the Getty Thesaurus of Geographic Names. - -2000-07-11 -2008-01-14 - - - - - -NLM -The set of conceptual resources specified by the National Library of Medicine Classification. - -2005-06-13 -2008-01-14 - - - - - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/dynresreq-default.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/dynresreq-default.cwl deleted file mode 100644 index f4401907..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/dynresreq-default.cwl +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - ResourceRequirement: - coresMin: $(inputs.special_file.size) - coresMax: $(inputs.special_file.size) - -inputs: - special_file: - type: File - default: - class: File - location: special_file - -outputs: - output: - type: stdout - -baseCommand: echo - -stdout: cores.txt - -arguments: [ $(runtime.cores) ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/dynresreq.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/dynresreq.cwl deleted file mode 100644 index e8c7752f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/dynresreq.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - ResourceRequirement: - coresMin: $(inputs.special_file.size) - coresMax: $(inputs.special_file.size) - -inputs: - special_file: File - -outputs: - output: - type: stdout - -baseCommand: echo - -stdout: cores.txt - -arguments: [ $(runtime.cores) ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/echo-file-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/echo-file-tool.cwl deleted file mode 100644 index f6e4f58c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/echo-file-tool.cwl +++ /dev/null @@ -1,13 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -baseCommand: [echo] -inputs: - in: - type: string - inputBinding: - position: 1 - name: string? -stdout: out.txt -outputs: - out: - type: stdout diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/echo-tool-default.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/echo-tool-default.cwl deleted file mode 100644 index 885960fc..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/echo-tool-default.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in: - type: string - default: tool_default - inputBinding: - position: 1 -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -baseCommand: [echo, -n] -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/echo-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/echo-tool.cwl deleted file mode 100644 index 5a9835b8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/echo-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in: - type: Any - inputBinding: {} -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -baseCommand: echo -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/env-tool1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/env-tool1.cwl deleted file mode 100644 index 96b0bc3d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/env-tool1.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in: string -outputs: - out: - type: File - outputBinding: - glob: out - -requirements: - EnvVarRequirement: - envDef: - TEST_ENV: $(inputs.in) - -baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"] - -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/env-tool2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/env-tool2.cwl deleted file mode 100644 index f568e545..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/env-tool2.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in: string -outputs: - out: - type: File - outputBinding: - glob: out - -hints: - EnvVarRequirement: - envDef: - TEST_ENV: $(inputs.in) - -baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"] - -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/envvar.yml b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/envvar.yml deleted file mode 100644 index 097c3f27..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/envvar.yml +++ /dev/null @@ -1,4 +0,0 @@ -class: EnvVarRequirement -envDef: - - envName: "TEST_ENV" - envValue: "hello test env" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/fail-unspecified-input.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/fail-unspecified-input.cwl deleted file mode 100644 index ae623c46..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/fail-unspecified-input.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in: string -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -stdout: out.txt -arguments: [echo, $(inputs.in), $(inputs.in2)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/foaf.rdf b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/foaf.rdf deleted file mode 100644 index 68d0700c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/foaf.rdf +++ /dev/null @@ -1,609 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Label Property - A foaf:LabelProperty is any RDF property with texual values that serve as labels. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/foo.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/foo.cwl deleted file mode 100644 index 9e19268d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/foo.cwl +++ /dev/null @@ -1,10 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in1: int -baseCommand: [echo] -outputs: - out1: - type: string - outputBinding: - outputEval: foo $(inputs.in1) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/gx_edam.ttl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/gx_edam.ttl deleted file mode 100644 index 8182f719..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/gx_edam.ttl +++ /dev/null @@ -1,7 +0,0 @@ -@prefix gx: . -@prefix owl: . -@prefix rdfs: . -@prefix edam: . - -gx:fasta a owl:Class . -gx:fasta owl:equivalentClass edam:format_1929 . diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/hello.txt b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/hello.txt deleted file mode 100644 index cd087558..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/hello.txt +++ /dev/null @@ -1 +0,0 @@ -Hello world! diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/inp-filelist.txt b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/inp-filelist.txt deleted file mode 100644 index 232ddf67..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/inp-filelist.txt +++ /dev/null @@ -1,9999 +0,0 @@ -example_input_file1.txt -example_input_file2.txt -example_input_file3.txt -example_input_file4.txt -example_input_file5.txt -example_input_file6.txt -example_input_file7.txt -example_input_file8.txt -example_input_file9.txt -example_input_file10.txt -example_input_file11.txt -example_input_file12.txt -example_input_file13.txt -example_input_file14.txt -example_input_file15.txt 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-class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: InlineJavascriptRequirement - -inputs: - - id: bar - type: Any - -outputs: - - id: t1 - type: Any - outputBinding: - outputEval: $(inputs.bar.class || inputs.bar) - -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/loadit.py b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/loadit.py deleted file mode 100644 index 2da9d7ed..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/loadit.py +++ /dev/null @@ -1,5 +0,0 @@ -import json -import sys -j = json.load(open(sys.argv[1])) -json.dump({"class": j["class"], - "basename": j["basename"]}, sys.stdout, sort_keys=True) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/mkdir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/mkdir.cwl deleted file mode 100644 index dbed864c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/mkdir.cwl +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -inputs: - dirname: string -outputs: - out: - type: Directory - outputBinding: - glob: $(inputs.dirname) -arguments: [mkdir, $(inputs.dirname)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/mkfilelist.py b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/mkfilelist.py deleted file mode 100644 index 3ae8896b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/mkfilelist.py +++ /dev/null @@ -1,6 +0,0 @@ -import json -ls = [] -for i in range(1, 10000): - ls.append("example_input_file%i.txt" % i) -f = open("cwl.output.json", "w") -json.dump({"filelist": ls, "bigstring": "\n".join(ls)}, f) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/null-expression3-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/null-expression3-tool.cwl deleted file mode 100644 index 6dbfda6c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/null-expression3-tool.cwl +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: ExpressionTool -requirements: { InlineJavascriptRequirement: {} } -cwlVersion: v1.2 - -inputs: [] - -outputs: - output: Any - -expression: "$({'output': null })" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/params_inc.yml b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/params_inc.yml deleted file mode 100644 index 930d2e89..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/params_inc.yml +++ /dev/null @@ -1,120 +0,0 @@ - - id: t1 - type: Any - outputBinding: - outputEval: $(inputs) - - id: t2 - type: Any - outputBinding: - outputEval: $(inputs.bar) - - id: t3 - type: Any - outputBinding: - outputEval: $(inputs['bar']) - - id: t4 - type: Any - outputBinding: - outputEval: $(inputs["bar"]) - - - id: t5 - type: Any - outputBinding: - outputEval: $(inputs.bar.baz) - - id: t6 - type: Any - outputBinding: - outputEval: $(inputs['bar'].baz) - - id: t7 - type: Any - outputBinding: - outputEval: $(inputs['bar']["baz"]) - - id: t8 - type: Any - outputBinding: - outputEval: $(inputs.bar['baz']) - - - id: t9 - type: Any - outputBinding: - outputEval: $(inputs.bar['b az']) - - id: t10 - type: Any - outputBinding: - outputEval: $(inputs.bar['b\'az']) - - id: t11 - type: Any - outputBinding: - outputEval: $(inputs.bar["b'az"]) - - id: t12 - type: "null" - outputBinding: - outputEval: $(inputs.bar['b"az']) - - - id: t13 - type: Any - outputBinding: - outputEval: -$(inputs.bar.baz) - - id: t14 - type: Any - outputBinding: - outputEval: -$(inputs['bar'].baz) - - id: t15 - type: Any - outputBinding: - outputEval: -$(inputs['bar']["baz"]) - - id: t16 - type: Any - outputBinding: - outputEval: -$(inputs.bar['baz']) - - - id: t17 - type: Any - outputBinding: - outputEval: $(inputs.bar.baz) $(inputs.bar.baz) - - id: t18 - type: Any - outputBinding: - outputEval: $(inputs['bar'].baz) $(inputs['bar'].baz) - - id: t19 - type: Any - outputBinding: - outputEval: $(inputs['bar']["baz"]) $(inputs['bar']["baz"]) - - id: t20 - type: Any - outputBinding: - outputEval: $(inputs.bar['baz']) $(inputs.bar['baz']) - - - id: t21 - type: Any - outputBinding: - outputEval: $(inputs.bar['b az']) $(inputs.bar['b az']) - - id: t22 - type: Any - outputBinding: - outputEval: $(inputs.bar['b\'az']) $(inputs.bar['b\'az']) - - id: t23 - type: Any - outputBinding: - outputEval: $(inputs.bar["b'az"]) $(inputs.bar["b'az"]) - - id: t24 - type: Any - outputBinding: - outputEval: $(inputs.bar['b"az']) $(inputs.bar['b"az']) - - - id: t25 - type: Any - outputBinding: - outputEval: $(inputs.bar.buz[1]) - - id: t26 - type: Any - outputBinding: - outputEval: $(inputs.bar.buz[1]) $(inputs.bar.buz[1]) - - - id: t27 - type: "null" - outputBinding: - outputEval: $(null) - - - id: t28 - type: int - outputBinding: - outputEval: $(inputs.bar.buz.length) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/parseInt-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/parseInt-tool.cwl deleted file mode 100755 index 844cc5d0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/parseInt-tool.cwl +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: ExpressionTool -requirements: - - class: InlineJavascriptRequirement -cwlVersion: v1.2 - -inputs: - file1: - type: File - loadContents: true - -outputs: - output: int - -expression: "$({'output': parseInt(inputs.file1.contents)})" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/record-in-format.cwl.json b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/record-in-format.cwl.json deleted file mode 100644 index d4b557c3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/record-in-format.cwl.json +++ /dev/null @@ -1,37 +0,0 @@ -{ - "class": "CommandLineTool", - "inputs": [ - { - "type": { - "type": "record", - "fields": [ - { - "type": "File", - "format": "http://example.com/format1", - "name": "#main/record_input/f1" - }, - { - "type": { - "type": "array", - "items": "File" - }, - "format": "http://example.com/format2", - "name": "#main/record_input/f2" - } - ] - }, - "id": "#main/record_input" - }, - { - "type": "File", - "format": "http://example.com/format1", - "id": "#main/regular_input" - } - ], - "outputs": [], - "arguments": [ - "true" - ], - "id": "#main", - "cwlVersion": "v1.2" -} \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/record-in-secondaryFiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/record-in-secondaryFiles.cwl deleted file mode 100644 index b9efc64a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/record-in-secondaryFiles.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - record_input: - type: - type: record - fields: - f1: - type: File - secondaryFiles: .s2 - f2: - type: - type: array - items: File - secondaryFiles: .s3 -outputs: [] -baseCommand: test -arguments: [-f, $(inputs.record_input.f1.path).s2, - '-a', '-f', '$(inputs.record_input.f2[0].path).s3', - '-a', '-f', '$(inputs.record_input.f2[1].path).s3'] \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/record-output.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/record-output.cwl deleted file mode 100644 index dbbc8390..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/record-output.cwl +++ /dev/null @@ -1,38 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: ShellCommandRequirement -inputs: - irec: - type: - name: irec - type: record - fields: - - name: ifoo - type: File - inputBinding: - position: 2 - - name: ibar - type: File - inputBinding: - position: 6 -outputs: - orec: - type: - name: orec - type: record - fields: - - name: ofoo - type: File - outputBinding: - glob: foo - - name: obar - type: File - outputBinding: - glob: bar -arguments: - - {valueFrom: "cat", position: 1} - - {valueFrom: "> foo", position: 3, shellQuote: false} - - {valueFrom: "&&", position: 4, shellQuote: false} - - {valueFrom: "cat", position: 5} - - {valueFrom: "> bar", position: 7, shellQuote: false} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/rename-inputs.yml b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/rename-inputs.yml deleted file mode 100644 index de72eec9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/rename-inputs.yml +++ /dev/null @@ -1,3 +0,0 @@ -inputWithSecondary: - class: File - location: secondary_file_test.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/rename.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/rename.cwl deleted file mode 100644 index 7bc0025a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/rename.cwl +++ /dev/null @@ -1,16 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -baseCommand: "true" -requirements: - InitialWorkDirRequirement: - listing: - - entryname: $(inputs.newname) - entry: $(inputs.srcfile) -inputs: - srcfile: File - newname: string -outputs: - outfile: - type: File - outputBinding: - glob: $(inputs.newname) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/revtool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/revtool.cwl deleted file mode 100644 index c4c0d035..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/revtool.cwl +++ /dev/null @@ -1,37 +0,0 @@ -# -# Simplest example command line program wrapper for the Unix tool "rev". -# -class: CommandLineTool -cwlVersion: v1.2 -doc: "Reverse each line using the `rev` command" - -# The "inputs" array defines the structure of the input object that describes -# the inputs to the underlying program. Here, there is one input field -# defined that will be called "input" and will contain a "File" object. -# -# The input binding indicates that the input value should be turned into a -# command line argument. In this example inputBinding is an empty object, -# which indicates that the file name should be added to the command line at -# a default location. -inputs: - input: - type: File - inputBinding: {} - -# The "outputs" array defines the structure of the output object that -# describes the outputs of the underlying program. Here, there is one -# output field defined that will be called "output", must be a "File" type, -# and after the program executes, the output value will be the file -# output.txt in the designated output directory. -outputs: - output: - type: File - outputBinding: - glob: output.txt - -# The actual program to execute. -baseCommand: rev - -# Specify that the standard output stream must be redirected to a file called -# output.txt in the designated output directory. -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/scatter-valueFrom-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/scatter-valueFrom-tool.cwl deleted file mode 100644 index 8d0fef14..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/scatter-valueFrom-tool.cwl +++ /dev/null @@ -1,15 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -inputs: - scattered_message: - type: string - inputBinding: - position: 2 - message: - type: string - inputBinding: - position: 1 -outputs: - out_message: - type: stdout -baseCommand: echo diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/schemadef-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/schemadef-tool.cwl deleted file mode 100644 index 90343981..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/schemadef-tool.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - - $import: schemadef-type.yml - -inputs: - - id: hello - type: "schemadef-type.yml#HelloType" - inputBinding: - valueFrom: $(self.a)/$(self.b) - -outputs: - - id: output - type: File - outputBinding: - glob: output.txt - -stdout: output.txt -baseCommand: echo diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/schemadef-type.yml b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/schemadef-type.yml deleted file mode 100644 index 45a82a75..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/schemadef-type.yml +++ /dev/null @@ -1,9 +0,0 @@ -class: SchemaDefRequirement -types: - - name: HelloType - type: record - fields: - - name: a - type: string - - name: b - type: string diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/schemadef_types_with_import-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/schemadef_types_with_import-tool.cwl deleted file mode 100644 index 1197249c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/schemadef_types_with_import-tool.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - - class: InlineJavascriptRequirement - - class: SchemaDefRequirement - types: - - $import: schemadef_types_with_import_readgroup.yml - -inputs: - - id: message - type: "schemadef_types_with_import_readgroup.yml#readgroups_bam_file" - inputBinding: - valueFrom: $(self.readgroup_meta_list[0]['DT']) - -outputs: - - id: out - type: string - outputBinding: - glob: output.txt - loadContents: true - outputEval: $(self[0].contents) - -stdout: output.txt -baseCommand: echo diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/schemadef_types_with_import_readgroup.yml b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/schemadef_types_with_import_readgroup.yml deleted file mode 100644 index c7ffe8ea..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/schemadef_types_with_import_readgroup.yml +++ /dev/null @@ -1,27 +0,0 @@ -- name: readgroup_meta - type: record - fields: - - name: CN - type: string - - name: DT - type: string - - name: ID - type: string - - name: LB - type: string - - name: PI - type: string - - name: PL - type: string - - name: SM - type: string - -- name: readgroups_bam_file - type: record - fields: - - name: bam - type: File - - name: readgroup_meta_list - type: - type: array - items: readgroup_meta diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/search.py b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/search.py deleted file mode 100755 index d402bc7c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/search.py +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env python - -# Toy program to search inverted index and print out each line the term -# appears. - -from __future__ import print_function - -import sys - -mainfile = sys.argv[1] -indexfile = sys.argv[1] + ".idx1" -term = sys.argv[2] - -main = open(mainfile) -index = open(indexfile) - -st = term + ": " - -for a in index: - if a.startswith(st): - n = [int(i) for i in a[len(st):].split(", ") if i] - linenum = 0 - for l in main: - linenum += 1 - if linenum in n: - print(linenum, l.rstrip()) - break diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/sorttool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/sorttool.cwl deleted file mode 100644 index e8c5dd48..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/sorttool.cwl +++ /dev/null @@ -1,35 +0,0 @@ -# Example command line program wrapper for the Unix tool "sort" -# demonstrating command line flags. -class: CommandLineTool -doc: "Sort lines using the `sort` command" -cwlVersion: v1.2 - -# This example is similar to the previous one, with an additional input -# parameter called "reverse". It is a boolean parameter, which is -# intepreted as a command line flag. The value of "prefix" is used for -# flag to put on the command line if "reverse" is true, if "reverse" is -# false, no flag is added. -# -# This example also introduced the "position" field. This indicates the -# sorting order of items on the command line. Lower numbers are placed -# before higher numbers. Here, the "-r" (same as "--reverse") flag (if -# present) will be added to the command line before the input file path. -inputs: - - id: reverse - type: boolean - inputBinding: - position: 1 - prefix: "-r" - - id: input - type: File - inputBinding: - position: 2 - -outputs: - - id: output - type: File - outputBinding: - glob: output.txt - -baseCommand: sort -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/special_file b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/special_file deleted file mode 100644 index f70d7bba..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/special_file +++ /dev/null @@ -1 +0,0 @@ -42 \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/testdir/b b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/testdir/b deleted file mode 100644 index e69de29b..00000000 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/testdir/c/d b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/testdir/c/d deleted file mode 100644 index e69de29b..00000000 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/touch.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/touch.cwl deleted file mode 100644 index f4714933..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/touch.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: CommandLineTool - -hints: - DockerRequirement: - dockerPull: debian:stretch-slim - -inputs: - name: - type: string - inputBinding: - position: 0 - -outputs: - empty_file: - type: File - outputBinding: - glob: $(inputs.name) - -baseCommand: [touch] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/underscore.js b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/underscore.js deleted file mode 100644 index 05bfdc0b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/underscore.js +++ /dev/null @@ -1,1416 +0,0 @@ -// Underscore.js 1.7.0 -// http://underscorejs.org -// (c) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors -// Underscore may be freely distributed under the MIT license. - -(function() { - - // Baseline setup - // -------------- - - // Establish the root object, `window` in the browser, or `exports` on the server. - var root = this; - - // Save the previous value of the `_` variable. - //var previousUnderscore = root._; - - // Save bytes in the minified (but not gzipped) version: - var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype; - - // Create quick reference variables for speed access to core prototypes. - var - push = ArrayProto.push, - slice = ArrayProto.slice, - concat = ArrayProto.concat, - toString = ObjProto.toString, - hasOwnProperty = ObjProto.hasOwnProperty; - - // All **ECMAScript 5** native function implementations that we hope to use - // are declared here. - var - nativeIsArray = Array.isArray, - nativeKeys = Object.keys, - nativeBind = FuncProto.bind; - - // Create a safe reference to the Underscore object for use below. - var _ = function(obj) { - if (obj instanceof _) return obj; - if (!(this instanceof _)) return new _(obj); - this._wrapped = obj; - }; - - // Export the Underscore object for **Node.js**, with - // backwards-compatibility for the old `require()` API. If we're in - // the browser, add `_` as a global object. - if (typeof exports !== 'undefined') { - if (typeof module !== 'undefined' && module.exports) { - exports = module.exports = _; - } - exports._ = _; - } else { - root._ = _; - } - - // Current version. - _.VERSION = '1.7.0'; - - // Internal function that returns an efficient (for current engines) version - // of the passed-in callback, to be repeatedly applied in other Underscore - // functions. - var createCallback = function(func, context, argCount) { - if (context === void 0) return func; - switch (argCount == null ? 3 : argCount) { - case 1: return function(value) { - return func.call(context, value); - }; - case 2: return function(value, other) { - return func.call(context, value, other); - }; - case 3: return function(value, index, collection) { - return func.call(context, value, index, collection); - }; - case 4: return function(accumulator, value, index, collection) { - return func.call(context, accumulator, value, index, collection); - }; - } - return function() { - return func.apply(context, arguments); - }; - }; - - // A mostly-internal function to generate callbacks that can be applied - // to each element in a collection, returning the desired result — either - // identity, an arbitrary callback, a property matcher, or a property accessor. - _.iteratee = function(value, context, argCount) { - if (value == null) return _.identity; - if (_.isFunction(value)) return createCallback(value, context, argCount); - if (_.isObject(value)) return _.matches(value); - return _.property(value); - }; - - // Collection Functions - // -------------------- - - // The cornerstone, an `each` implementation, aka `forEach`. - // Handles raw objects in addition to array-likes. Treats all - // sparse array-likes as if they were dense. - _.each = _.forEach = function(obj, iteratee, context) { - if (obj == null) return obj; - iteratee = createCallback(iteratee, context); - var i, length = obj.length; - if (length === +length) { - for (i = 0; i < length; i++) { - iteratee(obj[i], i, obj); - } - } else { - var keys = _.keys(obj); - for (i = 0, length = keys.length; i < length; i++) { - iteratee(obj[keys[i]], keys[i], obj); - } - } - return obj; - }; - - // Return the results of applying the iteratee to each element. - _.map = _.collect = function(obj, iteratee, context) { - if (obj == null) return []; - iteratee = _.iteratee(iteratee, context); - var keys = obj.length !== +obj.length && _.keys(obj), - length = (keys || obj).length, - results = Array(length), - currentKey; - for (var index = 0; index < length; index++) { - currentKey = keys ? keys[index] : index; - results[index] = iteratee(obj[currentKey], currentKey, obj); - } - return results; - }; - - var reduceError = 'Reduce of empty array with no initial value'; - - // **Reduce** builds up a single result from a list of values, aka `inject`, - // or `foldl`. - _.reduce = _.foldl = _.inject = function(obj, iteratee, memo, context) { - if (obj == null) obj = []; - iteratee = createCallback(iteratee, context, 4); - var keys = obj.length !== +obj.length && _.keys(obj), - length = (keys || obj).length, - index = 0, currentKey; - if (arguments.length < 3) { - if (!length) throw new TypeError(reduceError); - memo = obj[keys ? keys[index++] : index++]; - } - for (; index < length; index++) { - currentKey = keys ? keys[index] : index; - memo = iteratee(memo, obj[currentKey], currentKey, obj); - } - return memo; - }; - - // The right-associative version of reduce, also known as `foldr`. - _.reduceRight = _.foldr = function(obj, iteratee, memo, context) { - if (obj == null) obj = []; - iteratee = createCallback(iteratee, context, 4); - var keys = obj.length !== + obj.length && _.keys(obj), - index = (keys || obj).length, - currentKey; - if (arguments.length < 3) { - if (!index) throw new TypeError(reduceError); - memo = obj[keys ? keys[--index] : --index]; - } - while (index--) { - currentKey = keys ? keys[index] : index; - memo = iteratee(memo, obj[currentKey], currentKey, obj); - } - return memo; - }; - - // Return the first value which passes a truth test. Aliased as `detect`. - _.find = _.detect = function(obj, predicate, context) { - var result; - predicate = _.iteratee(predicate, context); - _.some(obj, function(value, index, list) { - if (predicate(value, index, list)) { - result = value; - return true; - } - }); - return result; - }; - - // Return all the elements that pass a truth test. - // Aliased as `select`. - _.filter = _.select = function(obj, predicate, context) { - var results = []; - if (obj == null) return results; - predicate = _.iteratee(predicate, context); - _.each(obj, function(value, index, list) { - if (predicate(value, index, list)) results.push(value); - }); - return results; - }; - - // Return all the elements for which a truth test fails. - _.reject = function(obj, predicate, context) { - return _.filter(obj, _.negate(_.iteratee(predicate)), context); - }; - - // Determine whether all of the elements match a truth test. - // Aliased as `all`. - _.every = _.all = function(obj, predicate, context) { - if (obj == null) return true; - predicate = _.iteratee(predicate, context); - var keys = obj.length !== +obj.length && _.keys(obj), - length = (keys || obj).length, - index, currentKey; - for (index = 0; index < length; index++) { - currentKey = keys ? keys[index] : index; - if (!predicate(obj[currentKey], currentKey, obj)) return false; - } - return true; - }; - - // Determine if at least one element in the object matches a truth test. - // Aliased as `any`. - _.some = _.any = function(obj, predicate, context) { - if (obj == null) return false; - predicate = _.iteratee(predicate, context); - var keys = obj.length !== +obj.length && _.keys(obj), - length = (keys || obj).length, - index, currentKey; - for (index = 0; index < length; index++) { - currentKey = keys ? keys[index] : index; - if (predicate(obj[currentKey], currentKey, obj)) return true; - } - return false; - }; - - // Determine if the array or object contains a given value (using `===`). - // Aliased as `include`. - _.contains = _.include = function(obj, target) { - if (obj == null) return false; - if (obj.length !== +obj.length) obj = _.values(obj); - return _.indexOf(obj, target) >= 0; - }; - - // Invoke a method (with arguments) on every item in a collection. - _.invoke = function(obj, method) { - var args = slice.call(arguments, 2); - var isFunc = _.isFunction(method); - return _.map(obj, function(value) { - return (isFunc ? method : value[method]).apply(value, args); - }); - }; - - // Convenience version of a common use case of `map`: fetching a property. - _.pluck = function(obj, key) { - return _.map(obj, _.property(key)); - }; - - // Convenience version of a common use case of `filter`: selecting only objects - // containing specific `key:value` pairs. - _.where = function(obj, attrs) { - return _.filter(obj, _.matches(attrs)); - }; - - // Convenience version of a common use case of `find`: getting the first object - // containing specific `key:value` pairs. - _.findWhere = function(obj, attrs) { - return _.find(obj, _.matches(attrs)); - }; - - // Return the maximum element (or element-based computation). - _.max = function(obj, iteratee, context) { - var result = -Infinity, lastComputed = -Infinity, - value, computed; - if (iteratee == null && obj != null) { - obj = obj.length === +obj.length ? obj : _.values(obj); - for (var i = 0, length = obj.length; i < length; i++) { - value = obj[i]; - if (value > result) { - result = value; - } - } - } else { - iteratee = _.iteratee(iteratee, context); - _.each(obj, function(value, index, list) { - computed = iteratee(value, index, list); - if (computed > lastComputed || computed === -Infinity && result === -Infinity) { - result = value; - lastComputed = computed; - } - }); - } - return result; - }; - - // Return the minimum element (or element-based computation). - _.min = function(obj, iteratee, context) { - var result = Infinity, lastComputed = Infinity, - value, computed; - if (iteratee == null && obj != null) { - obj = obj.length === +obj.length ? obj : _.values(obj); - for (var i = 0, length = obj.length; i < length; i++) { - value = obj[i]; - if (value < result) { - result = value; - } - } - } else { - iteratee = _.iteratee(iteratee, context); - _.each(obj, function(value, index, list) { - computed = iteratee(value, index, list); - if (computed < lastComputed || computed === Infinity && result === Infinity) { - result = value; - lastComputed = computed; - } - }); - } - return result; - }; - - // Shuffle a collection, using the modern version of the - // [Fisher-Yates shuffle](http://en.wikipedia.org/wiki/Fisher–Yates_shuffle). - _.shuffle = function(obj) { - var set = obj && obj.length === +obj.length ? obj : _.values(obj); - var length = set.length; - var shuffled = Array(length); - for (var index = 0, rand; index < length; index++) { - rand = _.random(0, index); - if (rand !== index) shuffled[index] = shuffled[rand]; - shuffled[rand] = set[index]; - } - return shuffled; - }; - - // Sample **n** random values from a collection. - // If **n** is not specified, returns a single random element. - // The internal `guard` argument allows it to work with `map`. - _.sample = function(obj, n, guard) { - if (n == null || guard) { - if (obj.length !== +obj.length) obj = _.values(obj); - return obj[_.random(obj.length - 1)]; - } - return _.shuffle(obj).slice(0, Math.max(0, n)); - }; - - // Sort the object's values by a criterion produced by an iteratee. - _.sortBy = function(obj, iteratee, context) { - iteratee = _.iteratee(iteratee, context); - return _.pluck(_.map(obj, function(value, index, list) { - return { - value: value, - index: index, - criteria: iteratee(value, index, list) - }; - }).sort(function(left, right) { - var a = left.criteria; - var b = right.criteria; - if (a !== b) { - if (a > b || a === void 0) return 1; - if (a < b || b === void 0) return -1; - } - return left.index - right.index; - }), 'value'); - }; - - // An internal function used for aggregate "group by" operations. - var group = function(behavior) { - return function(obj, iteratee, context) { - var result = {}; - iteratee = _.iteratee(iteratee, context); - _.each(obj, function(value, index) { - var key = iteratee(value, index, obj); - behavior(result, value, key); - }); - return result; - }; - }; - - // Groups the object's values by a criterion. Pass either a string attribute - // to group by, or a function that returns the criterion. - _.groupBy = group(function(result, value, key) { - if (_.has(result, key)) result[key].push(value); else result[key] = [value]; - }); - - // Indexes the object's values by a criterion, similar to `groupBy`, but for - // when you know that your index values will be unique. - _.indexBy = group(function(result, value, key) { - result[key] = value; - }); - - // Counts instances of an object that group by a certain criterion. Pass - // either a string attribute to count by, or a function that returns the - // criterion. - _.countBy = group(function(result, value, key) { - if (_.has(result, key)) result[key]++; else result[key] = 1; - }); - - // Use a comparator function to figure out the smallest index at which - // an object should be inserted so as to maintain order. Uses binary search. - _.sortedIndex = function(array, obj, iteratee, context) { - iteratee = _.iteratee(iteratee, context, 1); - var value = iteratee(obj); - var low = 0, high = array.length; - while (low < high) { - var mid = low + high >>> 1; - if (iteratee(array[mid]) < value) low = mid + 1; else high = mid; - } - return low; - }; - - // Safely create a real, live array from anything iterable. - _.toArray = function(obj) { - if (!obj) return []; - if (_.isArray(obj)) return slice.call(obj); - if (obj.length === +obj.length) return _.map(obj, _.identity); - return _.values(obj); - }; - - // Return the number of elements in an object. - _.size = function(obj) { - if (obj == null) return 0; - return obj.length === +obj.length ? obj.length : _.keys(obj).length; - }; - - // Split a collection into two arrays: one whose elements all satisfy the given - // predicate, and one whose elements all do not satisfy the predicate. - _.partition = function(obj, predicate, context) { - predicate = _.iteratee(predicate, context); - var pass = [], fail = []; - _.each(obj, function(value, key, obj) { - (predicate(value, key, obj) ? pass : fail).push(value); - }); - return [pass, fail]; - }; - - // Array Functions - // --------------- - - // Get the first element of an array. Passing **n** will return the first N - // values in the array. Aliased as `head` and `take`. The **guard** check - // allows it to work with `_.map`. - _.first = _.head = _.take = function(array, n, guard) { - if (array == null) return void 0; - if (n == null || guard) return array[0]; - if (n < 0) return []; - return slice.call(array, 0, n); - }; - - // Returns everything but the last entry of the array. Especially useful on - // the arguments object. Passing **n** will return all the values in - // the array, excluding the last N. The **guard** check allows it to work with - // `_.map`. - _.initial = function(array, n, guard) { - return slice.call(array, 0, Math.max(0, array.length - (n == null || guard ? 1 : n))); - }; - - // Get the last element of an array. Passing **n** will return the last N - // values in the array. The **guard** check allows it to work with `_.map`. - _.last = function(array, n, guard) { - if (array == null) return void 0; - if (n == null || guard) return array[array.length - 1]; - return slice.call(array, Math.max(array.length - n, 0)); - }; - - // Returns everything but the first entry of the array. Aliased as `tail` and `drop`. - // Especially useful on the arguments object. Passing an **n** will return - // the rest N values in the array. The **guard** - // check allows it to work with `_.map`. - _.rest = _.tail = _.drop = function(array, n, guard) { - return slice.call(array, n == null || guard ? 1 : n); - }; - - // Trim out all falsy values from an array. - _.compact = function(array) { - return _.filter(array, _.identity); - }; - - // Internal implementation of a recursive `flatten` function. - var flatten = function(input, shallow, strict, output) { - if (shallow && _.every(input, _.isArray)) { - return concat.apply(output, input); - } - for (var i = 0, length = input.length; i < length; i++) { - var value = input[i]; - if (!_.isArray(value) && !_.isArguments(value)) { - if (!strict) output.push(value); - } else if (shallow) { - push.apply(output, value); - } else { - flatten(value, shallow, strict, output); - } - } - return output; - }; - - // Flatten out an array, either recursively (by default), or just one level. - _.flatten = function(array, shallow) { - return flatten(array, shallow, false, []); - }; - - // Return a version of the array that does not contain the specified value(s). - _.without = function(array) { - return _.difference(array, slice.call(arguments, 1)); - }; - - // Produce a duplicate-free version of the array. If the array has already - // been sorted, you have the option of using a faster algorithm. - // Aliased as `unique`. - _.uniq = _.unique = function(array, isSorted, iteratee, context) { - if (array == null) return []; - if (!_.isBoolean(isSorted)) { - context = iteratee; - iteratee = isSorted; - isSorted = false; - } - if (iteratee != null) iteratee = _.iteratee(iteratee, context); - var result = []; - var seen = []; - for (var i = 0, length = array.length; i < length; i++) { - var value = array[i]; - if (isSorted) { - if (!i || seen !== value) result.push(value); - seen = value; - } else if (iteratee) { - var computed = iteratee(value, i, array); - if (_.indexOf(seen, computed) < 0) { - seen.push(computed); - result.push(value); - } - } else if (_.indexOf(result, value) < 0) { - result.push(value); - } - } - return result; - }; - - // Produce an array that contains the union: each distinct element from all of - // the passed-in arrays. - _.union = function() { - return _.uniq(flatten(arguments, true, true, [])); - }; - - // Produce an array that contains every item shared between all the - // passed-in arrays. - _.intersection = function(array) { - if (array == null) return []; - var result = []; - var argsLength = arguments.length; - for (var i = 0, length = array.length; i < length; i++) { - var item = array[i]; - if (_.contains(result, item)) continue; - for (var j = 1; j < argsLength; j++) { - if (!_.contains(arguments[j], item)) break; - } - if (j === argsLength) result.push(item); - } - return result; - }; - - // Take the difference between one array and a number of other arrays. - // Only the elements present in just the first array will remain. - _.difference = function(array) { - var rest = flatten(slice.call(arguments, 1), true, true, []); - return _.filter(array, function(value){ - return !_.contains(rest, value); - }); - }; - - // Zip together multiple lists into a single array -- elements that share - // an index go together. - _.zip = function(array) { - if (array == null) return []; - var length = _.max(arguments, 'length').length; - var results = Array(length); - for (var i = 0; i < length; i++) { - results[i] = _.pluck(arguments, i); - } - return results; - }; - - // Converts lists into objects. Pass either a single array of `[key, value]` - // pairs, or two parallel arrays of the same length -- one of keys, and one of - // the corresponding values. - _.object = function(list, values) { - if (list == null) return {}; - var result = {}; - for (var i = 0, length = list.length; i < length; i++) { - if (values) { - result[list[i]] = values[i]; - } else { - result[list[i][0]] = list[i][1]; - } - } - return result; - }; - - // Return the position of the first occurrence of an item in an array, - // or -1 if the item is not included in the array. - // If the array is large and already in sort order, pass `true` - // for **isSorted** to use binary search. - _.indexOf = function(array, item, isSorted) { - if (array == null) return -1; - var i = 0, length = array.length; - if (isSorted) { - if (typeof isSorted == 'number') { - i = isSorted < 0 ? Math.max(0, length + isSorted) : isSorted; - } else { - i = _.sortedIndex(array, item); - return array[i] === item ? i : -1; - } - } - for (; i < length; i++) if (array[i] === item) return i; - return -1; - }; - - _.lastIndexOf = function(array, item, from) { - if (array == null) return -1; - var idx = array.length; - if (typeof from == 'number') { - idx = from < 0 ? idx + from + 1 : Math.min(idx, from + 1); - } - while (--idx >= 0) if (array[idx] === item) return idx; - return -1; - }; - - // Generate an integer Array containing an arithmetic progression. A port of - // the native Python `range()` function. See - // [the Python documentation](http://docs.python.org/library/functions.html#range). - _.range = function(start, stop, step) { - if (arguments.length <= 1) { - stop = start || 0; - start = 0; - } - step = step || 1; - - var length = Math.max(Math.ceil((stop - start) / step), 0); - var range = Array(length); - - for (var idx = 0; idx < length; idx++, start += step) { - range[idx] = start; - } - - return range; - }; - - // Function (ahem) Functions - // ------------------ - - // Reusable constructor function for prototype setting. - var Ctor = function(){}; - - // Create a function bound to a given object (assigning `this`, and arguments, - // optionally). Delegates to **ECMAScript 5**'s native `Function.bind` if - // available. - _.bind = function(func, context) { - var args, bound; - if (nativeBind && func.bind === nativeBind) return nativeBind.apply(func, slice.call(arguments, 1)); - if (!_.isFunction(func)) throw new TypeError('Bind must be called on a function'); - args = slice.call(arguments, 2); - bound = function() { - if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments))); - Ctor.prototype = func.prototype; - var self = new Ctor; - Ctor.prototype = null; - var result = func.apply(self, args.concat(slice.call(arguments))); - if (_.isObject(result)) return result; - return self; - }; - return bound; - }; - - // Partially apply a function by creating a version that has had some of its - // arguments pre-filled, without changing its dynamic `this` context. _ acts - // as a placeholder, allowing any combination of arguments to be pre-filled. - _.partial = function(func) { - var boundArgs = slice.call(arguments, 1); - return function() { - var position = 0; - var args = boundArgs.slice(); - for (var i = 0, length = args.length; i < length; i++) { - if (args[i] === _) args[i] = arguments[position++]; - } - while (position < arguments.length) args.push(arguments[position++]); - return func.apply(this, args); - }; - }; - - // Bind a number of an object's methods to that object. Remaining arguments - // are the method names to be bound. Useful for ensuring that all callbacks - // defined on an object belong to it. - _.bindAll = function(obj) { - var i, length = arguments.length, key; - if (length <= 1) throw new Error('bindAll must be passed function names'); - for (i = 1; i < length; i++) { - key = arguments[i]; - obj[key] = _.bind(obj[key], obj); - } - return obj; - }; - - // Memoize an expensive function by storing its results. - _.memoize = function(func, hasher) { - var memoize = function(key) { - var cache = memoize.cache; - var address = hasher ? hasher.apply(this, arguments) : key; - if (!_.has(cache, address)) cache[address] = func.apply(this, arguments); - return cache[address]; - }; - memoize.cache = {}; - return memoize; - }; - - // Delays a function for the given number of milliseconds, and then calls - // it with the arguments supplied. - _.delay = function(func, wait) { - var args = slice.call(arguments, 2); - return setTimeout(function(){ - return func.apply(null, args); - }, wait); - }; - - // Defers a function, scheduling it to run after the current call stack has - // cleared. - _.defer = function(func) { - return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1))); - }; - - // Returns a function, that, when invoked, will only be triggered at most once - // during a given window of time. Normally, the throttled function will run - // as much as it can, without ever going more than once per `wait` duration; - // but if you'd like to disable the execution on the leading edge, pass - // `{leading: false}`. To disable execution on the trailing edge, ditto. - _.throttle = function(func, wait, options) { - var context, args, result; - var timeout = null; - var previous = 0; - if (!options) options = {}; - var later = function() { - previous = options.leading === false ? 0 : _.now(); - timeout = null; - result = func.apply(context, args); - if (!timeout) context = args = null; - }; - return function() { - var now = _.now(); - if (!previous && options.leading === false) previous = now; - var remaining = wait - (now - previous); - context = this; - args = arguments; - if (remaining <= 0 || remaining > wait) { - clearTimeout(timeout); - timeout = null; - previous = now; - result = func.apply(context, args); - if (!timeout) context = args = null; - } else if (!timeout && options.trailing !== false) { - timeout = setTimeout(later, remaining); - } - return result; - }; - }; - - // Returns a function, that, as long as it continues to be invoked, will not - // be triggered. The function will be called after it stops being called for - // N milliseconds. If `immediate` is passed, trigger the function on the - // leading edge, instead of the trailing. - _.debounce = function(func, wait, immediate) { - var timeout, args, context, timestamp, result; - - var later = function() { - var last = _.now() - timestamp; - - if (last < wait && last > 0) { - timeout = setTimeout(later, wait - last); - } else { - timeout = null; - if (!immediate) { - result = func.apply(context, args); - if (!timeout) context = args = null; - } - } - }; - - return function() { - context = this; - args = arguments; - timestamp = _.now(); - var callNow = immediate && !timeout; - if (!timeout) timeout = setTimeout(later, wait); - if (callNow) { - result = func.apply(context, args); - context = args = null; - } - - return result; - }; - }; - - // Returns the first function passed as an argument to the second, - // allowing you to adjust arguments, run code before and after, and - // conditionally execute the original function. - _.wrap = function(func, wrapper) { - return _.partial(wrapper, func); - }; - - // Returns a negated version of the passed-in predicate. - _.negate = function(predicate) { - return function() { - return !predicate.apply(this, arguments); - }; - }; - - // Returns a function that is the composition of a list of functions, each - // consuming the return value of the function that follows. - _.compose = function() { - var args = arguments; - var start = args.length - 1; - return function() { - var i = start; - var result = args[start].apply(this, arguments); - while (i--) result = args[i].call(this, result); - return result; - }; - }; - - // Returns a function that will only be executed after being called N times. - _.after = function(times, func) { - return function() { - if (--times < 1) { - return func.apply(this, arguments); - } - }; - }; - - // Returns a function that will only be executed before being called N times. - _.before = function(times, func) { - var memo; - return function() { - if (--times > 0) { - memo = func.apply(this, arguments); - } else { - func = null; - } - return memo; - }; - }; - - // Returns a function that will be executed at most one time, no matter how - // often you call it. Useful for lazy initialization. - _.once = _.partial(_.before, 2); - - // Object Functions - // ---------------- - - // Retrieve the names of an object's properties. - // Delegates to **ECMAScript 5**'s native `Object.keys` - _.keys = function(obj) { - if (!_.isObject(obj)) return []; - if (nativeKeys) return nativeKeys(obj); - var keys = []; - for (var key in obj) if (_.has(obj, key)) keys.push(key); - return keys; - }; - - // Retrieve the values of an object's properties. - _.values = function(obj) { - var keys = _.keys(obj); - var length = keys.length; - var values = Array(length); - for (var i = 0; i < length; i++) { - values[i] = obj[keys[i]]; - } - return values; - }; - - // Convert an object into a list of `[key, value]` pairs. - _.pairs = function(obj) { - var keys = _.keys(obj); - var length = keys.length; - var pairs = Array(length); - for (var i = 0; i < length; i++) { - pairs[i] = [keys[i], obj[keys[i]]]; - } - return pairs; - }; - - // Invert the keys and values of an object. The values must be serializable. - _.invert = function(obj) { - var result = {}; - var keys = _.keys(obj); - for (var i = 0, length = keys.length; i < length; i++) { - result[obj[keys[i]]] = keys[i]; - } - return result; - }; - - // Return a sorted list of the function names available on the object. - // Aliased as `methods` - _.functions = _.methods = function(obj) { - var names = []; - for (var key in obj) { - if (_.isFunction(obj[key])) names.push(key); - } - return names.sort(); - }; - - // Extend a given object with all the properties in passed-in object(s). - _.extend = function(obj) { - if (!_.isObject(obj)) return obj; - var source, prop; - for (var i = 1, length = arguments.length; i < length; i++) { - source = arguments[i]; - for (prop in source) { - if (hasOwnProperty.call(source, prop)) { - obj[prop] = source[prop]; - } - } - } - return obj; - }; - - // Return a copy of the object only containing the whitelisted properties. - _.pick = function(obj, iteratee, context) { - var result = {}, key; - if (obj == null) return result; - if (_.isFunction(iteratee)) { - iteratee = createCallback(iteratee, context); - for (key in obj) { - var value = obj[key]; - if (iteratee(value, key, obj)) result[key] = value; - } - } else { - var keys = concat.apply([], slice.call(arguments, 1)); - obj = new Object(obj); - for (var i = 0, length = keys.length; i < length; i++) { - key = keys[i]; - if (key in obj) result[key] = obj[key]; - } - } - return result; - }; - - // Return a copy of the object without the blacklisted properties. - _.omit = function(obj, iteratee, context) { - if (_.isFunction(iteratee)) { - iteratee = _.negate(iteratee); - } else { - var keys = _.map(concat.apply([], slice.call(arguments, 1)), String); - iteratee = function(value, key) { - return !_.contains(keys, key); - }; - } - return _.pick(obj, iteratee, context); - }; - - // Fill in a given object with default properties. - _.defaults = function(obj) { - if (!_.isObject(obj)) return obj; - for (var i = 1, length = arguments.length; i < length; i++) { - var source = arguments[i]; - for (var prop in source) { - if (obj[prop] === void 0) obj[prop] = source[prop]; - } - } - return obj; - }; - - // Create a (shallow-cloned) duplicate of an object. - _.clone = function(obj) { - if (!_.isObject(obj)) return obj; - return _.isArray(obj) ? obj.slice() : _.extend({}, obj); - }; - - // Invokes interceptor with the obj, and then returns obj. - // The primary purpose of this method is to "tap into" a method chain, in - // order to perform operations on intermediate results within the chain. - _.tap = function(obj, interceptor) { - interceptor(obj); - return obj; - }; - - // Internal recursive comparison function for `isEqual`. - var eq = function(a, b, aStack, bStack) { - // Identical objects are equal. `0 === -0`, but they aren't identical. - // See the [Harmony `egal` proposal](http://wiki.ecmascript.org/doku.php?id=harmony:egal). - if (a === b) return a !== 0 || 1 / a === 1 / b; - // A strict comparison is necessary because `null == undefined`. - if (a == null || b == null) return a === b; - // Unwrap any wrapped objects. - if (a instanceof _) a = a._wrapped; - if (b instanceof _) b = b._wrapped; - // Compare `[[Class]]` names. - var className = toString.call(a); - if (className !== toString.call(b)) return false; - switch (className) { - // Strings, numbers, regular expressions, dates, and booleans are compared by value. - case '[object RegExp]': - // RegExps are coerced to strings for comparison (Note: '' + /a/i === '/a/i') - case '[object String]': - // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is - // equivalent to `new String("5")`. - return '' + a === '' + b; - case '[object Number]': - // `NaN`s are equivalent, but non-reflexive. - // Object(NaN) is equivalent to NaN - if (+a !== +a) return +b !== +b; - // An `egal` comparison is performed for other numeric values. - return +a === 0 ? 1 / +a === 1 / b : +a === +b; - case '[object Date]': - case '[object Boolean]': - // Coerce dates and booleans to numeric primitive values. Dates are compared by their - // millisecond representations. Note that invalid dates with millisecond representations - // of `NaN` are not equivalent. - return +a === +b; - } - if (typeof a != 'object' || typeof b != 'object') return false; - // Assume equality for cyclic structures. The algorithm for detecting cyclic - // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`. - var length = aStack.length; - while (length--) { - // Linear search. Performance is inversely proportional to the number of - // unique nested structures. - if (aStack[length] === a) return bStack[length] === b; - } - // Objects with different constructors are not equivalent, but `Object`s - // from different frames are. - var aCtor = a.constructor, bCtor = b.constructor; - if ( - aCtor !== bCtor && - // Handle Object.create(x) cases - 'constructor' in a && 'constructor' in b && - !(_.isFunction(aCtor) && aCtor instanceof aCtor && - _.isFunction(bCtor) && bCtor instanceof bCtor) - ) { - return false; - } - // Add the first object to the stack of traversed objects. - aStack.push(a); - bStack.push(b); - var size, result; - // Recursively compare objects and arrays. - if (className === '[object Array]') { - // Compare array lengths to determine if a deep comparison is necessary. - size = a.length; - result = size === b.length; - if (result) { - // Deep compare the contents, ignoring non-numeric properties. - while (size--) { - if (!(result = eq(a[size], b[size], aStack, bStack))) break; - } - } - } else { - // Deep compare objects. - var keys = _.keys(a), key; - size = keys.length; - // Ensure that both objects contain the same number of properties before comparing deep equality. - result = _.keys(b).length === size; - if (result) { - while (size--) { - // Deep compare each member - key = keys[size]; - if (!(result = _.has(b, key) && eq(a[key], b[key], aStack, bStack))) break; - } - } - } - // Remove the first object from the stack of traversed objects. - aStack.pop(); - bStack.pop(); - return result; - }; - - // Perform a deep comparison to check if two objects are equal. - _.isEqual = function(a, b) { - return eq(a, b, [], []); - }; - - // Is a given array, string, or object empty? - // An "empty" object has no enumerable own-properties. - _.isEmpty = function(obj) { - if (obj == null) return true; - if (_.isArray(obj) || _.isString(obj) || _.isArguments(obj)) return obj.length === 0; - for (var key in obj) if (_.has(obj, key)) return false; - return true; - }; - - // Is a given value a DOM element? - _.isElement = function(obj) { - return !!(obj && obj.nodeType === 1); - }; - - // Is a given value an array? - // Delegates to ECMA5's native Array.isArray - _.isArray = nativeIsArray || function(obj) { - return toString.call(obj) === '[object Array]'; - }; - - // Is a given variable an object? - _.isObject = function(obj) { - var type = typeof obj; - return type === 'function' || type === 'object' && !!obj; - }; - - // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp. - _.each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp'], function(name) { - _['is' + name] = function(obj) { - return toString.call(obj) === '[object ' + name + ']'; - }; - }); - - // Define a fallback version of the method in browsers (ahem, IE), where - // there isn't any inspectable "Arguments" type. - if (!_.isArguments(arguments)) { - _.isArguments = function(obj) { - return _.has(obj, 'callee'); - }; - } - - // Optimize `isFunction` if appropriate. Work around an IE 11 bug. - if (typeof /./ !== 'function') { - _.isFunction = function(obj) { - return typeof obj == 'function' || false; - }; - } - - // Is a given object a finite number? - _.isFinite = function(obj) { - return isFinite(obj) && !isNaN(parseFloat(obj)); - }; - - // Is the given value `NaN`? (NaN is the only number which does not equal itself). - _.isNaN = function(obj) { - return _.isNumber(obj) && obj !== +obj; - }; - - // Is a given value a boolean? - _.isBoolean = function(obj) { - return obj === true || obj === false || toString.call(obj) === '[object Boolean]'; - }; - - // Is a given value equal to null? - _.isNull = function(obj) { - return obj === null; - }; - - // Is a given variable undefined? - _.isUndefined = function(obj) { - return obj === void 0; - }; - - // Shortcut function for checking if an object has a given property directly - // on itself (in other words, not on a prototype). - _.has = function(obj, key) { - return obj != null && hasOwnProperty.call(obj, key); - }; - - // Utility Functions - // ----------------- - - // Run Underscore.js in *noConflict* mode, returning the `_` variable to its - // previous owner. Returns a reference to the Underscore object. - _.noConflict = function() { - root._ = previousUnderscore; - return this; - }; - - // Keep the identity function around for default iteratees. - _.identity = function(value) { - return value; - }; - - // Predicate-generating functions. Often useful outside of Underscore. - _.constant = function(value) { - return function() { - return value; - }; - }; - - _.noop = function(){}; - - _.property = function(key) { - return function(obj) { - return obj[key]; - }; - }; - - // Returns a predicate for checking whether an object has a given set of `key:value` pairs. - _.matches = function(attrs) { - var pairs = _.pairs(attrs), length = pairs.length; - return function(obj) { - if (obj == null) return !length; - obj = new Object(obj); - for (var i = 0; i < length; i++) { - var pair = pairs[i], key = pair[0]; - if (pair[1] !== obj[key] || !(key in obj)) return false; - } - return true; - }; - }; - - // Run a function **n** times. - _.times = function(n, iteratee, context) { - var accum = Array(Math.max(0, n)); - iteratee = createCallback(iteratee, context, 1); - for (var i = 0; i < n; i++) accum[i] = iteratee(i); - return accum; - }; - - // Return a random integer between min and max (inclusive). - _.random = function(min, max) { - if (max == null) { - max = min; - min = 0; - } - return min + Math.floor(Math.random() * (max - min + 1)); - }; - - // A (possibly faster) way to get the current timestamp as an integer. - _.now = Date.now || function() { - return new Date().getTime(); - }; - - // List of HTML entities for escaping. - var escapeMap = { - '&': '&', - '<': '<', - '>': '>', - '"': '"', - "'": ''', - '`': '`' - }; - var unescapeMap = _.invert(escapeMap); - - // Functions for escaping and unescaping strings to/from HTML interpolation. - var createEscaper = function(map) { - var escaper = function(match) { - return map[match]; - }; - // Regexes for identifying a key that needs to be escaped - var source = '(?:' + _.keys(map).join('|') + ')'; - var testRegexp = RegExp(source); - var replaceRegexp = RegExp(source, 'g'); - return function(string) { - string = string == null ? '' : '' + string; - return testRegexp.test(string) ? string.replace(replaceRegexp, escaper) : string; - }; - }; - _.escape = createEscaper(escapeMap); - _.unescape = createEscaper(unescapeMap); - - // If the value of the named `property` is a function then invoke it with the - // `object` as context; otherwise, return it. - _.result = function(object, property) { - if (object == null) return void 0; - var value = object[property]; - return _.isFunction(value) ? object[property]() : value; - }; - - // Generate a unique integer id (unique within the entire client session). - // Useful for temporary DOM ids. - var idCounter = 0; - _.uniqueId = function(prefix) { - var id = ++idCounter + ''; - return prefix ? prefix + id : id; - }; - - // By default, Underscore uses ERB-style template delimiters, change the - // following template settings to use alternative delimiters. - _.templateSettings = { - evaluate : /<%([\s\S]+?)%>/g, - interpolate : /<%=([\s\S]+?)%>/g, - escape : /<%-([\s\S]+?)%>/g - }; - - // When customizing `templateSettings`, if you don't want to define an - // interpolation, evaluation or escaping regex, we need one that is - // guaranteed not to match. - var noMatch = /(.)^/; - - // Certain characters need to be escaped so that they can be put into a - // string literal. - var escapes = { - "'": "'", - '\\': '\\', - '\r': 'r', - '\n': 'n', - '\u2028': 'u2028', - '\u2029': 'u2029' - }; - - var escaper = /\\|'|\r|\n|\u2028|\u2029/g; - - var escapeChar = function(match) { - return '\\' + escapes[match]; - }; - - // JavaScript micro-templating, similar to John Resig's implementation. - // Underscore templating handles arbitrary delimiters, preserves whitespace, - // and correctly escapes quotes within interpolated code. - // NB: `oldSettings` only exists for backwards compatibility. - _.template = function(text, settings, oldSettings) { - if (!settings && oldSettings) settings = oldSettings; - settings = _.defaults({}, settings, _.templateSettings); - - // Combine delimiters into one regular expression via alternation. - var matcher = RegExp([ - (settings.escape || noMatch).source, - (settings.interpolate || noMatch).source, - (settings.evaluate || noMatch).source - ].join('|') + '|$', 'g'); - - // Compile the template source, escaping string literals appropriately. - var index = 0; - var source = "__p+='"; - text.replace(matcher, function(match, escape, interpolate, evaluate, offset) { - source += text.slice(index, offset).replace(escaper, escapeChar); - index = offset + match.length; - - if (escape) { - source += "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'"; - } else if (interpolate) { - source += "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'"; - } else if (evaluate) { - source += "';\n" + evaluate + "\n__p+='"; - } - - // Adobe VMs need the match returned to produce the correct offest. - return match; - }); - source += "';\n"; - - // If a variable is not specified, place data values in local scope. - if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n'; - - source = "var __t,__p='',__j=Array.prototype.join," + - "print=function(){__p+=__j.call(arguments,'');};\n" + - source + 'return __p;\n'; - - try { - var render = new Function(settings.variable || 'obj', '_', source); - } catch (e) { - e.source = source; - throw e; - } - - var template = function(data) { - return render.call(this, data, _); - }; - - // Provide the compiled source as a convenience for precompilation. - var argument = settings.variable || 'obj'; - template.source = 'function(' + argument + '){\n' + source + '}'; - - return template; - }; - - // Add a "chain" function. Start chaining a wrapped Underscore object. - _.chain = function(obj) { - var instance = _(obj); - instance._chain = true; - return instance; - }; - - // OOP - // --------------- - // If Underscore is called as a function, it returns a wrapped object that - // can be used OO-style. This wrapper holds altered versions of all the - // underscore functions. Wrapped objects may be chained. - - // Helper function to continue chaining intermediate results. - var result = function(obj) { - return this._chain ? _(obj).chain() : obj; - }; - - // Add your own custom functions to the Underscore object. - _.mixin = function(obj) { - _.each(_.functions(obj), function(name) { - var func = _[name] = obj[name]; - _.prototype[name] = function() { - var args = [this._wrapped]; - push.apply(args, arguments); - return result.call(this, func.apply(_, args)); - }; - }); - }; - - // Add all of the Underscore functions to the wrapper object. - _.mixin(_); - - // Add all mutator Array functions to the wrapper. - _.each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) { - var method = ArrayProto[name]; - _.prototype[name] = function() { - var obj = this._wrapped; - method.apply(obj, arguments); - if ((name === 'shift' || name === 'splice') && obj.length === 0) delete obj[0]; - return result.call(this, obj); - }; - }); - - // Add all accessor Array functions to the wrapper. - _.each(['concat', 'join', 'slice'], function(name) { - var method = ArrayProto[name]; - _.prototype[name] = function() { - return result.call(this, method.apply(this._wrapped, arguments)); - }; - }); - - // Extracts the result from a wrapped and chained object. - _.prototype.value = function() { - return this._wrapped; - }; - - // AMD registration happens at the end for compatibility with AMD loaders - // that may not enforce next-turn semantics on modules. Even though general - // practice for AMD registration is to be anonymous, underscore registers - // as a named module because, like jQuery, it is a base library that is - // popular enough to be bundled in a third party lib, but not be part of - // an AMD load request. Those cases could generate an error when an - // anonymous define() is called outside of a loader request. - if (typeof define === 'function' && define.amd) { - define('underscore', [], function() { - return _; - }); - } -}.call(this)); diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/updatedir_inplace.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/updatedir_inplace.cwl deleted file mode 100755 index fe4f284d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/updatedir_inplace.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.r) - entryname: inp - writable: true - InplaceUpdateRequirement: - inplaceUpdate: true -inputs: - r: Directory -outputs: - out: - type: Directory - outputBinding: - glob: inp -arguments: [touch, inp/blurb] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/updateval.py b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/updateval.py deleted file mode 100644 index abd9a401..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/updateval.py +++ /dev/null @@ -1,6 +0,0 @@ -import sys -f = open(sys.argv[1], "r+") -val = int(f.read()) -f.seek(0) -f.write(str(val+1)) -f.close() diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/updateval_inplace.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/updateval_inplace.cwl deleted file mode 100755 index d3b45048..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/updateval_inplace.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.r) - writable: true - InplaceUpdateRequirement: - inplaceUpdate: true -hints: - DockerRequirement: - dockerPull: "python:2.7.15-alpine3.7" -inputs: - r: File - script: - type: File - default: - class: File - location: updateval.py -outputs: - out: - type: File - outputBinding: - glob: $(inputs.r.basename) -arguments: [python, $(inputs.script), $(inputs.r.basename)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_action.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_action.cwl deleted file mode 100644 index 29a6418a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_action.cwl +++ /dev/null @@ -1,10 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -inputs: - initial_file: File - out_file_name: string -outputs: - processed_file: stdout -stdout: $(inputs.out_file_name) -arguments: [echo, $(inputs.initial_file.basename)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_anon_enum_inside_array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_anon_enum_inside_array.cwl deleted file mode 100644 index 6d23520f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_anon_enum_inside_array.cwl +++ /dev/null @@ -1,25 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -inputs: - first: - type: - type: record - fields: - species: - - type: enum - symbols: [homo_sapiens, mus_musculus] - - "null" - second: - type: - - "null" - - type: enum - symbols: [homo_sapiens, mus_musculus] -baseCommand: echo -arguments: - - prefix: first - valueFrom: $(inputs.first.species) - - prefix: second - valueFrom: $(inputs.second) -outputs: - result: stdout - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_anon_enum_inside_array_inside_schemadef.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_anon_enum_inside_array_inside_schemadef.cwl deleted file mode 100644 index 44e8fe7d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_anon_enum_inside_array_inside_schemadef.cwl +++ /dev/null @@ -1,27 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -requirements: - SchemaDefRequirement: - types: - - name: vcf2maf_params - type: record - fields: - species: - - "null" - - type: enum - symbols: [homo_sapiens, mus_musculus] - ncbi_build: - - "null" - - type: enum - symbols: [GRCh37, GRCh38, GRCm38] -inputs: - first: vcf2maf_params -baseCommand: echo -arguments: - - prefix: species - valueFrom: $(inputs.first.species) - - prefix: ncbi_build - valueFrom: $(inputs.first.ncbi_build) -outputs: - result: stdout - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_any-type-compat.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_any-type-compat.cwl deleted file mode 100644 index 5b0c2541..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_any-type-compat.cwl +++ /dev/null @@ -1,22 +0,0 @@ -cwlVersion: v1.2 -class: Workflow - -steps: [] -inputs: - input1: - type: Any - input2: - type: Any[] - input3: - type: Any - -outputs: - - id: output1 - type: string[] - outputSource: input1 - - id: output2 - type: string[] - outputSource: input2 - - id: output3 - type: string - outputSource: input3 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bar.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bar.cwl deleted file mode 100644 index 6fa2a718..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bar.cwl +++ /dev/null @@ -1,10 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in1: int -baseCommand: [echo] -outputs: - out1: - type: string - outputBinding: - outputEval: bar $(inputs.in1) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_basename-fields-test.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_basename-fields-test.cwl deleted file mode 100644 index 99f54329..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_basename-fields-test.cwl +++ /dev/null @@ -1,33 +0,0 @@ -cwlVersion: v1.2 -class: Workflow - -requirements: - - class: StepInputExpressionRequirement - -inputs: - tool: File - -outputs: - rootFile: - type: File - outputSource: root/out - extFile: - type: File - outputSource: ext/out - -steps: - root: - run: echo-file-tool.cwl - in: - tool: tool - in: - valueFrom: $(inputs.tool.nameroot) - out: [out] - ext: - run: echo-file-tool.cwl - in: - tool: tool - in: - valueFrom: $(inputs.tool.nameext) - out: [out] - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bash-dollar-quote.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bash-dollar-quote.cwl deleted file mode 100644 index c171acd6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bash-dollar-quote.cwl +++ /dev/null @@ -1,55 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: script.sh - entry: | - echo \$(echo \ - "My country, 'tis of thee," \ - "Sweet land of liberty" | rev) - echo '$(inputs.val)' # produce val - echo '\$(inputs.val)' # produce $(inputs.val) - echo - echo '\\$(inputs.val)' # produce \val - echo '\\\$(inputs.val)' # produce \$(inputs.val) - echo - echo '\\\\$(inputs.val)' # produce \\val - echo '\\\\\$(inputs.val)' # produce \\$(inputs.val) - echo - echo '\\\\\\$(inputs.val)' # produce \\\val - echo '\\\\\\\$(inputs.val)' # produce \\\$(inputs.val) - echo - echo '\\\\\\\\$(inputs.val)' # produce \\\\val - echo '\\\\\\\\\$(inputs.val)' # produce \\\\$(inputs.val) - echo - echo '\\\\\\\\\\$(inputs.val)' # produce \\\\\val - echo '\\\\\\\\\\\$(inputs.val)' # produce \\\\\$(inputs.val) - echo '\' # produce \ - echo '\\' # produce \ - echo '\\\' # produce \\ - echo '\\\\' # produce \\ - echo '\\\\\' # produce \\\ - echo '\\\\\\' # produce \\\ - echo '\\\\\\\' # produce \\\\ - echo '\\\\\\\\' # produce \\\\ - echo '\\\\\\\\\' # produce \\\\\ - echo '\\\\\\\\\\' # produce \\\\\ - echo '$' # produce $ - echo '\$' # produce \$ - echo '\\$' # produce \$ - echo '$$' # produce $$ - echo '$$$' # produce $$$ - -baseCommand: ["bash", "script.sh"] - -inputs: - val: - type: string - default: "val" - -outputs: - out: stdout - -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bash-line-continuation-with-expression.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bash-line-continuation-with-expression.cwl deleted file mode 100644 index 89c9688f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bash-line-continuation-with-expression.cwl +++ /dev/null @@ -1,22 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InitialWorkDirRequirement: - listing: - - entryname: script.sh - entry: | - echo \ - "My country, 'tis of thee," \ - "Sweet land of $(inputs.liberty)" - -baseCommand: ["bash", "script.sh"] - -inputs: - liberty: - type: string? - default: liberty - -outputs: - out: stdout - -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bash-line-continuation.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bash-line-continuation.cwl deleted file mode 100644 index 4e033948..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bash-line-continuation.cwl +++ /dev/null @@ -1,19 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InitialWorkDirRequirement: - listing: - - entryname: script.sh - entry: | - echo \ - "My country, 'tis of thee," \ - "Sweet land of liberty" - -baseCommand: ["bash", "script.sh"] - -inputs: [] - -outputs: - out: stdout - -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_binding-test.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_binding-test.cwl deleted file mode 100755 index 90ef6d11..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_binding-test.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -hints: - - class: DockerRequirement - dockerPull: python:2-slim -inputs: - - id: reference - type: File - inputBinding: { position: 2 } - - - id: reads - type: - type: array - items: File - inputBinding: { prefix: "-YYY" } - inputBinding: { position: 3, prefix: "-XXX" } - - - id: "#args.py" - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - -outputs: - args: string[] - -baseCommand: python -arguments: ["bwa", "mem"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bool-empty-inputbinding.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bool-empty-inputbinding.cwl deleted file mode 100644 index d22605a2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bool-empty-inputbinding.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -hints: - - class: DockerRequirement - dockerPull: python:2-slim -inputs: -- id: flag - type: boolean - inputBinding: {} -- id: "args.py" - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 -outputs: -- id: args - type: string[] -baseCommand: python -arguments: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bwa-mem-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bwa-mem-tool.cwl deleted file mode 100755 index d76f3180..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_bwa-mem-tool.cwl +++ /dev/null @@ -1,61 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 - -class: CommandLineTool - -hints: - - class: ResourceRequirement - coresMin: 2 - - class: DockerRequirement - dockerPull: python:2-slim - -inputs: - - id: reference - type: File - inputBinding: { position: 2 } - - - id: reads - type: - type: array - items: File - inputBinding: { position: 3 } - - - id: minimum_seed_length - type: int - inputBinding: { position: 1, prefix: -m } - - - id: min_std_max_min - type: { type: array, items: int } - inputBinding: - position: 1 - prefix: -I - itemSeparator: "," - - - id: args.py - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - -outputs: - - id: sam - type: ["null", File] - outputBinding: { glob: output.sam } - - id: args - type: - type: array - items: string - -baseCommand: python - -arguments: - - bwa - - mem - - valueFrom: $(runtime.cores) - position: 1 - prefix: -t - -stdout: output.sam diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat-from-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat-from-dir.cwl deleted file mode 100644 index 27af5345..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat-from-dir.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 - -inputs: - dir1: Directory - -outputs: - output: - type: stdout - -baseCommand: [cat] - -stdin: $(inputs.dir1.listing[0].path) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat-tool-shortcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat-tool-shortcut.cwl deleted file mode 100755 index 3f07cebb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat-tool-shortcut.cwl +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - - class: DockerRequirement - dockerPull: debian:stretch-slim - -inputs: - file1: stdin - -outputs: - output: - type: File - outputBinding: { glob: output } - -baseCommand: [cat] - -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat-tool.cwl deleted file mode 100644 index ca2687fe..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 - -inputs: - file1: File - -outputs: - output: - type: File - outputBinding: { glob: output } - -baseCommand: [cat] - -stdin: $(inputs.file1.path) -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat.cwl deleted file mode 100644 index 9425e565..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat.cwl +++ /dev/null @@ -1,12 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in1: int - in2: int - in3: int -baseCommand: [echo] -outputs: - out1: - type: string - outputBinding: - outputEval: $(inputs.in1)$(inputs.in2)$(inputs.in3) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat1-testcli.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat1-testcli.cwl deleted file mode 100755 index b82ffbed..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat1-testcli.cwl +++ /dev/null @@ -1,41 +0,0 @@ -#!/usr/bin/env cwl-runner -{ - "class": "CommandLineTool", - "cwlVersion": "v1.2", - "doc": "Print the contents of a file to stdout using 'cat' running in a docker container.", - "hints": [ - { - "class": "DockerRequirement", - "dockerPull": "python:2-slim" - } - ], - "inputs": [ - { - "id": "file1", - "type": "File", - "inputBinding": {"position": 1} - }, - { - "id": "numbering", - "type": ["null", "boolean"], - "inputBinding": { - "position": 0, - "prefix": "-n" - } - }, - { - id: "args.py", - type: File, - default: { - class: File, - location: args.py - }, - inputBinding: { - position: -1 - } - } - ], - "outputs": [{"id": "args", "type": "string[]"}], - "baseCommand": "python", - "arguments": ["cat"] -} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-from-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-from-dir.cwl deleted file mode 100755 index fc7bb661..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-from-dir.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -inputs: - dir1: - type: Directory - inputBinding: - valueFrom: $(self.listing[0].path) -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-nodocker.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-nodocker.cwl deleted file mode 100755 index 03cfa7b4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-nodocker.cwl +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "Print the contents of a file to stdout using 'cat'." -inputs: - file1: - type: File - label: Input File - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-tool-docker.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-tool-docker.cwl deleted file mode 100755 index 03c0ea4a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-tool-docker.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." -requirements: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - label: Input File - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-tool-mediumcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-tool-mediumcut.cwl deleted file mode 100755 index 353e6800..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-tool-mediumcut.cwl +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." -requirements: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - label: Input File - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: stdout -baseCommand: cat -stdout: cat-out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-tool-shortcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-tool-shortcut.cwl deleted file mode 100755 index 45e1d959..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-tool-shortcut.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." -requirements: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - label: Input File - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: stdout -baseCommand: cat diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-tool.cwl deleted file mode 100755 index 270640ca..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat3-tool.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - label: Input File - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat4-from-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat4-from-dir.cwl deleted file mode 100755 index 077310cd..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat4-from-dir.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -inputs: - dir1: - type: Directory - inputBinding: - valueFrom: $(self.listing[0].listing[0].path) -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat4-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat4-tool.cwl deleted file mode 100755 index 29b6a154..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat4-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "Print the contents of a file to stdout using 'cat' running in a docker container if docker is available." -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: File -outputs: - output_txt: - type: File - outputBinding: - glob: output.txt -baseCommand: cat -stdout: output.txt -stdin: $(inputs.file1.path) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat5-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat5-tool.cwl deleted file mode 100755 index 22bec9c3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cat5-tool.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -$namespaces: - ex: http://example.com/ -cwlVersion: v1.2 -class: CommandLineTool -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." -hints: - DockerRequirement: - dockerPull: "debian:stretch-slim" - ex:BlibberBlubberFakeRequirement: - fakeField: fraggleFroogle -inputs: - file1: - type: File - label: "Input File" - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_check.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_check.cwl deleted file mode 100644 index da8b5c9f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_check.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - p: File - checkname: string -outputs: [] -arguments: - - sh - - "-c" - - | - name=`basename $(inputs.p.path)` - ls -l $(inputs.p.path) - if test $name = $(inputs.checkname) ; then - echo success - else - echo expected basename to be $(inputs.checkname) but was $name - exit 1 - fi diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_colon:test.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_colon:test.cwl deleted file mode 100755 index 7b675b06..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_colon:test.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -hints: - DockerRequirement: - dockerPull: docker.io/bash:4.4 -inputs: - input_file: File - outdir_name: string - -baseCommand: [ bash, -c ] -stdout: re:sult -arguments: - - | - mkdir $(inputs.outdir_name); - cp $(inputs.input_file.path) $(inputs.outdir_name)/; - echo Status: done! -outputs: - log: stdout - result: - type: Directory - outputBinding: - glob: $(inputs.outdir_name) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_colon_test_output.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_colon_test_output.cwl deleted file mode 100755 index 5e84b81f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_colon_test_output.cwl +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -hints: - DockerRequirement: - dockerPull: docker.io/bash:4.4 -inputs: - input_file: File - outdir_name: string - -baseCommand: [ bash, -c ] -arguments: - - | - mkdir $(inputs.outdir_name); - cp $(inputs.input_file.path) $(inputs.outdir_name)/; -outputs: - result: - type: Directory - outputBinding: - glob: $(inputs.outdir_name) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-001.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-001.cwl deleted file mode 100644 index de1e9793..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-001.cwl +++ /dev/null @@ -1,22 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: int - -steps: - - step1: - in: - in1: val - a_new_var: val - run: foo.cwl - when: $(inputs.a_new_var > 2) - out: [out1] - -outputs: - out1: - type: string? - outputSource: step1/out1 - -requirements: - InlineJavascriptRequirement: {} \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-001_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-001_nojs.cwl deleted file mode 100644 index 0173b293..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-001_nojs.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - test: boolean - -steps: - - step1: - in: - in1: - default: 23 - extra: test - run: foo.cwl - when: $(inputs.extra) - out: [out1] - -outputs: - out1: - type: string? - outputSource: step1/out1 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-002.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-002.cwl deleted file mode 100644 index 7549a5fb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-002.cwl +++ /dev/null @@ -1,22 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: int - -steps: - - step1: - in: - in1: val - a_new_var: val - run: foo.cwl - when: $(inputs.a_new_var > 2) - out: [out1] - -outputs: - out1: - type: string - outputSource: step1/out1 - -requirements: - InlineJavascriptRequirement: {} \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-002_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-002_nojs.cwl deleted file mode 100644 index e5ee4b5e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-002_nojs.cwl +++ /dev/null @@ -1,22 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: int - test: - type: boolean - default: false - -steps: - - step1: - in: - in1: val - a_new_var: test - run: foo.cwl - when: $(inputs.a_new_var) - out: [out1] - -outputs: - out1: - type: string - outputSource: step1/out1 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-003.1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-003.1.cwl deleted file mode 100644 index cd04dbb5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-003.1.cwl +++ /dev/null @@ -1,34 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: int - -steps: - - step1: - in: - in1: val - a_new_var: val - run: foo.cwl - when: $(inputs.in1 < 1) - out: [out1] - - step2: - in: - in1: val - a_new_var: val - run: foo.cwl - when: $(inputs.a_new_var > 2) - out: [out1] - -outputs: - out1: - type: string - outputSource: - - step1/out1 - - step2/out1 - pickValue: first_non_null - -requirements: - InlineJavascriptRequirement: {} - MultipleInputFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-003.1_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-003.1_nojs.cwl deleted file mode 100644 index 3b8b49ee..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-003.1_nojs.cwl +++ /dev/null @@ -1,37 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: - type: int - default: 23 - test1: boolean - test2: boolean - -steps: - - step1: - in: - in1: val - a_new_var: test1 - run: foo.cwl - when: $(inputs.a_new_var) - out: [out1] - - step2: - in: - in1: val - a_new_var: test2 - run: foo.cwl - when: $(inputs.a_new_var) - out: [out1] - -outputs: - out1: - type: string - outputSource: - - step1/out1 - - step2/out1 - pickValue: first_non_null - -requirements: - MultipleInputFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-003.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-003.cwl deleted file mode 100644 index 009e0134..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-003.cwl +++ /dev/null @@ -1,29 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: int - def: - type: string - default: "Direct" - -steps: - - step1: - in: - in1: val - a_new_var: val - run: foo.cwl - when: $(inputs.a_new_var > 2) - out: [out1] - -outputs: - out1: - type: string - outputSource: - - step1/out1 - - def - pickValue: first_non_null - -requirements: - InlineJavascriptRequirement: {} - MultipleInputFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-003_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-003_nojs.cwl deleted file mode 100644 index 617603c8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-003_nojs.cwl +++ /dev/null @@ -1,31 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: - type: int - default: 23 - test: boolean - def: - type: string - default: "Direct" - -steps: - - step1: - in: - in1: val - a_new_var: test - run: foo.cwl - when: $(inputs.a_new_var) - out: [out1] - -outputs: - out1: - type: string - outputSource: - - step1/out1 - - def - pickValue: first_non_null - -requirements: - MultipleInputFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-004.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-004.cwl deleted file mode 100644 index 630d1065..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-004.cwl +++ /dev/null @@ -1,29 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: int - def: - type: string - default: "Direct" - -steps: - - step1: - in: - in1: val - a_new_var: val - run: foo.cwl - when: $(inputs.a_new_var > 2) - out: [out1] - -outputs: - out1: - type: string - outputSource: - - step1/out1 - - def - pickValue: the_only_non_null - -requirements: - InlineJavascriptRequirement: {} - MultipleInputFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-004_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-004_nojs.cwl deleted file mode 100644 index 5cb51464..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-004_nojs.cwl +++ /dev/null @@ -1,31 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: - type: int - default: 23 - test: boolean - def: - type: string - default: "Direct" - -steps: - - step1: - in: - in1: val - a_new_var: test - run: foo.cwl - when: $(inputs.a_new_var) - out: [out1] - -outputs: - out1: - type: string - outputSource: - - step1/out1 - - def - pickValue: the_only_non_null - -requirements: - MultipleInputFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-006.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-006.cwl deleted file mode 100644 index b4dfdee3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-006.cwl +++ /dev/null @@ -1,34 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: int - -steps: - - step1: - in: - in1: val - a_new_var: val - run: foo.cwl - when: $(inputs.a_new_var > 2) - out: [out1] - - step2: - in: - in1: val - a_new_var: val - run: bar.cwl - when: $(inputs.a_new_var > 0) - out: [out1] - -outputs: - out1: - type: string - outputSource: - - step1/out1 - - step2/out1 - pickValue: the_only_non_null - -requirements: - InlineJavascriptRequirement: {} - MultipleInputFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-006_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-006_nojs.cwl deleted file mode 100644 index 98afc79d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-006_nojs.cwl +++ /dev/null @@ -1,36 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - test1: boolean - test2: boolean - val: - type: int - default: 23 - -steps: - step1: - in: - in1: val - a_new_var: test1 - run: foo.cwl - when: $(inputs.a_new_var) - out: [out1] - - step2: - in: - in1: val - a_new_var: test2 - run: bar.cwl - when: $(inputs.a_new_var) - out: [out1] - -outputs: - out1: - type: string - outputSource: - - step1/out1 - - step2/out1 - pickValue: the_only_non_null - -requirements: - MultipleInputFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-007.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-007.cwl deleted file mode 100644 index 99b731ff..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-007.cwl +++ /dev/null @@ -1,34 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: int - -steps: - - step1: - in: - in1: val - a_new_var: val - run: foo.cwl - when: $(inputs.a_new_var > 2) - out: [out1] - - step2: - in: - in1: val - a_new_var: val - run: bar.cwl - when: $(inputs.a_new_var > 0) - out: [out1] - -outputs: - out1: - type: string[] - outputSource: - - step1/out1 - - step2/out1 - pickValue: all_non_null - -requirements: - InlineJavascriptRequirement: {} - MultipleInputFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-007_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-007_nojs.cwl deleted file mode 100644 index b7ebfd7a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-007_nojs.cwl +++ /dev/null @@ -1,37 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: - type: int - default: 23 - test1: boolean - test2: boolean - -steps: - - step1: - in: - in1: val - a_new_var: test1 - run: foo.cwl - when: $(inputs.a_new_var) - out: [out1] - - step2: - in: - in1: val - a_new_var: test2 - run: bar.cwl - when: $(inputs.a_new_var) - out: [out1] - -outputs: - out1: - type: string[] - outputSource: - - step1/out1 - - step2/out1 - pickValue: all_non_null - -requirements: - MultipleInputFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-009.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-009.cwl deleted file mode 100644 index e1f17af4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-009.cwl +++ /dev/null @@ -1,26 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - data: int[] - val: int - -steps: - - step1: - in: - in1: data - a_new_var: val - run: foo.cwl - when: $(inputs.a_new_var > 3) - out: [out1] - scatter: in1 - -outputs: - out1: - type: string[] - outputSource: step1/out1 - pickValue: all_non_null - -requirements: - InlineJavascriptRequirement: {} - ScatterFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-009_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-009_nojs.cwl deleted file mode 100644 index 418243df..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-009_nojs.cwl +++ /dev/null @@ -1,27 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - data: - type: int[] - default: [1, 2, 3, 4, 5, 6] - test: boolean - -steps: - - step1: - in: - in1: data - a_new_var: test - run: foo.cwl - when: $(inputs.a_new_var) - out: [out1] - scatter: in1 - -outputs: - out1: - type: string[] - outputSource: step1/out1 - pickValue: all_non_null - -requirements: - ScatterFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-010.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-010.cwl deleted file mode 100644 index eeb7ac4f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-010.cwl +++ /dev/null @@ -1,26 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: int[] - -steps: - - step1: - in: - in1: val - a_new_var: val - run: foo.cwl - when: $(inputs.a_new_var > 3) - out: [out1] - scatter: [in1, a_new_var] - scatterMethod: dotproduct - -outputs: - out1: - type: string[] - outputSource: step1/out1 - pickValue: all_non_null - -requirements: - InlineJavascriptRequirement: {} - ScatterFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-010_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-010_nojs.cwl deleted file mode 100644 index b962c0ad..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-010_nojs.cwl +++ /dev/null @@ -1,30 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: - type: int[] - default: [1, 2, 3, 4, 5, 6] - test: - type: boolean[] - default: [false, false, false, true, true, true] - -steps: - - step1: - in: - in1: val - a_new_var: test - run: foo.cwl - when: $(inputs.a_new_var) - out: [out1] - scatter: [in1, a_new_var] - scatterMethod: dotproduct - -outputs: - out1: - type: string[] - outputSource: step1/out1 - pickValue: all_non_null - -requirements: - ScatterFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-011.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-011.cwl deleted file mode 100644 index cf99cc85..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-011.cwl +++ /dev/null @@ -1,35 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - in1: int[] - in2: int[] - in3: int[] - -steps: - - step1: - in: - in1: in1 - in2: in2 - in3: in3 - run: cat.cwl - when: $(inputs.in3 % 2 == 0) - out: [out1] - scatter: [in1, in2, in3] - scatterMethod: nested_crossproduct - -outputs: - out1: - type: - type: array - items: - type: array - items: - type: array - items: string - outputSource: step1/out1 - pickValue: all_non_null - -requirements: - InlineJavascriptRequirement: {} - ScatterFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-011_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-011_nojs.cwl deleted file mode 100644 index 21c3e0e7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-011_nojs.cwl +++ /dev/null @@ -1,44 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - in1: - type: int[] - default: [1, 2] - in2: - type: int[] - default: [1, 2, 3] - in3: - type: int - default: 23 - test: - type: boolean[] - default: [false, true, false, true] - -steps: - - step1: - in: - in1: in1 - in2: in2 - in3: in3 - another_input: test - run: cat.cwl - when: $(inputs.another_input) - out: [out1] - scatter: [in1, in2, another_input] - scatterMethod: nested_crossproduct - -outputs: - out1: - type: - type: array - items: - type: array - items: - type: array - items: string - outputSource: step1/out1 - pickValue: all_non_null - -requirements: - ScatterFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-012.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-012.cwl deleted file mode 100644 index aa9a56db..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-012.cwl +++ /dev/null @@ -1,22 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: int - -steps: - - step1: - in: - in1: val - a_new_var: val - run: foo.cwl - when: $(inputs.a_new_var % 2) - out: [out1] - -outputs: - out1: - type: string? - outputSource: step1/out1 - -requirements: - InlineJavascriptRequirement: {} \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-012_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-012_nojs.cwl deleted file mode 100644 index 954c6c65..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-012_nojs.cwl +++ /dev/null @@ -1,23 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - val: - type: int - default: 23 - test: - type: int - default: 1 -steps: - - step1: - in: - in1: val - a_new_var: test - run: foo.cwl - when: $(inputs.a_new_var) - out: [out1] - -outputs: - out1: - type: string? - outputSource: step1/out1 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-013.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-013.cwl deleted file mode 100644 index c9ad07f2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-013.cwl +++ /dev/null @@ -1,36 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - in1: int[] - -steps: - - step1: - in: - in1: in1 - run: foo.cwl - when: $(inputs.in1 % 2 == 0) - out: [out1] - scatter: in1 - - step2: - in: - in1: in1 - run: bar.cwl - when: $(inputs.in1 % 2 == 1) - out: [out1] - scatter: in1 - -outputs: - out1: - type: string[] - outputSource: - - step1/out1 - - step2/out1 - linkMerge: merge_flattened - pickValue: all_non_null - -requirements: - InlineJavascriptRequirement: {} - ScatterFeatureRequirement: {} - MultipleInputFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-013_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-013_nojs.cwl deleted file mode 100644 index cd70cfff..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-wf-013_nojs.cwl +++ /dev/null @@ -1,47 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - in1: - type: int[] - default: [1, 2, 3, 4, 5, 6] - test1: - type: boolean[] - default: [false, true, false, true, false, true] - test2: - type: boolean[] - default: [true, false, true, false, true, false] - -steps: - - step1: - in: - in1: in1 - another_var: test1 - run: foo.cwl - when: $(inputs.another_var) - out: [out1] - scatter: [ in1, another_var ] - scatterMethod: dotproduct - - step2: - in: - in1: in1 - another_var: test2 - run: bar.cwl - when: $(inputs.another_var) - out: [out1] - scatter: [ in1, another_var ] - scatterMethod: dotproduct - -outputs: - out1: - type: string[] - outputSource: - - step1/out1 - - step2/out1 - linkMerge: merge_flattened - pickValue: all_non_null - -requirements: - ScatterFeatureRequirement: {} - MultipleInputFeatureRequirement: {} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-with-defaults.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-with-defaults.cwl deleted file mode 100644 index 8b9bf621..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cond-with-defaults.cwl +++ /dev/null @@ -1,49 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -requirements: - MultipleInputFeatureRequirement: {} - InlineJavascriptRequirement: {} - StepInputExpressionRequirement: {} - ScatterFeatureRequirement: {} - -inputs: - forward_reads: File? - reverse_reads: File? - single_reads: File? - -outputs: - out_file: - type: File[] - outputSource: - - step_paired/processed_file - - step_single/processed_file - linkMerge: merge_flattened - pickValue: all_non_null - -steps: - - step_paired: - run: action.cwl - when: $(inputs.single === null) - scatter: [initial_file, suffix] - scatterMethod: dotproduct - in: - single: single_reads - suffix: - default: ["1", "2"] - initial_file: - - forward_reads - - reverse_reads - out_file_name: { valueFrom: "filename_paired$(inputs.suffix)" } - out: [ processed_file ] - - step_single: - run: action.cwl - when: $(inputs.single !== null) - in: - single: single_reads - initial_file: single_reads - out_file_name: { default: 'filename_single' } - out: [ processed_file ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cores_float.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cores_float.cwl deleted file mode 100644 index 23939b32..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cores_float.cwl +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - ResourceRequirement: - coresMin: 1.25 - coresMax: 1.75 - -inputs: [] - -outputs: - output: - type: stdout - -baseCommand: echo - -stdout: cores.txt - -arguments: [ $(runtime.cores) ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines1-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines1-wf-noET.cwl deleted file mode 100755 index b48f06bc..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines1-wf-noET.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: - type: File - -outputs: - wc_output: - type: File - outputSource: step1/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: file1 - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines1-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines1-wf.cwl deleted file mode 100755 index bb4adbb6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines1-wf.cwl +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: - type: File - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: file1 - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines10-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines10-wf.cwl deleted file mode 100755 index 66470a2e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines10-wf.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -inputs: - file1: File -outputs: - count_output: {type: int, outputSource: step0/count_output} -requirements: - SubworkflowFeatureRequirement: {} -steps: - step0: - in: {file1: file1} - out: [count_output] - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step2/output} - steps: - step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} - step2: {run: parseInt-tool.cwl, in: {file1: step1/output}, out: [output]} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-extra-step-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-extra-step-wf-noET.cwl deleted file mode 100755 index 0f7bf7ac..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-extra-step-wf-noET.cwl +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: File? - -outputs: - wc_output: - type: File - outputSource: step1/output - -steps: - step0: - run: cat-tool.cwl - in: - file1: file1 - out: [ output ] - step1: - run: wc-tool.cwl - in: - file1: - source: step0/output - default: - class: File - location: whale.txt - out: [output] - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-extra-step-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-extra-step-wf.cwl deleted file mode 100755 index 0ac1c65b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-extra-step-wf.cwl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: File? - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step0: - run: cat-tool.cwl - in: - file1: file1 - out: [ output ] - step1: - run: wc-tool.cwl - in: - file1: - source: step0/output - default: - class: File - location: whale.txt - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-null-step-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-null-step-wf-noET.cwl deleted file mode 100755 index 13e8a340..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-null-step-wf-noET.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: [] - -outputs: - wc_output: - type: File - outputSource: step1/output - -steps: - step0: - run: null-expression3-tool.cwl - in: [] - out: [ output ] - - step1: - run: wc-tool.cwl - in: - file1: - source: step0/output - default: - class: File - location: whale.txt - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-null-step-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-null-step-wf.cwl deleted file mode 100755 index a24a71e3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-null-step-wf.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: [] - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step0: - run: null-expression3-tool.cwl - in: [] - out: [ output ] - - step1: - run: wc-tool.cwl - in: - file1: - source: step0/output - default: - class: File - location: whale.txt - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-wf-noET.cwl deleted file mode 100755 index 40aab14c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-wf-noET.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: File? - -outputs: - wc_output: - type: File - outputSource: step1/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: - source: file1 - default: - class: File - location: whale.txt - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-wf.cwl deleted file mode 100755 index d3b1b1ab..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines11-wf.cwl +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: File? - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: - source: file1 - default: - class: File - location: whale.txt - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines12-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines12-wf.cwl deleted file mode 100755 index 6f226d65..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines12-wf.cwl +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -requirements: - - class: MultipleInputFeatureRequirement - -inputs: - file1: - - type: array - items: File - file2: - - type: array - items: File - -outputs: - count_output: - type: int - outputSource: step1/output - -steps: - step1: - run: wc3-tool.cwl - in: - file1: - source: [file1, file2] - linkMerge: merge_flattened - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines13-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines13-wf.cwl deleted file mode 100644 index 86d57701..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines13-wf.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: File - -outputs: - count_output: - type: int - outputSource: step1/output - -steps: - step1: - run: wc2-tool.cwl - in: - file1: - source: [file1] - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines14-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines14-wf.cwl deleted file mode 100644 index 7d963b64..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines14-wf.cwl +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: - type: File - file2: - type: File - -outputs: - count_output: - type: int[] - outputSource: step1/count_output - -requirements: - ScatterFeatureRequirement: {} - SubworkflowFeatureRequirement: {} - MultipleInputFeatureRequirement: {} - -steps: - step1: - in: - file1: [file1, file2] - out: [count_output] - scatter: file1 - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step2/output} - steps: - step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} - step2: {run: parseInt-tool.cwl, in: {file1: step1/output}, out: [output]} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines15-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines15-wf.cwl deleted file mode 100644 index 07975bef..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines15-wf.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -inputs: - file1: File -outputs: - count_output: {type: int, outputSource: step1/count_output} -requirements: - SubworkflowFeatureRequirement: {} -steps: - step1: - in: {file1: file1} - out: [count_output] - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step1/count_output} - steps: - step1: - in: {file1: file1} - out: [count_output] - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step2/output} - steps: - step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} - step2: {run: parseInt-tool.cwl, in: {file1: step1/output}, out: [output]} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines16-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines16-wf.cwl deleted file mode 100644 index 8b8dc72d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines16-wf.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -inputs: - file1: File -outputs: - count_output: {type: int, outputSource: step1/count_output} -requirements: - SubworkflowFeatureRequirement: {} -steps: - step1: - in: {file1: file1} - out: [count_output] - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step2/count_output} - steps: - step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} - step2: - in: {file1: step1/output} - out: [count_output] - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step1/output} - steps: - step1: {run: parseInt-tool.cwl, in: {file1: file1}, out: [output]} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines17-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines17-wf.cwl deleted file mode 100644 index f423a4b6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines17-wf.cwl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -inputs: - file1: File -outputs: - count_output: {type: int, outputSource: step1/count_output} -requirements: - SubworkflowFeatureRequirement: {} -steps: - step1: - in: {file1: file1} - out: [count_output] - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step2/output} - steps: - step1: - in: {file1: file1} - out: [wc_output] - run: - class: Workflow - inputs: - file1: File - outputs: - wc_output: {type: File, outputSource: step1/output} - steps: - step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} - - step2: {run: parseInt-tool.cwl, in: {file1: step1/wc_output}, out: [output]} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines18-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines18-wf.cwl deleted file mode 100644 index 44c54469..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines18-wf.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: - type: File[] - -outputs: - count_output: - type: int[] - outputSource: step1/count_output - -requirements: - ScatterFeatureRequirement: {} - SubworkflowFeatureRequirement: {} - MultipleInputFeatureRequirement: {} - -steps: - step1: - in: {file1: file1} - out: [count_output] - scatter: file1 - run: - class: Workflow - inputs: - file1: File - outputs: - count_output: {type: int, outputSource: step2/output} - steps: - step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} - step2: {run: parseInt-tool.cwl, in: {file1: step1/output}, out: [output]} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines19-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines19-wf.cwl deleted file mode 100644 index 544a9114..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines19-wf.cwl +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: File - -outputs: - count_output: - type: int - outputSource: step1/output - -steps: - step1: - run: wc3-tool.cwl - in: - file1: - source: [file1] - linkMerge: merge_nested - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines2-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines2-wf.cwl deleted file mode 100755 index 8f2c7365..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines2-wf.cwl +++ /dev/null @@ -1,50 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} - -inputs: - file1: - type: File - -outputs: - count_output: - type: int - outputSource: step2/parseInt_output - -steps: - step1: - in: - wc_file1: file1 - out: [wc_output] - run: - id: wc - class: CommandLineTool - inputs: - wc_file1: - type: File - inputBinding: {} - outputs: - wc_output: - type: File - outputBinding: - glob: output.txt - stdout: output.txt - baseCommand: wc - - step2: - in: - parseInt_file1: step1/wc_output - out: [parseInt_output] - run: - class: ExpressionTool - inputs: - parseInt_file1: - type: File - loadContents: true - outputs: - parseInt_output: - type: int - expression: > - ${return {'parseInt_output': parseInt(inputs.parseInt_file1.contents)};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines3-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines3-wf.cwl deleted file mode 100755 index 905cbfc1..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines3-wf.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: - type: File[] - -outputs: - count_output: - type: int[] - outputSource: step1/output - -requirements: - ScatterFeatureRequirement: {} - -steps: - step1: - run: wc2-tool.cwl - scatter: file1 - in: - file1: file1 - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines4-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines4-wf.cwl deleted file mode 100755 index 29b448ec..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines4-wf.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: - type: File - file2: - type: File - -outputs: - count_output: - type: int[] - outputSource: step1/output - -requirements: - - class: ScatterFeatureRequirement - - class: MultipleInputFeatureRequirement - -steps: - step1: - run: wc2-tool.cwl - scatter: file1 - in: - file1: [file1, file2] - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines5-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines5-wf.cwl deleted file mode 100755 index dbf85558..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines5-wf.cwl +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: - type: File - default: {class: File, location: hello.txt} -outputs: - count_output: - type: int - outputSource: step1/output -steps: - step1: - run: wc2-tool.cwl - in: - file1: file1 - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines6-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines6-wf.cwl deleted file mode 100755 index fac839e2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines6-wf.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: File[] - file2: File[] - -outputs: - count_output: - type: int[] - outputSource: step1/output - -requirements: - - class: ScatterFeatureRequirement - - class: MultipleInputFeatureRequirement - -steps: - step1: - run: wc3-tool.cwl - scatter: file1 - in: - file1: - source: [file1, file2] - linkMerge: merge_nested - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines7-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines7-wf.cwl deleted file mode 100755 index 2d89118b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines7-wf.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -requirements: - - class: MultipleInputFeatureRequirement - -inputs: - file1: - type: File[] - file2: - type: File[] - -outputs: - count_output: - type: int - outputSource: step1/output - -steps: - step1: - run: wc3-tool.cwl - in: - file1: - source: [file1, file2] - linkMerge: merge_flattened - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines8-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines8-wf-noET.cwl deleted file mode 100755 index 3329a9dd..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines8-wf-noET.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: File - -outputs: - wc_output: - type: File - outputSource: step1/wc_output - -requirements: - - class: SubworkflowFeatureRequirement - -steps: - step1: - run: count-lines1-wf-noET.cwl - in: - file1: file1 - out: [wc_output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines8-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines8-wf.cwl deleted file mode 100755 index 54defcc9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines8-wf.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - file1: File - -outputs: - count_output: - type: int - outputSource: step1/count_output - -requirements: - - class: SubworkflowFeatureRequirement - -steps: - step1: - run: count-lines1-wf.cwl - in: - file1: file1 - out: [count_output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines9-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines9-wf-noET.cwl deleted file mode 100755 index 17d0e95b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines9-wf-noET.cwl +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: [] - -outputs: - wc_output: - type: File - outputSource: step1/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: - default: - class: File - location: whale.txt - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines9-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines9-wf.cwl deleted file mode 100755 index 1ea1cfc9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_count-lines9-wf.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: [] - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: - default: - class: File - location: whale.txt - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cwloutput-nolimit.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cwloutput-nolimit.cwl deleted file mode 100644 index a2fb3bc9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_cwloutput-nolimit.cwl +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - DockerRequirement: - dockerPull: "python:3-slim" -inputs: - script: - type: File - default: {class: File, location: mkfilelist.py} -outputs: - filelist: string[] -arguments: [python, $(inputs.script)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_default_path.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_default_path.cwl deleted file mode 100644 index cab6a9ca..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_default_path.cwl +++ /dev/null @@ -1,10 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -inputs: - - id: "file1" - type: File - default: - class: File - path: whale.txt -outputs: [] -arguments: [cat,$(inputs.file1.path)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir.cwl deleted file mode 100644 index d9829910..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir.cwl +++ /dev/null @@ -1,17 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: ShellCommandRequirement -inputs: - indir: Directory -outputs: - outlist: - type: File - outputBinding: - glob: output.txt -arguments: ["cd", "$(inputs.indir.path)", - {shellQuote: false, valueFrom: "&&"}, - "find", ".", - {shellQuote: false, valueFrom: "|"}, - "sort"] -stdout: output.txt \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir2.cwl deleted file mode 100644 index eaade67e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir2.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - ShellCommandRequirement: {} -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - indir: Directory -outputs: - outlist: - type: File - outputBinding: - glob: output.txt -arguments: ["cd", "$(inputs.indir.path)", - {shellQuote: false, valueFrom: "&&"}, - "find", ".", - {shellQuote: false, valueFrom: "|"}, - "sort"] -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir3.cwl deleted file mode 100644 index 2966859b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir3.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -baseCommand: [tar, xvf] -inputs: - inf: - type: File - inputBinding: - position: 1 -outputs: - outdir: - type: Directory - outputBinding: - glob: . diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir4.cwl deleted file mode 100644 index 9ba7b938..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir4.cwl +++ /dev/null @@ -1,17 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: ShellCommandRequirement -inputs: - inf: File -outputs: - outlist: - type: File - outputBinding: - glob: output.txt -arguments: ["cd", "$(inputs.inf.dirname)/xtestdir", - {shellQuote: false, valueFrom: "&&"}, - "find", ".", - {shellQuote: false, valueFrom: "|"}, - "sort"] -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir5.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir5.cwl deleted file mode 100644 index e85726fe..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir5.cwl +++ /dev/null @@ -1,19 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: ShellCommandRequirement - - class: InitialWorkDirRequirement - listing: $(inputs.indir.listing) -inputs: - indir: - type: Directory - loadListing: shallow_listing -outputs: - outlist: - type: File - outputBinding: - glob: output.txt -arguments: ["find", "-L", ".", "!", "-path", "*.txt", - {shellQuote: false, valueFrom: "|"}, - "sort"] -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir6.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir6.cwl deleted file mode 100644 index 66a3a1f8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir6.cwl +++ /dev/null @@ -1,21 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: ShellCommandRequirement -inputs: - indir: - type: Directory - inputBinding: - prefix: cd - position: -1 -outputs: - outlist: - type: File - outputBinding: - glob: output.txt -arguments: [ - {shellQuote: false, valueFrom: "&&"}, - "find", ".", - {shellQuote: false, valueFrom: "|"}, - "sort"] -stdout: output.txt \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir7.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir7.cwl deleted file mode 100644 index 0c326401..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dir7.cwl +++ /dev/null @@ -1,12 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} -inputs: - files: File[] -outputs: - dir: Directory -expression: | - ${ - return {"dir": {"class": "Directory", "basename": "a_directory", "listing": inputs.files}}; - } \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_docker-array-secondaryfiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_docker-array-secondaryfiles.cwl deleted file mode 100644 index 8615d641..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_docker-array-secondaryfiles.cwl +++ /dev/null @@ -1,50 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 - -requirements: - - class: DockerRequirement - dockerPull: debian:stretch-slim - - class: InlineJavascriptRequirement - - class: ShellCommandRequirement - -class: CommandLineTool - -inputs: - fasta_path: - type: - type: array - items: File - secondaryFiles: - - pattern: .fai - required: true - - pattern: .crai - required: false - - .bai? - - "${ if (inputs.require_dat) {return '.dat'} else {return null} }" - - "${ return null; }" - - pattern: .dat2 - required: $(inputs.require_dat) - require_dat: boolean? - -outputs: - bai_list: - type: File - outputBinding: - glob: "fai.list" - secondaryFiles: - - .bai? - - pattern: "${ return null }" - -arguments: - - valueFrom: ${ - var fai_list = ""; - for (var i = 0; i < inputs.fasta_path.length; i ++) { - fai_list += " cat " + inputs.fasta_path[i].path +".fai" + " >> fai.list && " - } - return fai_list.slice(0,-3) - } - position: 1 - shellQuote: false - -baseCommand: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_docker-output-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_docker-output-dir.cwl deleted file mode 100644 index 339493fd..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_docker-output-dir.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - DockerRequirement: - dockerPull: debian:stretch-slim - dockerOutputDirectory: /other -inputs: [] -outputs: - thing: - type: File - outputBinding: - glob: thing -baseCommand: ["touch", "/other/thing"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_docker-run-cmd.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_docker-run-cmd.cwl deleted file mode 100644 index e4432b86..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_docker-run-cmd.cwl +++ /dev/null @@ -1,12 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - DockerRequirement: - dockerPull: bash:4.4.12 -inputs: [] -outputs: - cow: - type: File - outputBinding: - glob: cow -baseCommand: ["-c", "echo 'moo' > cow"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-default.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-default.cwl deleted file mode 100644 index f4401907..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-default.cwl +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - ResourceRequirement: - coresMin: $(inputs.special_file.size) - coresMax: $(inputs.special_file.size) - -inputs: - special_file: - type: File - default: - class: File - location: special_file - -outputs: - output: - type: stdout - -baseCommand: echo - -stdout: cores.txt - -arguments: [ $(runtime.cores) ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-dir.cwl deleted file mode 100644 index a1817efb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-dir.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - InlineJavascriptRequirement: {} - ResourceRequirement: - coresMin: $(inputs.dir.listing[0].size) - coresMax: $(inputs.dir.listing[0].size) - -inputs: - dir: Directory - -outputs: - output: - type: stdout - -baseCommand: echo - -stdout: cores.txt - -arguments: [ $(runtime.cores) ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-workflow-inputdefault.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-workflow-inputdefault.cwl deleted file mode 100644 index 05647a85..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-workflow-inputdefault.cwl +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - special_file: - type: File - default: - class: File - path: special_file - -outputs: - cores: - type: File - outputSource: report/output - -steps: - count: - in: - special_file: special_file - out: [output] - run: dynresreq.cwl - - report: - in: - file1: count/output - out: [output] - run: cat-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-workflow-stepdefault.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-workflow-stepdefault.cwl deleted file mode 100644 index 9e985d2a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-workflow-stepdefault.cwl +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - special_file: File? -outputs: - cores: - type: File - outputSource: report/output - -steps: - count: - in: - special_file: - source: special_file - default: - class: File - location: special_file - out: [output] - run: dynresreq.cwl - - report: - in: - file1: count/output - out: [output] - run: cat-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-workflow-tooldefault.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-workflow-tooldefault.cwl deleted file mode 100644 index 86d8cf77..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-workflow-tooldefault.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - special_file: File? -outputs: - cores: - type: File - outputSource: report/output - -steps: - count: - in: - special_file: special_file - out: [output] - run: dynresreq-default.cwl - - report: - in: - file1: count/output - out: [output] - run: cat-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-workflow.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-workflow.cwl deleted file mode 100644 index 95271d88..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq-workflow.cwl +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - special_file: File - -outputs: - cores: - type: File - outputSource: report/output - -steps: - count: - in: - special_file: special_file - out: [output] - run: dynresreq.cwl - - report: - in: - file1: count/output - out: [output] - run: cat-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq.cwl deleted file mode 100644 index e8c7752f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_dynresreq.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - ResourceRequirement: - coresMin: $(inputs.special_file.size) - coresMax: $(inputs.special_file.size) - -inputs: - special_file: File - -outputs: - output: - type: stdout - -baseCommand: echo - -stdout: cores.txt - -arguments: [ $(runtime.cores) ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-file-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-file-tool.cwl deleted file mode 100644 index f6e4f58c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-file-tool.cwl +++ /dev/null @@ -1,13 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -baseCommand: [echo] -inputs: - in: - type: string - inputBinding: - position: 1 - name: string? -stdout: out.txt -outputs: - out: - type: stdout diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-position-expr.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-position-expr.cwl deleted file mode 100644 index 6c230dd2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-position-expr.cwl +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} -inputs: - one: - type: int - inputBinding: - position: $(self) - two: - type: int - inputBinding: - valueFrom: sensation! - position: ${return self+1;} -arguments: - - position: ${return 2;} - valueFrom: singular - - position: ${return null;} - valueFrom: 🕺 -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -baseCommand: echo -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-tool-default.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-tool-default.cwl deleted file mode 100644 index 885960fc..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-tool-default.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in: - type: string - default: tool_default - inputBinding: - position: 1 -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -baseCommand: [echo, -n] -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-tool-packed.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-tool-packed.cwl deleted file mode 100644 index f9f2c336..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-tool-packed.cwl +++ /dev/null @@ -1,31 +0,0 @@ -cwlVersion: v1.2 -$graph: - - class: CommandLineTool - id: first - inputs: - in: - type: Any - outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) - baseCommand: [ echo, first ] - stdout: out.txt - - class: CommandLineTool - id: main - inputs: - in: - type: Any - inputBinding: {} - outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) - baseCommand: echo - stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-tool-packed2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-tool-packed2.cwl deleted file mode 100644 index d352567e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-tool-packed2.cwl +++ /dev/null @@ -1,31 +0,0 @@ -cwlVersion: v1.2 -$graph: - - class: CommandLineTool - id: first - inputs: - in: - type: Any - outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) - baseCommand: [ echo, first ] - stdout: out.txt - - class: CommandLineTool - id: '#main' - inputs: - in: - type: Any - inputBinding: {} - outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) - baseCommand: echo - stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-tool.cwl deleted file mode 100644 index 5a9835b8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in: - type: Any - inputBinding: {} -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -baseCommand: echo -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-wf-default.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-wf-default.cwl deleted file mode 100644 index 13f4030b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_echo-wf-default.cwl +++ /dev/null @@ -1,19 +0,0 @@ - -class: Workflow -cwlVersion: v1.2 - -inputs: [] - -steps: - step1: - run: echo-tool-default.cwl - in: - in: - default: workflow_default - out: [out] - -outputs: - default_output: - type: string - outputSource: step1/out - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_empty-array-input.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_empty-array-input.cwl deleted file mode 100644 index 8d6271ba..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_empty-array-input.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 -class: CommandLineTool - -hints: - - class: DockerRequirement - dockerPull: python:2-slim - -inputs: - - id: array - type: { type: array, items: int } - inputBinding: - position: 1 - prefix: -I - itemSeparator: "," - - - id: args.py - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - -outputs: - - id: args - type: - type: array - items: string - -baseCommand: python diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-tool1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-tool1.cwl deleted file mode 100644 index 96b0bc3d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-tool1.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in: string -outputs: - out: - type: File - outputBinding: - glob: out - -requirements: - EnvVarRequirement: - envDef: - TEST_ENV: $(inputs.in) - -baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"] - -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-tool2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-tool2.cwl deleted file mode 100644 index f568e545..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-tool2.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in: string -outputs: - out: - type: File - outputBinding: - glob: out - -hints: - EnvVarRequirement: - envDef: - TEST_ENV: $(inputs.in) - -baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"] - -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-tool3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-tool3.cwl deleted file mode 100644 index 90279cf2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-tool3.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in: string -outputs: - out: - type: File - outputBinding: - glob: out - -baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"] - -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-tool4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-tool4.cwl deleted file mode 100644 index 3d21190f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-tool4.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in: string -outputs: - out: - type: File - outputBinding: - glob: out - -requirements: - EnvVarRequirement: - envDef: - TEST_ENV: conflict_original - -baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"] - -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-wf1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-wf1.cwl deleted file mode 100644 index 4da70cde..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-wf1.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - in: string - -outputs: - out: - type: File - outputSource: step1/out - -requirements: - EnvVarRequirement: - envDef: - TEST_ENV: override - -steps: - step1: - run: env-tool1.cwl - in: - in: in - out: [out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-wf2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-wf2.cwl deleted file mode 100644 index b9408fc4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-wf2.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - in: string - -outputs: - out: - type: File - outputSource: step1/out - -requirements: - EnvVarRequirement: - envDef: - TEST_ENV: override - -steps: - step1: - run: env-tool2.cwl - in: - in: in - out: [out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-wf3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-wf3.cwl deleted file mode 100644 index 94dd7e1f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_env-wf3.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - in: string - -outputs: - out: - type: File - outputSource: step1/out - -steps: - step1: - run: env-tool2.cwl - requirements: - EnvVarRequirement: - envDef: - TEST_ENV: override - in: - in: in - out: [out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_envvar.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_envvar.cwl deleted file mode 100644 index 50399567..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_envvar.cwl +++ /dev/null @@ -1,11 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: - ShellCommandRequirement: {} -arguments: [ - echo, {valueFrom: '"HOME=$HOME"', shellQuote: false}, {valueFrom: '"TMPDIR=$TMPDIR"', shellQuote: false}, - {valueFrom: '&&', shellQuote: false}, - test, {valueFrom: '"$HOME"', shellQuote: false}, "=", $(runtime.outdir), - "-a", {valueFrom: '"$TMPDIR"', shellQuote: false}, "=", $(runtime.tmpdir)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_envvar2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_envvar2.cwl deleted file mode 100644 index cf81a45f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_envvar2.cwl +++ /dev/null @@ -1,14 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: - ShellCommandRequirement: {} -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -arguments: [ - echo, {valueFrom: '"HOME=$HOME"', shellQuote: false}, {valueFrom: '"TMPDIR=$TMPDIR"', shellQuote: false}, - {valueFrom: '&&', shellQuote: false}, - test, {valueFrom: '"$HOME"', shellQuote: false}, "=", $(runtime.outdir), - "-a", {valueFrom: '"$TMPDIR"', shellQuote: false}, "=", $(runtime.tmpdir)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_envvar3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_envvar3.cwl deleted file mode 100644 index 53c2e492..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_envvar3.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: - results: - type: File - outputBinding: { glob: results } -requirements: - ShellCommandRequirement: {} -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -arguments: - - shellQuote: false - valueFrom: | - echo HOME=$HOME TMPDIR=$TMPDIR > log - if [ "$HOME" = "$(runtime.outdir)" ] && [ "$TMPDIR" = "$(runtime.tmpdir)" ] - then - echo success > results - else - echo failure > results - fi diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_exit-success.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_exit-success.cwl deleted file mode 100644 index 54f51542..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_exit-success.cwl +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: CommandLineTool - -inputs: [] -baseCommand: "false" -outputs: [] - -successCodes: [ 1 ] -permanentFailCodes: [ 0 ] -temporaryFailCodes: [ 42 ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_exitcode.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_exitcode.cwl deleted file mode 100644 index 8c142bef..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_exitcode.cwl +++ /dev/null @@ -1,12 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -requirements: - ShellCommandRequirement: {} -inputs: [] -outputs: - code: - type: int - outputBinding: - outputEval: $(runtime.exitCode) -successCodes: [7] -arguments: ["exit", "7"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_fail-unconnected.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_fail-unconnected.cwl deleted file mode 100644 index aaccde20..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_fail-unconnected.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - inp1: - type: string - default: hello inp1 - inp2: - type: string - default: hello inp2 -outputs: - out: - type: string - outputSource: step1/out -steps: - step1: - in: - in: inp1 - in2: inp2 - out: [out] - run: fail-unspecified-input.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_fail-unspecified-input.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_fail-unspecified-input.cwl deleted file mode 100644 index ae623c46..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_fail-unspecified-input.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in: string -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -stdout: out.txt -arguments: [echo, $(inputs.in), $(inputs.in2)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_file-literal-ex.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_file-literal-ex.cwl deleted file mode 100644 index b8fc37a1..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_file-literal-ex.cwl +++ /dev/null @@ -1,11 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} -inputs: [] -outputs: - lit: File -expression: | - ${ - return {"lit": {"class": "File", "basename": "a_file", "contents": "Hello file literal."}}; - } \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_foo.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_foo.cwl deleted file mode 100644 index 9e19268d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_foo.cwl +++ /dev/null @@ -1,10 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - in1: int -baseCommand: [echo] -outputs: - out1: - type: string - outputBinding: - outputEval: foo $(inputs.in1) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_formattest.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_formattest.cwl deleted file mode 100644 index 4b435639..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_formattest.cwl +++ /dev/null @@ -1,20 +0,0 @@ -$namespaces: - edam: "http://edamontology.org/" -cwlVersion: v1.2 -class: CommandLineTool -doc: "Reverse each line using the `rev` command" -inputs: - input: - type: File - inputBinding: {} - format: edam:format_2330 - -outputs: - output: - type: File - outputBinding: - glob: output.txt - format: edam:format_2330 - -baseCommand: rev -stdout: output.txt \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_formattest2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_formattest2.cwl deleted file mode 100644 index 7d2ddccc..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_formattest2.cwl +++ /dev/null @@ -1,26 +0,0 @@ -$namespaces: - edam: http://edamontology.org/ -$schemas: - - EDAM.owl -class: CommandLineTool -cwlVersion: v1.2 -doc: "Reverse each line using the `rev` command" -hints: - DockerRequirement: - dockerPull: "debian:stretch-slim" - -inputs: - input: - type: File - inputBinding: {} - format: edam:format_2330 - -outputs: - output: - type: File - outputBinding: - glob: output.txt - format: $(inputs.input.format) - -baseCommand: rev -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_formattest3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_formattest3.cwl deleted file mode 100644 index 55be2546..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_formattest3.cwl +++ /dev/null @@ -1,28 +0,0 @@ -$namespaces: - edam: http://edamontology.org/ - gx: http://galaxyproject.org/formats/ -$schemas: - - EDAM.owl - - gx_edam.ttl -class: CommandLineTool -cwlVersion: v1.2 -doc: "Reverse each line using the `rev` command" -hints: - DockerRequirement: - dockerPull: "debian:stretch-slim" - -inputs: - input: - type: File - inputBinding: {} - format: gx:fasta - -outputs: - output: - type: File - outputBinding: - glob: output.txt - format: $(inputs.input.format) - -baseCommand: rev -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_glob-expr-list.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_glob-expr-list.cwl deleted file mode 100644 index 90c51ca0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_glob-expr-list.cwl +++ /dev/null @@ -1,16 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 - -inputs: - ids: - type: string[] - inputBinding: - position: 1 - -outputs: - files: - type: File[] - outputBinding: - glob: $(inputs.ids) - -baseCommand: touch diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_glob-path-error.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_glob-path-error.cwl deleted file mode 100644 index 6a2e3331..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_glob-path-error.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 - -requirements: - - class: DockerRequirement - dockerPull: debian:stretch-slim - -class: CommandLineTool - -inputs: [] - -outputs: - - id: OUTPUT - type: File - outputBinding: - glob: /etc/passwd - -baseCommand: [echo] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_glob_directory.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_glob_directory.cwl deleted file mode 100644 index 901d9e2f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_glob_directory.cwl +++ /dev/null @@ -1,10 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: CommandLineTool - -inputs: [] -baseCommand: [mkdir, a_dir, b_dir, c_dir] -outputs: - directories: - type: Directory[] - outputBinding: { glob: '[a,b,c]_dir' } diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_glob_test.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_glob_test.cwl deleted file mode 100644 index 968bd5ba..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_glob_test.cwl +++ /dev/null @@ -1,10 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: CommandLineTool - -inputs: [] -baseCommand: [touch, z, y, x, w, c, b, a] -outputs: - letters: - type: File[] - outputBinding: { glob: '*' } diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_import_schema-def.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_import_schema-def.cwl deleted file mode 100644 index 039872ee..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_import_schema-def.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 - -class: Workflow - -requirements: - SchemaDefRequirement: - types: - - $import: capture_kit.yml - -inputs: - bam: string - capture_kit: capture_kit.yml#capture_kit - -outputs: - output_bam: - type: File - outputSource: touch_bam/empty_file - -steps: - touch_bam: - run: touch.cwl - in: - name: bam - out: [ empty_file ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_import_schema-def2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_import_schema-def2.cwl deleted file mode 100644 index 139ac59e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_import_schema-def2.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 - -class: Workflow - -requirements: - SchemaDefRequirement: - types: - - $import: capture_kit.yml - -inputs: - bam: string - capture_kit[]: capture_kit.yml#capture_kit - -outputs: - output_bam: - type: File - outputSource: touch_bam/empty_file - -steps: - touch_bam: - run: touch.cwl - in: - name: bam - out: [ empty_file ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_import_schema-def_packed.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_import_schema-def_packed.cwl deleted file mode 100644 index 0757ace6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_import_schema-def_packed.cwl +++ /dev/null @@ -1,89 +0,0 @@ -{ - "cwlVersion": "v1.2", - "$graph": [ - { - "inputs": [ - { - "type": "string", - "id": "#main/bam" - }, - { - "type": "#capture_kit.yml/capture_kit", - "id": "#main/capture_kit" - } - ], - "requirements": [ - { - "class": "SchemaDefRequirement", - "types": [ - { - "fields": [ - { - "type": "string", - "name": "#capture_kit.yml/capture_kit/bait" - } - ], - "type": "record", - "name": "#capture_kit.yml/capture_kit" - } - ] - } - ], - "outputs": [ - { - "outputSource": "#main/touch_bam/empty_file", - "type": "File", - "id": "#main/output_bam" - } - ], - "class": "Workflow", - "steps": [ - { - "out": [ - "#main/touch_bam/empty_file" - ], - "run": "#touch.cwl", - "id": "#main/touch_bam", - "in": [ - { - "source": "#main/bam", - "id": "#main/touch_bam/name" - } - ] - } - ], - "id": "#main" - }, - { - "inputs": [ - { - "inputBinding": { - "position": 0 - }, - "type": "string", - "id": "#touch.cwl/name" - } - ], - "outputs": [ - { - "outputBinding": { - "glob": "$(inputs.name)" - }, - "type": "File", - "id": "#touch.cwl/empty_file" - } - ], - "baseCommand": [ - "touch" - ], - "class": "CommandLineTool", - "id": "#touch.cwl", - "hints": [ - { - "dockerPull": "debian:stretch-slim", - "class": "DockerRequirement" - } - ] - } - ] -} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_imported-hint.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_imported-hint.cwl deleted file mode 100755 index 9a1b6a9f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_imported-hint.cwl +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: CommandLineTool -inputs: [] -outputs: - out: stdout - -hints: -- $import: envvar.yml - -baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"] - -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_initialwork-path.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_initialwork-path.cwl deleted file mode 100644 index 7ccd7d91..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_initialwork-path.cwl +++ /dev/null @@ -1,15 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.file1) - entryname: bob.txt - ShellCommandRequirement: {} -inputs: - file1: File -outputs: [] -arguments: - - shellQuote: false - valueFrom: | - test "$(inputs.file1.path)" = "$(runtime.outdir)/bob.txt" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_initialworkdir-glob-fullpath.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_initialworkdir-glob-fullpath.cwl deleted file mode 100644 index 074f8778..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_initialworkdir-glob-fullpath.cwl +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 - -requirements: - - class: InitialWorkDirRequirement - listing: - - $(inputs.INPUT) - -class: CommandLineTool - -inputs: - - id: INPUT - type: File - -outputs: - - id: OUTPUT - type: File - outputBinding: - glob: $(runtime.outdir)/$(inputs.INPUT.basename) - secondaryFiles: - - .fai - -arguments: - - valueFrom: $(inputs.INPUT.basename).fai - position: 0 - -baseCommand: [touch] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_initialworkdirrequirement-docker-out.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_initialworkdirrequirement-docker-out.cwl deleted file mode 100644 index 922652c5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_initialworkdirrequirement-docker-out.cwl +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 - -requirements: - - class: DockerRequirement - dockerPull: debian:stretch-slim - - class: InitialWorkDirRequirement - listing: - - $(inputs.INPUT) - -class: CommandLineTool - -inputs: - - id: INPUT - type: File - -outputs: - - id: OUTPUT - type: File - outputBinding: - glob: $(inputs.INPUT.basename) - secondaryFiles: - - .fai - -arguments: - - valueFrom: $(inputs.INPUT.basename).fai - position: 0 - -baseCommand: [touch] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_inline-js.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_inline-js.cwl deleted file mode 100755 index abc85e44..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_inline-js.cwl +++ /dev/null @@ -1,45 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool - -requirements: - - class: InlineJavascriptRequirement -hints: - - class: DockerRequirement - dockerPull: python:2-slim - -inputs: - - id: args.py - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - -outputs: - - id: args - type: - type: array - items: string - -baseCommand: python - -arguments: - - prefix: -A - valueFrom: $(1+1) - - prefix: -B - valueFrom: $("/foo/bar/baz".split('/').slice(-1)[0]) - - prefix: -C - valueFrom: | - ${ - var r = []; - for (var i = 10; i >= 1; i--) { - r.push(i); - } - return r; - } - # Test errors similar to https://github.com/common-workflow-language/cwltool/issues/648 are fixed - - prefix: -D - valueFrom: $(true) - - prefix: -E - valueFrom: $(false) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_inp_update_wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_inp_update_wf.cwl deleted file mode 100644 index 73eb1fd5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_inp_update_wf.cwl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -inputs: [] -outputs: - a: - type: int - outputSource: step3/output - b: - type: int - outputSource: step4/output -steps: - step1: - in: - in: {default: "3"} - out: [out] - run: echo-file-tool.cwl - step2: - in: - r: step1/out - out: [out] - run: updateval_inplace.cwl - step3: - in: - file1: step1/out - wait: step2/out - out: [output] - run: parseInt-tool.cwl - step4: - in: - file1: step2/out - out: [output] - run: parseInt-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_inpdir_update_wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_inpdir_update_wf.cwl deleted file mode 100644 index 22da9ee7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_inpdir_update_wf.cwl +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -inputs: [] -requirements: - InlineJavascriptRequirement: {} -outputs: - a: - type: File[] - outputSource: step3/d1out - b: - type: File[] - outputSource: step3/d2out -steps: - step1: - in: - dirname: {default: step1dir} - out: [out] - run: mkdir.cwl - step2: - in: - r: step1/out - out: [out] - run: updatedir_inplace.cwl - step3: - in: - d1: step1/out - d2: step2/out - out: [d1out, d2out] - run: - class: ExpressionTool - inputs: - d1: - type: Directory - loadListing: shallow_listing - d2: - type: Directory - loadListing: shallow_listing - outputs: - d1out: File[] - d2out: File[] - expression: "$({d1out: inputs.d1.listing, d2out: inputs.d2.listing})" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-any-1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-any-1.cwl deleted file mode 100644 index 80f70e23..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-any-1.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: InlineJavascriptRequirement - -inputs: - - id: bar - type: Any - -outputs: - - id: t1 - type: Any - outputBinding: - outputEval: $(inputs.bar.class || inputs.bar) - -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-any-wf-1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-any-wf-1.cwl deleted file mode 100644 index 5835c8af..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-any-wf-1.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - bar: - type: Any - -outputs: - t1: - type: Any - outputSource: step1/t1 - -steps: - step1: - in: - bar: bar - out: [t1] - run: io-any-1.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-file-default-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-file-default-wf.cwl deleted file mode 100644 index 7d5a2baa..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-file-default-wf.cwl +++ /dev/null @@ -1,34 +0,0 @@ -cwlVersion: v1.2 -class: Workflow - -inputs: - file1: - type: File - default: - class: File - path: whale.txt - -outputs: - o: - type: File - outputSource: step1/o - -steps: - step1: - in: - catfile1: file1 - out: [o] - run: - class: CommandLineTool - - inputs: - catfile1: - type: File - - outputs: - o: - type: File - outputBinding: { glob: output } - - arguments: [cat, $(inputs.catfile1.path)] - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-file-or-files.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-file-or-files.cwl deleted file mode 100644 index 347934af..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-file-or-files.cwl +++ /dev/null @@ -1,43 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 - -requirements: - - class: InlineJavascriptRequirement - -class: CommandLineTool - -inputs: - - id: input - type: - - "null" - - File - - type: array - items: File - -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} - -arguments: - - valueFrom: | - ${ - var cmd = []; - if (inputs.input === null) { - cmd.push('echo'); - cmd.push('no_inputs'); - } else { - cmd.push('cat'); - if (Array.isArray(inputs.input)) { - for (var i = 0; i < inputs.input.length; i++) { - cmd.push(inputs.input[i].path); - } - } else { - cmd.push(inputs.input.path); - } - } - return cmd; - } -baseCommand: [] -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-int-default-tool-and-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-int-default-tool-and-wf.cwl deleted file mode 100644 index 2657ee49..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-int-default-tool-and-wf.cwl +++ /dev/null @@ -1,49 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - i: - type: int - default: 4 - -outputs: - o: - type: int - outputSource: step2/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int - outputs: - o: - type: int - expression: > - ${return {'o': (inputs.i || 2)};} - step2: - in: - i: step1/o - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int - i2: - type: int - default: 5 - outputs: - o: - type: int - expression: > - ${return {'o': inputs.i * 2 + inputs.i2};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-int-default-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-int-default-wf.cwl deleted file mode 100644 index 67ef860e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-int-default-wf.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - i: - type: int - default: 4 - -outputs: - o: - type: int - outputSource: step1/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int - outputs: - o: - type: int - expression: > - ${return {'o': (inputs.i || 2) * 2};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-int-optional-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-int-optional-wf.cwl deleted file mode 100644 index 94029b3b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-int-optional-wf.cwl +++ /dev/null @@ -1,31 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - i: - type: int? - -outputs: - o: - type: int - outputSource: step1/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int? - outputs: - o: - type: int - expression: > - ${return {'o': (inputs.i || 2) * 2};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-int-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-int-wf.cwl deleted file mode 100644 index 49176eec..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-int-wf.cwl +++ /dev/null @@ -1,31 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - i: - type: int - -outputs: - o: - type: int - outputSource: step1/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int - outputs: - o: - type: int - expression: > - ${return {'o': inputs.i * 2};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-union-input-default-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-union-input-default-wf.cwl deleted file mode 100644 index fbe1e154..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_io-union-input-default-wf.cwl +++ /dev/null @@ -1,38 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - bar: - type: - - File - - 'null' - - string - default: the default value - -outputs: - o: - type: string - outputSource: step1/o - -steps: - step1: - in: - i: bar - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: - - File - - 'null' - - string - outputs: - o: - type: string - expression: > - ${return {'o': (inputs.i.class || inputs.i)};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-container-entryname1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-container-entryname1.cwl deleted file mode 100644 index 2cfd3a31..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-container-entryname1.cwl +++ /dev/null @@ -1,23 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -doc: | - When executing in a container, entryname can have an absolute path - to a mount location inside the container. -inputs: - filelist: File -outputs: - head: - type: File - outputBinding: - glob: head.txt -requirements: - DockerRequirement: - dockerPull: "debian:10" - dockerOutputDirectory: /output - InitialWorkDirRequirement: - listing: - - entryname: /tmp2j3y7rpb/input/stuff.txt # Give it a weird prefix to minimize chance of conflict with a real file - entry: $(inputs.filelist) - ShellCommandRequirement: {} -arguments: - - {shellQuote: false, valueFrom: "head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt"} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-container-entryname2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-container-entryname2.cwl deleted file mode 100644 index d2492511..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-container-entryname2.cwl +++ /dev/null @@ -1,20 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -doc: | - Must fail if entryname is an absolute path and DockerRequirement is - not in the 'requirements' section. -inputs: - filelist: File -outputs: - head: - type: File - outputBinding: - glob: head.txt -requirements: - InitialWorkDirRequirement: - listing: - - entryname: /tmp2j3y7rpb/input/stuff.txt # Give it a weird prefix to minimize chance of conflict with a real file - entry: $(inputs.filelist) - ShellCommandRequirement: {} -arguments: - - {shellQuote: false, valueFrom: "head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt"} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-container-entryname3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-container-entryname3.cwl deleted file mode 100644 index d6aaf993..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-container-entryname3.cwl +++ /dev/null @@ -1,24 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -doc: | - Must fail if entryname is an absolute path and DockerRequirement is - not in the 'requirements' section. -inputs: - filelist: File -outputs: - head: - type: File - outputBinding: - glob: head.txt -hints: - DockerRequirement: - dockerPull: "debian:10" - dockerOutputDirectory: /output -requirements: - InitialWorkDirRequirement: - listing: - - entryname: /tmp2j3y7rpb/input/stuff.txt # Give it a weird prefix to minimize chance of conflict with a real file - entry: $(inputs.filelist) - ShellCommandRequirement: {} -arguments: - - {shellQuote: false, valueFrom: "head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt"} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-container-entryname4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-container-entryname4.cwl deleted file mode 100644 index 7ecdda16..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-container-entryname4.cwl +++ /dev/null @@ -1,19 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -doc: | - Must fail if entryname starts with ../ -inputs: - filelist: File -outputs: - head: - type: File - outputBinding: - glob: head.txt -requirements: - InitialWorkDirRequirement: - listing: - - entryname: ../input/stuff.txt # Illegal - entry: $(inputs.filelist) - ShellCommandRequirement: {} -arguments: - - {shellQuote: false, valueFrom: "head -n10 ../input/stuff.txt > head.txt"} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-fileobjs1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-fileobjs1.cwl deleted file mode 100644 index 4ccc561c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-fileobjs1.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: Can have a file declared directly in InitialWorkDir -requirements: - InitialWorkDirRequirement: - listing: - - class: File - location: inp-filelist.txt - - class: Directory - location: testdir -inputs: [] -outputs: - filelist: - type: File - outputBinding: - glob: inp-filelist.txt - testdir: - type: Directory - outputBinding: - glob: testdir -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-fileobjs2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-fileobjs2.cwl deleted file mode 100644 index c8eb2e39..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-fileobjs2.cwl +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: Can have a file declared directly in InitialWorkDir -requirements: - InitialWorkDirRequirement: - listing: - - [{class: File, location: ../loadContents/inp-filelist.txt}, - {class: Directory, location: ../testdir}] -inputs: [] -outputs: - filelist: - type: File - outputBinding: - glob: inp-filelist.txt - testdir: - type: Directory - outputBinding: - glob: testdir -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump1-nl.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump1-nl.cwl deleted file mode 100644 index e473d966..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump1-nl.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: "out-filelist.json" - entry: | - ${ - var ls = []; - for (var i = 1; i < 10000; i++) { - ls.push("example_input_file"+i+".txt"); - } - return ls; - } -inputs: [] -outputs: - filelist: - type: File - outputBinding: - glob: out-filelist.json -arguments: ["true"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump1.cwl deleted file mode 100644 index 35fefa69..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump1.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: "out-filelist.json" - entry: |- - ${ - var ls = []; - for (var i = 1; i < 10000; i++) { - ls.push("example_input_file"+i+".txt"); - } - return ls; - } -inputs: [] -outputs: - filelist: - type: File - outputBinding: - glob: out-filelist.json -arguments: ["true"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump2-nl.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump2-nl.cwl deleted file mode 100644 index 2c32523c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump2-nl.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: "out-filelist.json" - entry: | - ${ - var ls = []; - for (var i = 1; i < 10000; i++) { - ls.push("example_input_file"+i+".txt"); - } - return {"filelist": ls}; - } -inputs: [] -outputs: - filelist: - type: File - outputBinding: - glob: out-filelist.json -arguments: ["true"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump2.cwl deleted file mode 100644 index 1166eba8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump2.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: "out-filelist.json" - entry: |- - ${ - var ls = []; - for (var i = 1; i < 10000; i++) { - ls.push("example_input_file"+i+".txt"); - } - return {"filelist": ls}; - } -inputs: [] -outputs: - filelist: - type: File - outputBinding: - glob: out-filelist.json -arguments: ["true"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump3-nl.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump3-nl.cwl deleted file mode 100644 index b0ba69df..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump3-nl.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: "out-number.json" - entry: | - ${ - return 44.4; - } -inputs: [] -outputs: - filelist: - type: File - outputBinding: - glob: out-number.json -arguments: ["true"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump3.cwl deleted file mode 100644 index f81e63c9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-jsondump3.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: "out-number.json" - entry: |- - ${ - return 44.4; - } -inputs: [] -outputs: - filelist: - type: File - outputBinding: - glob: out-number.json -arguments: ["true"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-nolimit.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-nolimit.cwl deleted file mode 100644 index e24ac39c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-nolimit.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: "out-filelist.txt" - entry: |- - ${ - var ls = ""; - for (var i = 1; i < 10000; i++) { - ls += "example_input_file"+i+".txt\n"; - } - return ls; - } -inputs: [] -outputs: - filelist: - type: File - outputBinding: - glob: out-filelist.txt -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-passthrough1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-passthrough1.cwl deleted file mode 100644 index 52823e5f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-passthrough1.cwl +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: | - YAML |- syntax does not add trailing newline so in the listing entry - below there is no whitespace surrounding the value - $(inputs.filelist), so it is evaluated as a File object. Compare to - iwd-passthrough2.cwl - -requirements: - InitialWorkDirRequirement: - listing: - - entryname: "renamed-filelist.txt" - entry: |- - $(inputs.filelist) -inputs: - filelist: - type: File -outputs: - filelist: - type: File - outputBinding: - glob: renamed-filelist.txt -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-passthrough2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-passthrough2.cwl deleted file mode 100644 index 88034e41..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-passthrough2.cwl +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: | - YAML | syntax adds a trailing newline, so in the listing entry - below, it becomes a string interpolation -- it evaluates to a string - consisting of $(inputs.filelist) serialized to JSON and then adding - a newline. Compare to iwd-passthrough1.cwl - -requirements: - DockerRequirement: - dockerPull: "python:3-slim" - InitialWorkDirRequirement: - listing: - - entryname: "renamed-filelist.txt" - entry: | - $(inputs.filelist) -inputs: - filelist: File - script: - type: File - default: - class: File - location: loadit.py -stdout: out.txt -outputs: - out: stdout -arguments: [python3, $(inputs.script), "renamed-filelist.txt"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-passthrough3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-passthrough3.cwl deleted file mode 100644 index a7e40137..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-passthrough3.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InitialWorkDirRequirement: - listing: - - entryname: "renamed-filelist.txt" - entry: $(inputs.filelist) -inputs: - filelist: - type: File -outputs: - filelist: - type: File - outputBinding: - glob: renamed-filelist.txt -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-passthrough4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-passthrough4.cwl deleted file mode 100644 index 1db004dd..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwd-passthrough4.cwl +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InitialWorkDirRequirement: - listing: - - $(inputs.filelist) -inputs: - filelist: - type: File -outputs: - filelist: - type: File - outputBinding: - glob: $(inputs.filelist.basename) -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwdr-entry.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwdr-entry.cwl deleted file mode 100644 index f5b2c245..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwdr-entry.cwl +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -baseCommand: ["cat", "example.conf"] - -requirements: - InitialWorkDirRequirement: - listing: - - entryname: example.conf - entry: | - CONFIGVAR=$(inputs.message) - -inputs: - message: string -outputs: - out: - type: File - outputBinding: - glob: example.conf diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwdr_dir_literal_real_file.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwdr_dir_literal_real_file.cwl deleted file mode 100644 index ae4c0f49..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwdr_dir_literal_real_file.cwl +++ /dev/null @@ -1,25 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - DockerRequirement: - dockerPull: debian:stable-slim - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: | - ${ - return [{"class": "Directory", - "basename": "subdir", - "listing": [ inputs.filelist ] - }]} - -inputs: - filelist: File - -outputs: - same: - type: File - outputBinding: - glob: subdir/$(inputs.filelist.basename) - -baseCommand: echo diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwdr_with_nested_dirs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwdr_with_nested_dirs.cwl deleted file mode 100644 index f6388217..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_iwdr_with_nested_dirs.cwl +++ /dev/null @@ -1,41 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: Workflow - -inputs: [] -outputs: - ya_empty: - type: File - outputSource: second/ya - -steps: - first: - run: - class: CommandLineTool - baseCommand: [ mkdir, -p, deeply/nested/dir/structure ] - inputs: [] - outputs: - deep_dir: - type: Directory - outputBinding: { glob: deeply } - in: {} - out: [ deep_dir ] - - second: - run: - class: CommandLineTool - baseCommand: [ touch, deeply/nested/dir/structure/ya ] - requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.dir) - writable: true - inputs: - dir: Directory - outputs: - ya: - type: File - outputBinding: { glob: deeply/nested/dir/structure/ya } - - in: { dir: first/deep_dir } - out: [ ya ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_js-input-record.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_js-input-record.cwl deleted file mode 100644 index 80e13174..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_js-input-record.cwl +++ /dev/null @@ -1,33 +0,0 @@ -cwlVersion: v1.0 - -class: CommandLineTool - -requirements: - - class: InlineJavascriptRequirement - -baseCommand: ['echo'] - -inputs: - message: - type: - type: record - name: message_object - fields: - text: - type: string - inputBinding: - position: 1 - newlines: - type: boolean? - inputBinding: - position: 0 - prefix: -n - -outputs: - out: - type: string - outputBinding: - glob: output.txt - loadContents: true - outputEval: $(self[0].contents) -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_js-quote.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_js-quote.cwl deleted file mode 100644 index 4258dde6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_js-quote.cwl +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -label: Check for a JS quoting bug - -requirements: - InitialWorkDirRequirement: - listing: - - entryname: file.txt - entry: | - ${return 'quote "' + inputs.quote + '"'} - - entryname: script.sh - entry: | - set -xe - cat file.txt - InlineJavascriptRequirement: {} - ResourceRequirement: - coresMin: 2 - ramMin: 1000 - -inputs: - quote: - type: string - default: Hello - -outputs: - out: - type: File - outputBinding: - glob: file.txt - -baseCommand: -- echo -arguments: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_linkfile.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_linkfile.cwl deleted file mode 100644 index 754269b6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_linkfile.cwl +++ /dev/null @@ -1,22 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool - -requirements: - InitialWorkDirRequirement: - listing: - - $(inputs.src) - -inputs: - src: - type: File - inputBinding: - position: 1 - valueFrom: $(self.nameroot).class - -baseCommand: touch - -outputs: - classfile: - type: File - outputBinding: - glob: "*.class" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_deep1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_deep1.cwl deleted file mode 100755 index 7696466e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_deep1.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - LoadListingRequirement: - loadListing: deep_listing - InlineJavascriptRequirement: {} -inputs: - d: Directory -outputs: - out: - type: boolean - outputBinding: - outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing.length === 1)' -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_deep2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_deep2.cwl deleted file mode 100755 index 6cfa5c69..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_deep2.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} -inputs: - d: - type: Directory - loadListing: deep_listing -outputs: - out: - type: boolean - outputBinding: - outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing.length === 1)' -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_none1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_none1.cwl deleted file mode 100755 index 7726adaf..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_none1.cwl +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} -inputs: - d: Directory -outputs: - out: - type: boolean - outputBinding: - outputEval: $(inputs.d.listing === undefined) -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_none2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_none2.cwl deleted file mode 100755 index bfbd0c88..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_none2.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - LoadListingRequirement: - loadListing: no_listing - InlineJavascriptRequirement: {} -inputs: - d: Directory -outputs: - out: - type: boolean - outputBinding: - outputEval: $(inputs.d.listing === undefined) -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_none3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_none3.cwl deleted file mode 100755 index 4eae7b06..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_none3.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} -inputs: - d: - type: Directory - loadListing: no_listing -outputs: - out: - type: boolean - outputBinding: - outputEval: $(inputs.d.listing === undefined) -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_shallow1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_shallow1.cwl deleted file mode 100755 index fe623082..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_shallow1.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - LoadListingRequirement: - loadListing: shallow_listing - InlineJavascriptRequirement: {} -inputs: - d: Directory -outputs: - out: - type: boolean - outputBinding: - outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing === undefined)' -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_shallow2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_shallow2.cwl deleted file mode 100755 index 6f782d0e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_listing_shallow2.cwl +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InlineJavascriptRequirement: {} -inputs: - d: - type: Directory - loadListing: shallow_listing -outputs: - out: - type: boolean - outputBinding: - outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing === undefined)' -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_loadContents-limit.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_loadContents-limit.cwl deleted file mode 100644 index 89c554ce..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_loadContents-limit.cwl +++ /dev/null @@ -1,9 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -inputs: - filelist: - type: File - loadContents: true -outputs: [] -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_metadata.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_metadata.cwl deleted file mode 100644 index 7a1a2e3c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_metadata.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner -$namespaces: - dct: http://purl.org/dc/terms/ - foaf: http://xmlns.com/foaf/0.1/ -$schemas: - - foaf.rdf - - dcterms.rdf - -cwlVersion: v1.2 -class: CommandLineTool -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." - -dct:creator: - id: "http://orcid.org/0000-0003-3566-7705" - class: foaf:Person - foaf:name: Peter Amstutz - foaf:mbox: "mailto:peter.amstutz@curoverse.com" - -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - inputBinding: {position: 1} - numbering: - type: boolean? - inputBinding: - position: 0 - prefix: -n -outputs: [] -baseCommand: cat diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_mkdir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_mkdir.cwl deleted file mode 100644 index dbed864c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_mkdir.cwl +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -inputs: - dirname: string -outputs: - out: - type: Directory - outputBinding: - glob: $(inputs.dirname) -arguments: [mkdir, $(inputs.dirname)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_multiple_input_feature_requirement.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_multiple_input_feature_requirement.cwl deleted file mode 100644 index 57b8c681..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_multiple_input_feature_requirement.cwl +++ /dev/null @@ -1,29 +0,0 @@ -cwlVersion: v1.2 -class: Workflow - -requirements: - - class: MultipleInputFeatureRequirement - -inputs: [] - -steps: - step1: - run: echo-tool.cwl - in: - in: - default: hello - out: [out] - step2: - run: echo-tool.cwl - in: - in: - default: world - out: [out] - -outputs: - hello_world_in_two_lines: - type: - type: array - items: string - # Only allowed with MultipleInputFeatureRequirement - outputSource: [step1/out, step2/out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_nameroot.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_nameroot.cwl deleted file mode 100644 index 81d4d8ce..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_nameroot.cwl +++ /dev/null @@ -1,9 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -inputs: - file1: File -outputs: - b: stdout -stdout: $(inputs.file1.nameroot).xtx -baseCommand: [] -arguments: [echo, $(inputs.file1.basename), $(inputs.file1.nameroot), $(inputs.file1.nameext)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_nested-array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_nested-array.cwl deleted file mode 100644 index e4601525..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_nested-array.cwl +++ /dev/null @@ -1,15 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -baseCommand: echo -inputs: - letters: - type: - type: array - items: - type: array - items: string - inputBinding: - position: 1 -stdout: echo.txt -outputs: - echo: stdout \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_networkaccess.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_networkaccess.cwl deleted file mode 100644 index 855c7286..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_networkaccess.cwl +++ /dev/null @@ -1,15 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - DockerRequirement: - dockerPull: python:3 - NetworkAccess: - networkAccess: true -inputs: [] -outputs: [] -baseCommand: python -arguments: - - "-c" - - valueFrom: | - import urllib.request - assert(urllib.request.urlopen("http://commonwl.org").code == 200) \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_networkaccess2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_networkaccess2.cwl deleted file mode 100644 index 9d5c8864..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_networkaccess2.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - DockerRequirement: - dockerPull: python:3 -inputs: [] -outputs: [] -baseCommand: python -arguments: - - "-c" - - valueFrom: | - import urllib.request - assert(urllib.request.urlopen("http://commonwl.org").code == 200) \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_no-inputs-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_no-inputs-tool.cwl deleted file mode 100644 index 3037ea21..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_no-inputs-tool.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "CommandLineTool without inputs." -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: [] -outputs: - output: - type: File - outputBinding: { glob: output } -baseCommand: [echo, cwl] -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_no-inputs-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_no-inputs-wf.cwl deleted file mode 100644 index 1495bb63..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_no-inputs-wf.cwl +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -doc: "Workflow without inputs." -inputs: [] -outputs: - output: - type: File - outputSource: step0/output -steps: - step0: - in: [] - out: [output] - run: - class: CommandLineTool - cwlVersion: v1.2 - doc: "CommandLineTool without inputs." - hints: - DockerRequirement: - dockerPull: debian:stretch-slim - inputs: [] - outputs: - output: - type: File - outputBinding: { glob: output } - baseCommand: [echo, cwl] - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_no-outputs-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_no-outputs-tool.cwl deleted file mode 100644 index eef1dcb3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_no-outputs-tool.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "CommandLineTool without outputs." -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - label: Input File - inputBinding: {position: 1} -outputs: [] -baseCommand: echo diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_no-outputs-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_no-outputs-wf.cwl deleted file mode 100644 index 8fbed130..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_no-outputs-wf.cwl +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -doc: "Workflow without outputs." -inputs: - file1: File -outputs: [] -steps: - step0: - in: {file1: file1} - out: [] - run: - class: CommandLineTool - cwlVersion: v1.2 - doc: "CommandLineTool without outputs." - hints: - DockerRequirement: - dockerPull: debian:stretch-slim - inputs: - file1: - type: File - label: Input File - inputBinding: {position: 1} - outputs: [] - baseCommand: echo \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_null-defined.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_null-defined.cwl deleted file mode 100644 index 3794639c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_null-defined.cwl +++ /dev/null @@ -1,15 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -requirements: - InlineJavascriptRequirement: {} -inputs: - file1: File? -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -stdout: out.txt -arguments: [echo, '$(inputs.file1 === null ? "t" : "f")'] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_null-expression1-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_null-expression1-tool.cwl deleted file mode 100644 index 0a3c7bef..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_null-expression1-tool.cwl +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: ExpressionTool -requirements: - - class: InlineJavascriptRequirement -cwlVersion: v1.2 - -inputs: - i1: - type: Any - default: "the-default" - -outputs: - output: int - -expression: "$({'output': (inputs.i1 == 'the-default' ? 1 : 2)})" \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_null-expression2-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_null-expression2-tool.cwl deleted file mode 100644 index 2b09ec04..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_null-expression2-tool.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: ExpressionTool -requirements: - - class: InlineJavascriptRequirement -cwlVersion: v1.2 - -inputs: - i1: Any - -outputs: - output: int - -expression: "$({'output': (inputs.i1 == 'the-default' ? 1 : 2)})" \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_null-expression3-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_null-expression3-tool.cwl deleted file mode 100644 index 6dbfda6c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_null-expression3-tool.cwl +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: ExpressionTool -requirements: { InlineJavascriptRequirement: {} } -cwlVersion: v1.2 - -inputs: [] - -outputs: - output: Any - -expression: "$({'output': null })" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_operation.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_operation.cwl deleted file mode 100644 index a9e6c5e6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_operation.cwl +++ /dev/null @@ -1,25 +0,0 @@ -# -# Example of an operation that has not yet been implemented -# -class: Operation -cwlVersion: v1.2 - -# an Operation is a placeholder for a CommandLineTool or -# Workflow to be added later, therefore its documentation -# are very important. -id: reverse -doc: "Reverse each line" - -# The "inputs" array work the same as in CommandLineTool, but do -# not have any inputBinding -inputs: - input: - type: File - -# The "outputs" array defines the structure of the output object, just like -# in CommandLineTool, but without outputBinding -outputs: - output: - type: File - -# There are no "run" or "steps" command (FIXME: Should they be allowed?) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_optional-numerical-output-0.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_optional-numerical-output-0.cwl deleted file mode 100644 index 192d23af..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_optional-numerical-output-0.cwl +++ /dev/null @@ -1,16 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -baseCommand: - - echo - - "0" -stdout: a.txt -requirements: -- class: InlineJavascriptRequirement -inputs: [] -outputs: - out: - type: float? - outputBinding: - glob: "a.txt" - loadContents: true - outputEval: "${\n return parseFloat(self[0].contents);\n}" \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_optional-output.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_optional-output.cwl deleted file mode 100644 index ccca38b4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_optional-output.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: "v1.2" -doc: "Print the contents of a file to stdout using 'cat' running in a docker container." -hints: - DockerRequirement: - dockerPull: debian:stretch-slim -inputs: - file1: - type: File - label: Input File - doc: "The file that will be copied using 'cat'" - inputBinding: {position: 1} -outputs: - output_file: - type: File - outputBinding: - glob: output.txt - secondaryFiles: - - .idx - optional_file: - type: File? - outputBinding: - glob: bumble.txt -baseCommand: cat -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_output-arrays-file-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_output-arrays-file-wf.cwl deleted file mode 100644 index 845fcebc..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_output-arrays-file-wf.cwl +++ /dev/null @@ -1,53 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - i: File - -outputs: - o: - type: File[] - outputSource: step2/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: File - loadContents: true - - outputs: - o: - type: string[] - expression: > - ${return {'o': inputs.i.contents.split(" ")};} - step2: - in: - i: - source: step1/o - out: [o] - run: - class: CommandLineTool - - inputs: - i: - type: string[] - inputBinding: - position: 1 - - outputs: - o: - type: File[] - outputBinding: - glob: $(inputs.i) - - baseCommand: touch diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_output-arrays-int-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_output-arrays-int-wf.cwl deleted file mode 100644 index 09bfdd5a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_output-arrays-int-wf.cwl +++ /dev/null @@ -1,60 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -requirements: - InlineJavascriptRequirement: {} - -inputs: - i: int - -outputs: - o: - type: int - outputSource: step3/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int - outputs: - o: - type: int[] - expression: > - ${return {'o': Array.apply(null, {length: inputs.i}).map(Number.call, Number)};} - step2: - in: - i: - source: step1/o - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int[] - outputs: - o: - type: int[] - expression: > - ${return {'o': inputs.i.map(function(x) { return (x + 1) * 2; })};} - step3: - in: - i: - source: step2/o - out: [o] - run: - class: ExpressionTool - inputs: - i: - type: int[] - outputs: - o: - type: int - expression: > - ${return {'o': inputs.i.reduce(function(a, b) { return a + b; })};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_output-arrays-int.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_output-arrays-int.cwl deleted file mode 100644 index f2c03f2e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_output-arrays-int.cwl +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 -class: ExpressionTool - -requirements: - InlineJavascriptRequirement: {} - -inputs: - i: - type: int - -outputs: - o: - type: int[] - -expression: > - ${return {'o': Array.apply(null, {length: inputs.i}).map(Number.call, Number)};} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_output_reference_workflow_input.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_output_reference_workflow_input.cwl deleted file mode 100644 index 808132aa..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_output_reference_workflow_input.cwl +++ /dev/null @@ -1,14 +0,0 @@ -cwlVersion: v1.2 -class: Workflow - -inputs: - first: - type: string - default: me - -steps: [] - -outputs: - last: - type: string - outputSource: first diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_action.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_action.cwl deleted file mode 100644 index 82f65ccf..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_action.cwl +++ /dev/null @@ -1,11 +0,0 @@ -arguments: [echo, $(inputs.initial_file.basename)] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: initial_file, type: File} -- {id: out_file_name, type: string} -outputs: -- {id: processed_file, type: stdout} -requirements: -- {class: InlineJavascriptRequirement} -stdout: $(inputs.out_file_name) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_anon_enum_inside_array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_anon_enum_inside_array.cwl deleted file mode 100644 index 2807a86c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_anon_enum_inside_array.cwl +++ /dev/null @@ -1,25 +0,0 @@ -arguments: -- {prefix: first, valueFrom: $(inputs.first.species)} -- {prefix: second, valueFrom: $(inputs.second)} -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: first - type: - fields: - - name: species - type: - - symbols: [homo_sapiens, mus_musculus] - type: enum - - 'null' - type: record -- id: second - type: - - 'null' - - symbols: [homo_sapiens, mus_musculus] - type: enum -outputs: -- {id: result, type: stdout} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_anon_enum_inside_array_inside_schemadef.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_anon_enum_inside_array_inside_schemadef.cwl deleted file mode 100644 index 65be0e26..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_anon_enum_inside_array_inside_schemadef.cwl +++ /dev/null @@ -1,26 +0,0 @@ -arguments: -- {prefix: species, valueFrom: $(inputs.first.species)} -- {prefix: ncbi_build, valueFrom: $(inputs.first.ncbi_build)} -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: first - type: - fields: - - name: species - type: - - 'null' - - symbols: [homo_sapiens, mus_musculus] - type: enum - - name: ncbi_build - type: - - 'null' - - symbols: [GRCh37, GRCh38, GRCm38] - type: enum - name: user_type_2 - type: record -outputs: -- {id: result, type: stdout} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_any-type-compat.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_any-type-compat.cwl deleted file mode 100644 index f264d4c7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_any-type-compat.cwl +++ /dev/null @@ -1,19 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: input1, type: Any} -- id: input2 - type: {items: Any, type: array} -- {id: input3, type: Any} -outputs: -- id: output1 - outputSource: input1 - type: {items: string, type: array} -- id: output2 - outputSource: input2 - type: {items: string, type: array} -- {id: output3, outputSource: input3, type: string} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bar.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bar.cwl deleted file mode 100644 index 1e9cc9d7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bar.cwl +++ /dev/null @@ -1,11 +0,0 @@ -baseCommand: [echo] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: in1, type: int} -outputs: -- id: out1 - outputBinding: {outputEval: bar $(inputs.in1)} - type: string -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_basename-fields-test.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_basename-fields-test.cwl deleted file mode 100644 index 2c9c6273..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_basename-fields-test.cwl +++ /dev/null @@ -1,50 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: tool, type: File} -outputs: -- {id: rootFile, outputSource: root/out, type: File} -- {id: extFile, outputSource: ext/out, type: File} -requirements: -- {class: StepInputExpressionRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: root - in: - - {id: tool, source: tool} - - {id: in, valueFrom: $(inputs.tool.nameroot)} - out: [out] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - id: in - inputBinding: {position: 1} - type: string - - id: name - type: ['null', string] - outputs: - - {id: out, type: stdout} - requirements: - - {class: InlineJavascriptRequirement} - stdout: out.txt -- id: ext - in: - - {id: tool, source: tool} - - {id: in, valueFrom: $(inputs.tool.nameext)} - out: [out] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - id: in - inputBinding: {position: 1} - type: string - - id: name - type: ['null', string] - outputs: - - {id: out, type: stdout} - requirements: - - {class: InlineJavascriptRequirement} - stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bash-dollar-quote.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bash-dollar-quote.cwl deleted file mode 100644 index ccd1f583..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bash-dollar-quote.cwl +++ /dev/null @@ -1,31 +0,0 @@ -baseCommand: [bash, script.sh] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {default: val, id: val, type: string} -outputs: -- {id: out, type: stdout} -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "echo \\$(echo \\\n \"My country, 'tis of thee,\" \\\n \"Sweet land\ - \ of liberty\" | rev)\necho '$(inputs.val)' # produce val\necho '\\$(inputs.val)'\ - \ # produce $(inputs.val)\necho\necho '\\\\$(inputs.val)' # produce \\\ - val\necho '\\\\\\$(inputs.val)' # produce \\$(inputs.val)\necho\necho '\\\\\ - \\\\$(inputs.val)' # produce \\\\val\necho '\\\\\\\\\\$(inputs.val)' # produce\ - \ \\\\$(inputs.val)\necho\necho '\\\\\\\\\\\\$(inputs.val)' # produce \\\\\\\ - val\necho '\\\\\\\\\\\\\\$(inputs.val)' # produce \\\\\\$(inputs.val)\necho\n\ - echo '\\\\\\\\\\\\\\\\$(inputs.val)' # produce \\\\\\\\val\necho '\\\\\\\\\\\ - \\\\\\\\$(inputs.val)' # produce \\\\\\\\$(inputs.val)\necho\necho '\\\\\\\\\ - \\\\\\\\\\\\$(inputs.val)' # produce \\\\\\\\\\val\necho '\\\\\\\\\\\\\\\\\\\ - \\\\$(inputs.val)' # produce \\\\\\\\\\$(inputs.val)\necho '\\' #\ - \ produce \\\necho '\\\\' # produce \\\necho '\\\\\\' # produce\ - \ \\\\\necho '\\\\\\\\' # produce \\\\\necho '\\\\\\\\\\' # produce\ - \ \\\\\\\necho '\\\\\\\\\\\\' # produce \\\\\\\necho '\\\\\\\\\\\\\\' \ - \ # produce \\\\\\\\\necho '\\\\\\\\\\\\\\\\' # produce \\\\\\\\\necho '\\\ - \\\\\\\\\\\\\\\\' # produce \\\\\\\\\\\necho '\\\\\\\\\\\\\\\\\\\\' # produce\ - \ \\\\\\\\\\\necho '$' # produce $\necho '\\$' # produce \\\ - $\necho '\\\\$' # produce \\$\necho '$$' # produce $$\necho '$$$'\ - \ # produce $$$\n", entryname: script.sh} -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bash-line-continuation-with-expression.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bash-line-continuation-with-expression.cwl deleted file mode 100644 index 0a380d35..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bash-line-continuation-with-expression.cwl +++ /dev/null @@ -1,16 +0,0 @@ -baseCommand: [bash, script.sh] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- default: liberty - id: liberty - type: ['null', string] -outputs: -- {id: out, type: stdout} -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: "echo \\\n \"My country, 'tis of thee,\" \\\n \"Sweet land of $(inputs.liberty)\"\ - \n", entryname: script.sh} -- {class: InlineJavascriptRequirement} -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bash-line-continuation.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bash-line-continuation.cwl deleted file mode 100644 index 30c4b5e4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bash-line-continuation.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: [bash, script.sh] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: out, type: stdout} -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: "echo \\\n \"My country, 'tis of thee,\" \\\n \"Sweet land of liberty\"\ - \n", entryname: script.sh} -- {class: InlineJavascriptRequirement} -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_binding-test.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_binding-test.cwl deleted file mode 100644 index 2318e3b4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_binding-test.cwl +++ /dev/null @@ -1,25 +0,0 @@ -arguments: [bwa, mem] -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -hints: -- {class: DockerRequirement, dockerPull: python:2-slim} -inputs: -- id: reference - inputBinding: {position: 2} - type: File -- id: reads - inputBinding: {position: 3, prefix: -XXX} - type: - inputBinding: {prefix: -YYY} - items: File - type: array -- default: {class: File, location: args.py} - id: '#args.py' - inputBinding: {position: -1} - type: File -outputs: -- id: args - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bool-empty-inputbinding.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bool-empty-inputbinding.cwl deleted file mode 100644 index 346b40ad..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bool-empty-inputbinding.cwl +++ /dev/null @@ -1,19 +0,0 @@ -arguments: [] -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -hints: -- {class: DockerRequirement, dockerPull: python:2-slim} -inputs: -- id: flag - inputBinding: {} - type: boolean -- default: {class: File, location: args.py} - id: args.py - inputBinding: {position: -1} - type: File -outputs: -- id: args - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bwa-mem-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bwa-mem-tool.cwl deleted file mode 100644 index a6299890..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_bwa-mem-tool.cwl +++ /dev/null @@ -1,36 +0,0 @@ -arguments: -- bwa -- mem -- {position: 1, prefix: -t, valueFrom: $(runtime.cores)} -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -hints: -- {class: ResourceRequirement, coresMin: 2} -- {class: DockerRequirement, dockerPull: python:2-slim} -inputs: -- id: reference - inputBinding: {position: 2} - type: File -- id: reads - inputBinding: {position: 3} - type: {items: File, type: array} -- id: minimum_seed_length - inputBinding: {position: 1, prefix: -m} - type: int -- id: min_std_max_min - inputBinding: {itemSeparator: ',', position: 1, prefix: -I} - type: {items: int, type: array} -- default: {class: File, location: args.py} - id: args.py - inputBinding: {position: -1} - type: File -outputs: -- id: sam - outputBinding: {glob: output.sam} - type: ['null', File] -- id: args - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.sam diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat-from-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat-from-dir.cwl deleted file mode 100644 index cd40599f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat-from-dir.cwl +++ /dev/null @@ -1,10 +0,0 @@ -baseCommand: [cat] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: dir1, type: Directory} -outputs: -- {id: output, type: stdout} -requirements: -- {class: InlineJavascriptRequirement} -stdin: $(inputs.dir1.listing[0].path) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat-tool-shortcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat-tool-shortcut.cwl deleted file mode 100644 index 0cf9b937..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat-tool-shortcut.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: [cat] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: file1, type: stdin} -outputs: -- id: output - outputBinding: {glob: output} - type: File -requirements: -- {class: DockerRequirement, dockerPull: debian:stretch-slim} -- {class: InlineJavascriptRequirement} -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat-tool.cwl deleted file mode 100644 index b996ad25..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat-tool.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: [cat] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- id: output - outputBinding: {glob: output} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdin: $(inputs.file1.path) -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat.cwl deleted file mode 100644 index 6961efb6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: [echo] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: in1, type: int} -- {id: in2, type: int} -- {id: in3, type: int} -outputs: -- id: out1 - outputBinding: {outputEval: $(inputs.in1)$(inputs.in2)$(inputs.in3)} - type: string -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat1-testcli.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat1-testcli.cwl deleted file mode 100644 index cd104883..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat1-testcli.cwl +++ /dev/null @@ -1,23 +0,0 @@ -arguments: [cat] -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -doc: Print the contents of a file to stdout using 'cat' running in a docker container. -hints: -- {class: DockerRequirement, dockerPull: python:2-slim} -inputs: -- id: file1 - inputBinding: {position: 1} - type: File -- id: numbering - inputBinding: {position: 0, prefix: -n} - type: ['null', boolean] -- default: {class: File, location: args.py} - id: args.py - inputBinding: {position: -1} - type: File -outputs: -- id: args - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-from-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-from-dir.cwl deleted file mode 100644 index cf3048ad..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-from-dir.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: cat -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: dir1 - inputBinding: {valueFrom: '$(self.listing[0].path)'} - type: Directory -outputs: -- id: output_file - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-nodocker.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-nodocker.cwl deleted file mode 100644 index d43d3b43..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-nodocker.cwl +++ /dev/null @@ -1,17 +0,0 @@ -baseCommand: cat -class: CommandLineTool -cwlVersion: v1.2 -doc: Print the contents of a file to stdout using 'cat'. -inputs: -- doc: The file that will be copied using 'cat' - id: file1 - inputBinding: {position: 1} - label: Input File - type: File -outputs: -- id: output_file - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-tool-docker.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-tool-docker.cwl deleted file mode 100644 index 96f1f40c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-tool-docker.cwl +++ /dev/null @@ -1,18 +0,0 @@ -baseCommand: cat -class: CommandLineTool -cwlVersion: v1.2 -doc: Print the contents of a file to stdout using 'cat' running in a docker container. -inputs: -- doc: The file that will be copied using 'cat' - id: file1 - inputBinding: {position: 1} - label: Input File - type: File -outputs: -- id: output_file - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: DockerRequirement, dockerPull: debian:stretch-slim} -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-tool-mediumcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-tool-mediumcut.cwl deleted file mode 100644 index aad55d3d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-tool-mediumcut.cwl +++ /dev/null @@ -1,16 +0,0 @@ -baseCommand: cat -class: CommandLineTool -cwlVersion: v1.2 -doc: Print the contents of a file to stdout using 'cat' running in a docker container. -inputs: -- doc: The file that will be copied using 'cat' - id: file1 - inputBinding: {position: 1} - label: Input File - type: File -outputs: -- {id: output_file, type: stdout} -requirements: -- {class: DockerRequirement, dockerPull: debian:stretch-slim} -- {class: InlineJavascriptRequirement} -stdout: cat-out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-tool-shortcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-tool-shortcut.cwl deleted file mode 100644 index a597d717..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-tool-shortcut.cwl +++ /dev/null @@ -1,15 +0,0 @@ -baseCommand: cat -class: CommandLineTool -cwlVersion: v1.2 -doc: Print the contents of a file to stdout using 'cat' running in a docker container. -inputs: -- doc: The file that will be copied using 'cat' - id: file1 - inputBinding: {position: 1} - label: Input File - type: File -outputs: -- {id: output_file, type: stdout} -requirements: -- {class: DockerRequirement, dockerPull: debian:stretch-slim} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-tool.cwl deleted file mode 100644 index f8a8f2f9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat3-tool.cwl +++ /dev/null @@ -1,19 +0,0 @@ -baseCommand: cat -class: CommandLineTool -cwlVersion: v1.2 -doc: Print the contents of a file to stdout using 'cat' running in a docker container. -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: -- doc: The file that will be copied using 'cat' - id: file1 - inputBinding: {position: 1} - label: Input File - type: File -outputs: -- id: output_file - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat4-from-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat4-from-dir.cwl deleted file mode 100644 index 7a884e4a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat4-from-dir.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: cat -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: dir1 - inputBinding: {valueFrom: '$(self.listing[0].listing[0].path)'} - type: Directory -outputs: -- id: output_file - outputBinding: {glob: output.txt} - type: File -requirements: [] -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat4-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat4-tool.cwl deleted file mode 100644 index 292c80ed..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat4-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -baseCommand: cat -class: CommandLineTool -cwlVersion: v1.2 -doc: Print the contents of a file to stdout using 'cat' running in a docker container - if docker is available. -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: -- {id: file1, type: File} -outputs: -- id: output_txt - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdin: $(inputs.file1.path) -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat5-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat5-tool.cwl deleted file mode 100644 index fc9f5dc6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cat5-tool.cwl +++ /dev/null @@ -1,21 +0,0 @@ -$namespaces: {ex: http://example.com/} -baseCommand: cat -class: CommandLineTool -cwlVersion: v1.2 -doc: Print the contents of a file to stdout using 'cat' running in a docker container. -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} - ex:BlibberBlubberFakeRequirement: {fakeField: fraggleFroogle} -inputs: -- doc: The file that will be copied using 'cat' - id: file1 - inputBinding: {position: 1} - label: Input File - type: File -outputs: -- id: output_file - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_check.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_check.cwl deleted file mode 100644 index eaa45cfb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_check.cwl +++ /dev/null @@ -1,10 +0,0 @@ -arguments: [sh, -c, "name=`basename $(inputs.p.path)`\nls -l $(inputs.p.path)\nif - test $name = $(inputs.checkname) ; then\n echo success\nelse\n echo expected - basename to be $(inputs.checkname) but was $name\n exit 1\nfi\n"] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: p, type: File} -- {id: checkname, type: string} -outputs: [] -requirements: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_colon:test.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_colon:test.cwl deleted file mode 100644 index 9f51d608..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_colon:test.cwl +++ /dev/null @@ -1,22 +0,0 @@ -arguments: ['mkdir $(inputs.outdir_name); - - cp $(inputs.input_file.path) $(inputs.outdir_name)/; - - echo Status: done! - - '] -baseCommand: [bash, -c] -class: CommandLineTool -cwlVersion: v1.2 -hints: - DockerRequirement: {dockerPull: 'docker.io/bash:4.4'} -inputs: -- {id: input_file, type: File} -- {id: outdir_name, type: string} -outputs: -- {id: log, type: stdout} -- id: result - outputBinding: {glob: $(inputs.outdir_name)} - type: Directory -requirements: [] -stdout: re:sult diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_colon_test_output.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_colon_test_output.cwl deleted file mode 100644 index 22e1a38d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_colon_test_output.cwl +++ /dev/null @@ -1,18 +0,0 @@ -arguments: ['mkdir $(inputs.outdir_name); - - cp $(inputs.input_file.path) $(inputs.outdir_name)/; - - '] -baseCommand: [bash, -c] -class: CommandLineTool -cwlVersion: v1.2 -hints: - DockerRequirement: {dockerPull: 'docker.io/bash:4.4'} -inputs: -- {id: input_file, type: File} -- {id: outdir_name, type: string} -outputs: -- id: result - outputBinding: {glob: $(inputs.outdir_name)} - type: Directory -requirements: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-001.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-001.cwl deleted file mode 100644 index 1382defb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-001.cwl +++ /dev/null @@ -1,29 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: val, type: int} -outputs: -- id: out1 - outputSource: step1/out1 - type: ['null', string] -requirements: -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var > 2) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-001_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-001_nojs.cwl deleted file mode 100644 index c3eafa3f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-001_nojs.cwl +++ /dev/null @@ -1,29 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: test, type: boolean} -outputs: -- id: out1 - outputSource: step1/out1 - type: ['null', string] -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {default: 23, id: in1} - - {id: extra, source: test} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.extra) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-002.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-002.cwl deleted file mode 100644 index b53e4cb2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-002.cwl +++ /dev/null @@ -1,27 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: val, type: int} -outputs: -- {id: out1, outputSource: step1/out1, type: string} -requirements: -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var > 2) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-002_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-002_nojs.cwl deleted file mode 100644 index 040e354e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-002_nojs.cwl +++ /dev/null @@ -1,28 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: val, type: int} -- {default: false, id: test, type: boolean} -outputs: -- {id: out1, outputSource: step1/out1, type: string} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: test} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-003.1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-003.1.cwl deleted file mode 100644 index 2bdf54c0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-003.1.cwl +++ /dev/null @@ -1,48 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: val, type: int} -outputs: -- id: out1 - outputSource: [step1/out1, step2/out1] - pickValue: first_non_null - type: string -requirements: -- {class: InlineJavascriptRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.in1 < 1) -- id: step2 - in: - - {id: in1, source: val} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var > 2) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-003.1_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-003.1_nojs.cwl deleted file mode 100644 index d1bc9c0c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-003.1_nojs.cwl +++ /dev/null @@ -1,50 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {default: 23, id: val, type: int} -- {id: test1, type: boolean} -- {id: test2, type: boolean} -outputs: -- id: out1 - outputSource: [step1/out1, step2/out1] - pickValue: first_non_null - type: string -requirements: -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: test1} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var) -- id: step2 - in: - - {id: in1, source: val} - - {id: a_new_var, source: test2} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-003.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-003.cwl deleted file mode 100644 index 2361069e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-003.cwl +++ /dev/null @@ -1,32 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: val, type: int} -- {default: Direct, id: def, type: string} -outputs: -- id: out1 - outputSource: [step1/out1, def] - pickValue: first_non_null - type: string -requirements: -- {class: InlineJavascriptRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var > 2) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-003_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-003_nojs.cwl deleted file mode 100644 index ff4bd814..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-003_nojs.cwl +++ /dev/null @@ -1,33 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {default: 23, id: val, type: int} -- {id: test, type: boolean} -- {default: Direct, id: def, type: string} -outputs: -- id: out1 - outputSource: [step1/out1, def] - pickValue: first_non_null - type: string -requirements: -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: test} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-004.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-004.cwl deleted file mode 100644 index 1be31810..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-004.cwl +++ /dev/null @@ -1,32 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: val, type: int} -- {default: Direct, id: def, type: string} -outputs: -- id: out1 - outputSource: [step1/out1, def] - pickValue: the_only_non_null - type: string -requirements: -- {class: InlineJavascriptRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var > 2) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-004_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-004_nojs.cwl deleted file mode 100644 index 6944c2c3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-004_nojs.cwl +++ /dev/null @@ -1,33 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {default: 23, id: val, type: int} -- {id: test, type: boolean} -- {default: Direct, id: def, type: string} -outputs: -- id: out1 - outputSource: [step1/out1, def] - pickValue: the_only_non_null - type: string -requirements: -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: test} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-006.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-006.cwl deleted file mode 100644 index 5b11d793..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-006.cwl +++ /dev/null @@ -1,48 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: val, type: int} -outputs: -- id: out1 - outputSource: [step1/out1, step2/out1] - pickValue: the_only_non_null - type: string -requirements: -- {class: InlineJavascriptRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var > 2) -- id: step2 - in: - - {id: in1, source: val} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: bar $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var > 0) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-006_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-006_nojs.cwl deleted file mode 100644 index 651fdb9a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-006_nojs.cwl +++ /dev/null @@ -1,50 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: test1, type: boolean} -- {id: test2, type: boolean} -- {default: 23, id: val, type: int} -outputs: -- id: out1 - outputSource: [step1/out1, step2/out1] - pickValue: the_only_non_null - type: string -requirements: -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: test1} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var) -- id: step2 - in: - - {id: in1, source: val} - - {id: a_new_var, source: test2} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: bar $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-007.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-007.cwl deleted file mode 100644 index 69e058fe..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-007.cwl +++ /dev/null @@ -1,48 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: val, type: int} -outputs: -- id: out1 - outputSource: [step1/out1, step2/out1] - pickValue: all_non_null - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var > 2) -- id: step2 - in: - - {id: in1, source: val} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: bar $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var > 0) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-007_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-007_nojs.cwl deleted file mode 100644 index 43e92a34..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-007_nojs.cwl +++ /dev/null @@ -1,50 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {default: 23, id: val, type: int} -- {id: test1, type: boolean} -- {id: test2, type: boolean} -outputs: -- id: out1 - outputSource: [step1/out1, step2/out1] - pickValue: all_non_null - type: {items: string, type: array} -requirements: -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: test1} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var) -- id: step2 - in: - - {id: in1, source: val} - - {id: a_new_var, source: test2} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: bar $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-009.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-009.cwl deleted file mode 100644 index 5eced09d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-009.cwl +++ /dev/null @@ -1,34 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: data - type: {items: int, type: array} -- {id: val, type: int} -outputs: -- id: out1 - outputSource: step1/out1 - pickValue: all_non_null - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} -- {class: ScatterFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: in1, source: data} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - scatter: in1 - when: $(inputs.a_new_var > 3) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-009_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-009_nojs.cwl deleted file mode 100644 index 28189ccd..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-009_nojs.cwl +++ /dev/null @@ -1,35 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- default: [1, 2, 3, 4, 5, 6] - id: data - type: {items: int, type: array} -- {id: test, type: boolean} -outputs: -- id: out1 - outputSource: step1/out1 - pickValue: all_non_null - type: {items: string, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in1, source: data} - - {id: a_new_var, source: test} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - scatter: in1 - when: $(inputs.a_new_var) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-010.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-010.cwl deleted file mode 100644 index dd69ce05..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-010.cwl +++ /dev/null @@ -1,34 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: val - type: {items: int, type: array} -outputs: -- id: out1 - outputSource: step1/out1 - pickValue: all_non_null - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} -- {class: ScatterFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - scatter: [in1, a_new_var] - scatterMethod: dotproduct - when: $(inputs.a_new_var > 3) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-010_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-010_nojs.cwl deleted file mode 100644 index 0ea64853..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-010_nojs.cwl +++ /dev/null @@ -1,38 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- default: [1, 2, 3, 4, 5, 6] - id: val - type: {items: int, type: array} -- default: [false, false, false, true, true, true] - id: test - type: {items: boolean, type: array} -outputs: -- id: out1 - outputSource: step1/out1 - pickValue: all_non_null - type: {items: string, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: test} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - scatter: [in1, a_new_var] - scatterMethod: dotproduct - when: $(inputs.a_new_var) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-011.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-011.cwl deleted file mode 100644 index 121d095b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-011.cwl +++ /dev/null @@ -1,45 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: in1 - type: {items: int, type: array} -- id: in2 - type: {items: int, type: array} -- id: in3 - type: {items: int, type: array} -outputs: -- id: out1 - outputSource: step1/out1 - pickValue: all_non_null - type: - items: - items: {items: string, type: array} - type: array - type: array -requirements: -- {class: InlineJavascriptRequirement} -- {class: ScatterFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: in1, source: in1} - - {id: in2, source: in2} - - {id: in3, source: in3} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - - {id: in2, type: int} - - {id: in3, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: $(inputs.in1)$(inputs.in2)$(inputs.in3)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - scatter: [in1, in2, in3] - scatterMethod: nested_crossproduct - when: $(inputs.in3 % 2 == 0) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-011_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-011_nojs.cwl deleted file mode 100644 index 40cf229c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-011_nojs.cwl +++ /dev/null @@ -1,50 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- default: [1, 2] - id: in1 - type: {items: int, type: array} -- default: [1, 2, 3] - id: in2 - type: {items: int, type: array} -- {default: 23, id: in3, type: int} -- default: [false, true, false, true] - id: test - type: {items: boolean, type: array} -outputs: -- id: out1 - outputSource: step1/out1 - pickValue: all_non_null - type: - items: - items: {items: string, type: array} - type: array - type: array -requirements: -- {class: ScatterFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in1, source: in1} - - {id: in2, source: in2} - - {id: in3, source: in3} - - {id: another_input, source: test} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - - {id: in2, type: int} - - {id: in3, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: $(inputs.in1)$(inputs.in2)$(inputs.in3)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - scatter: [in1, in2, another_input] - scatterMethod: nested_crossproduct - when: $(inputs.another_input) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-012.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-012.cwl deleted file mode 100644 index 5b765d77..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-012.cwl +++ /dev/null @@ -1,29 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: val, type: int} -outputs: -- id: out1 - outputSource: step1/out1 - type: ['null', string] -requirements: -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: val} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var % 2) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-012_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-012_nojs.cwl deleted file mode 100644 index b69b29b6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-012_nojs.cwl +++ /dev/null @@ -1,30 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {default: 23, id: val, type: int} -- {default: 1, id: test, type: int} -outputs: -- id: out1 - outputSource: step1/out1 - type: ['null', string] -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in1, source: val} - - {id: a_new_var, source: test} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - when: $(inputs.a_new_var) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-013.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-013.cwl deleted file mode 100644 index 63cb0b52..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-013.cwl +++ /dev/null @@ -1,51 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: in1 - type: {items: int, type: array} -outputs: -- id: out1 - linkMerge: merge_flattened - outputSource: [step1/out1, step2/out1] - pickValue: all_non_null - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} -- {class: ScatterFeatureRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: in1, source: in1} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - scatter: in1 - when: $(inputs.in1 % 2 == 0) -- id: step2 - in: - - {id: in1, source: in1} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: bar $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - scatter: in1 - when: $(inputs.in1 % 2 == 1) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-013_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-013_nojs.cwl deleted file mode 100644 index 6d859456..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-wf-013_nojs.cwl +++ /dev/null @@ -1,62 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- default: [1, 2, 3, 4, 5, 6] - id: in1 - type: {items: int, type: array} -- default: [false, true, false, true, false, true] - id: test1 - type: {items: boolean, type: array} -- default: [true, false, true, false, true, false] - id: test2 - type: {items: boolean, type: array} -outputs: -- id: out1 - linkMerge: merge_flattened - outputSource: [step1/out1, step2/out1] - pickValue: all_non_null - type: {items: string, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in1, source: in1} - - {id: another_var, source: test1} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - scatter: [in1, another_var] - scatterMethod: dotproduct - when: $(inputs.another_var) -- id: step2 - in: - - {id: in1, source: in1} - - {id: another_var, source: test2} - out: [out1] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - {id: in1, type: int} - outputs: - - id: out1 - outputBinding: {outputEval: bar $(inputs.in1)} - type: string - requirements: - - {class: InlineJavascriptRequirement} - scatter: [in1, another_var] - scatterMethod: dotproduct - when: $(inputs.another_var) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-with-defaults.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-with-defaults.cwl deleted file mode 100644 index 8d94a283..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cond-with-defaults.cwl +++ /dev/null @@ -1,63 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: forward_reads - type: ['null', File] -- id: reverse_reads - type: ['null', File] -- id: single_reads - type: ['null', File] -outputs: -- id: out_file - linkMerge: merge_flattened - outputSource: [step_paired/processed_file, step_single/processed_file] - pickValue: all_non_null - type: {items: File, type: array} -requirements: -- {class: MultipleInputFeatureRequirement} -- {class: InlineJavascriptRequirement} -- {class: StepInputExpressionRequirement} -- {class: ScatterFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step_paired - in: - - {id: single, source: single_reads} - - default: ['1', '2'] - id: suffix - - id: initial_file - source: [forward_reads, reverse_reads] - - {id: out_file_name, valueFrom: filename_paired$(inputs.suffix)} - out: [processed_file] - run: - arguments: [echo, $(inputs.initial_file.basename)] - class: CommandLineTool - inputs: - - {id: initial_file, type: File} - - {id: out_file_name, type: string} - outputs: - - {id: processed_file, type: stdout} - requirements: - - {class: InlineJavascriptRequirement} - stdout: $(inputs.out_file_name) - scatter: [initial_file, suffix] - scatterMethod: dotproduct - when: $(inputs.single === null) -- id: step_single - in: - - {id: single, source: single_reads} - - {id: initial_file, source: single_reads} - - {default: filename_single, id: out_file_name} - out: [processed_file] - run: - arguments: [echo, $(inputs.initial_file.basename)] - class: CommandLineTool - inputs: - - {id: initial_file, type: File} - - {id: out_file_name, type: string} - outputs: - - {id: processed_file, type: stdout} - requirements: - - {class: InlineJavascriptRequirement} - stdout: $(inputs.out_file_name) - when: $(inputs.single !== null) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cores_float.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cores_float.cwl deleted file mode 100644 index c304c0e0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cores_float.cwl +++ /dev/null @@ -1,11 +0,0 @@ -arguments: [$(runtime.cores)] -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: output, type: stdout} -requirements: -- {class: ResourceRequirement, coresMax: 1.75, coresMin: 1.25} -- {class: InlineJavascriptRequirement} -stdout: cores.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines1-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines1-wf-noET.cwl deleted file mode 100644 index 3947d4e3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines1-wf-noET.cwl +++ /dev/null @@ -1,27 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: wc_output, outputSource: step1/output, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines1-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines1-wf.cwl deleted file mode 100644 index 938b5e49..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines1-wf.cwl +++ /dev/null @@ -1,40 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: count_output, outputSource: step2/output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output -- id: step2 - in: - - {id: file1, source: step1/output} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines10-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines10-wf.cwl deleted file mode 100644 index 6212f8df..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines10-wf.cwl +++ /dev/null @@ -1,54 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: count_output, outputSource: step0/count_output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step0 - in: - - {id: file1, source: file1} - out: [count_output] - run: - class: Workflow - inputs: - - {id: file1, type: File} - outputs: - - {id: count_output, outputSource: step2/output, type: int} - requirements: - - {class: SubworkflowFeatureRequirement} - - {class: InlineJavascriptRequirement} - steps: - - id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output - - id: step2 - in: - - {id: file1, source: step1/output} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-extra-step-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-extra-step-wf-noET.cwl deleted file mode 100644 index bed82b5a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-extra-step-wf-noET.cwl +++ /dev/null @@ -1,47 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: file1 - type: ['null', File] -outputs: -- {id: wc_output, outputSource: step1/output, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step0 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: [cat] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output -- id: step1 - in: - - default: {class: File, location: whale.txt} - id: file1 - source: step0/output - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-extra-step-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-extra-step-wf.cwl deleted file mode 100644 index eabd2945..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-extra-step-wf.cwl +++ /dev/null @@ -1,60 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: file1 - type: ['null', File] -outputs: -- {id: count_output, outputSource: step2/output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step0 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: [cat] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output -- id: step1 - in: - - default: {class: File, location: whale.txt} - id: file1 - source: step0/output - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output -- id: step2 - in: - - {id: file1, source: step1/output} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-null-step-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-null-step-wf-noET.cwl deleted file mode 100644 index dd211382..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-null-step-wf-noET.cwl +++ /dev/null @@ -1,39 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: wc_output, outputSource: step1/output, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step0 - in: [] - out: [output] - run: - class: ExpressionTool - expression: "$({'output': null })" - inputs: [] - outputs: - - {id: output, type: Any} - requirements: - - {class: InlineJavascriptRequirement} -- id: step1 - in: - - default: {class: File, location: whale.txt} - id: file1 - source: step0/output - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-null-step-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-null-step-wf.cwl deleted file mode 100644 index f1cbba3d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-null-step-wf.cwl +++ /dev/null @@ -1,52 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: count_output, outputSource: step2/output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step0 - in: [] - out: [output] - run: - class: ExpressionTool - expression: "$({'output': null })" - inputs: [] - outputs: - - {id: output, type: Any} - requirements: - - {class: InlineJavascriptRequirement} -- id: step1 - in: - - default: {class: File, location: whale.txt} - id: file1 - source: step0/output - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output -- id: step2 - in: - - {id: file1, source: step1/output} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-wf-noET.cwl deleted file mode 100644 index 2ea3eea8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-wf-noET.cwl +++ /dev/null @@ -1,30 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: file1 - type: ['null', File] -outputs: -- {id: wc_output, outputSource: step1/output, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - default: {class: File, location: whale.txt} - id: file1 - source: file1 - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-wf.cwl deleted file mode 100644 index 70aa7417..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines11-wf.cwl +++ /dev/null @@ -1,43 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: file1 - type: ['null', File] -outputs: -- {id: count_output, outputSource: step2/output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - default: {class: File, location: whale.txt} - id: file1 - source: file1 - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output -- id: step2 - in: - - {id: file1, source: step1/output} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines12-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines12-wf.cwl deleted file mode 100644 index 6ea0d6c7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines12-wf.cwl +++ /dev/null @@ -1,38 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: file1 - type: - - {items: File, type: array} -- id: file2 - type: - - {items: File, type: array} -outputs: -- {id: count_output, outputSource: step1/output, type: int} -requirements: -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - id: file1 - linkMerge: merge_flattened - source: [file1, file2] - out: [output] - run: - baseCommand: wc - class: CommandLineTool - inputs: - - id: file1 - inputBinding: {} - type: {items: File, type: array} - outputs: - - id: output - outputBinding: {glob: output.txt, loadContents: true, outputEval: "${\n var\ - \ s = self[0].contents.split(/\\r?\\n/);\n return parseInt(s[s.length-2]);\n\ - }\n"} - type: int - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines13-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines13-wf.cwl deleted file mode 100644 index f95b32ff..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines13-wf.cwl +++ /dev/null @@ -1,29 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: count_output, outputSource: step1/output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - id: file1 - source: [file1] - out: [output] - run: - baseCommand: wc - class: CommandLineTool - inputs: - - id: file1 - inputBinding: {} - type: File - outputs: - - id: output - outputBinding: {glob: output.txt, loadContents: true, outputEval: '$(parseInt(self[0].contents))'} - type: int - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines14-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines14-wf.cwl deleted file mode 100644 index a39b6570..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines14-wf.cwl +++ /dev/null @@ -1,61 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -- {id: file2, type: File} -outputs: -- id: count_output - outputSource: step1/count_output - type: {items: int, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - id: file1 - source: [file1, file2] - out: [count_output] - run: - class: Workflow - inputs: - - {id: file1, type: File} - outputs: - - {id: count_output, outputSource: step2/output, type: int} - requirements: - - {class: SubworkflowFeatureRequirement} - - {class: InlineJavascriptRequirement} - steps: - - id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output - - id: step2 - in: - - {id: file1, source: step1/output} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} - scatter: file1 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines15-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines15-wf.cwl deleted file mode 100644 index 0ffddeb3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines15-wf.cwl +++ /dev/null @@ -1,68 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: count_output, outputSource: step1/count_output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: file1, source: file1} - out: [count_output] - run: - class: Workflow - inputs: - - {id: file1, type: File} - outputs: - - {id: count_output, outputSource: step1/count_output, type: int} - requirements: - - {class: SubworkflowFeatureRequirement} - - {class: InlineJavascriptRequirement} - steps: - - id: step1 - in: - - {id: file1, source: file1} - out: [count_output] - run: - class: Workflow - inputs: - - {id: file1, type: File} - outputs: - - {id: count_output, outputSource: step2/output, type: int} - requirements: - - {class: SubworkflowFeatureRequirement} - - {class: InlineJavascriptRequirement} - steps: - - id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output - - id: step2 - in: - - {id: file1, source: step1/output} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines16-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines16-wf.cwl deleted file mode 100644 index 202b1c92..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines16-wf.cwl +++ /dev/null @@ -1,68 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: count_output, outputSource: step1/count_output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: file1, source: file1} - out: [count_output] - run: - class: Workflow - inputs: - - {id: file1, type: File} - outputs: - - {id: count_output, outputSource: step2/count_output, type: int} - requirements: - - {class: SubworkflowFeatureRequirement} - - {class: InlineJavascriptRequirement} - steps: - - id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output - - id: step2 - in: - - {id: file1, source: step1/output} - out: [count_output] - run: - class: Workflow - inputs: - - {id: file1, type: File} - outputs: - - {id: count_output, outputSource: step1/output, type: int} - requirements: - - {class: SubworkflowFeatureRequirement} - - {class: InlineJavascriptRequirement} - steps: - - id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines17-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines17-wf.cwl deleted file mode 100644 index 2637d9ad..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines17-wf.cwl +++ /dev/null @@ -1,68 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: count_output, outputSource: step1/count_output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: file1, source: file1} - out: [count_output] - run: - class: Workflow - inputs: - - {id: file1, type: File} - outputs: - - {id: count_output, outputSource: step2/output, type: int} - requirements: - - {class: SubworkflowFeatureRequirement} - - {class: InlineJavascriptRequirement} - steps: - - id: step1 - in: - - {id: file1, source: file1} - out: [wc_output] - run: - class: Workflow - inputs: - - {id: file1, type: File} - outputs: - - {id: wc_output, outputSource: step1/output, type: File} - requirements: - - {class: SubworkflowFeatureRequirement} - - {class: InlineJavascriptRequirement} - steps: - - id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output - - id: step2 - in: - - {id: file1, source: step1/wc_output} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines18-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines18-wf.cwl deleted file mode 100644 index 588b6714..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines18-wf.cwl +++ /dev/null @@ -1,60 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: file1 - type: {items: File, type: array} -outputs: -- id: count_output - outputSource: step1/count_output - type: {items: int, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: file1, source: file1} - out: [count_output] - run: - class: Workflow - inputs: - - {id: file1, type: File} - outputs: - - {id: count_output, outputSource: step2/output, type: int} - requirements: - - {class: SubworkflowFeatureRequirement} - - {class: InlineJavascriptRequirement} - steps: - - id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output - - id: step2 - in: - - {id: file1, source: step1/output} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} - scatter: file1 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines19-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines19-wf.cwl deleted file mode 100644 index fd38b512..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines19-wf.cwl +++ /dev/null @@ -1,32 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: count_output, outputSource: step1/output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - id: file1 - linkMerge: merge_nested - source: [file1] - out: [output] - run: - baseCommand: wc - class: CommandLineTool - inputs: - - id: file1 - inputBinding: {} - type: {items: File, type: array} - outputs: - - id: output - outputBinding: {glob: output.txt, loadContents: true, outputEval: "${\n var\ - \ s = self[0].contents.split(/\\r?\\n/);\n return parseInt(s[s.length-2]);\n\ - }\n"} - type: int - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines2-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines2-wf.cwl deleted file mode 100644 index 4318d848..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines2-wf.cwl +++ /dev/null @@ -1,42 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: count_output, outputSource: step2/parseInt_output, type: int} -requirements: -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: wc_file1, source: file1} - out: [wc_output] - run: - baseCommand: wc - class: CommandLineTool - id: wc - inputs: - - id: wc_file1 - inputBinding: {} - type: File - outputs: - - id: wc_output - outputBinding: {glob: output.txt} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt -- id: step2 - in: - - {id: parseInt_file1, source: step1/wc_output} - out: [parseInt_output] - run: - class: ExpressionTool - expression: "${return {'parseInt_output': parseInt(inputs.parseInt_file1.contents)};}\n" - inputs: - - {id: parseInt_file1, loadContents: true, type: File} - outputs: - - {id: parseInt_output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines3-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines3-wf.cwl deleted file mode 100644 index 43e79786..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines3-wf.cwl +++ /dev/null @@ -1,33 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: file1 - type: {items: File, type: array} -outputs: -- id: count_output - outputSource: step1/output - type: {items: int, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: wc - class: CommandLineTool - inputs: - - id: file1 - inputBinding: {} - type: File - outputs: - - id: output - outputBinding: {glob: output.txt, loadContents: true, outputEval: '$(parseInt(self[0].contents))'} - type: int - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt - scatter: file1 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines4-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines4-wf.cwl deleted file mode 100644 index 038cc5d4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines4-wf.cwl +++ /dev/null @@ -1,35 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -- {id: file2, type: File} -outputs: -- id: count_output - outputSource: step1/output - type: {items: int, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - id: file1 - source: [file1, file2] - out: [output] - run: - baseCommand: wc - class: CommandLineTool - inputs: - - id: file1 - inputBinding: {} - type: File - outputs: - - id: output - outputBinding: {glob: output.txt, loadContents: true, outputEval: '$(parseInt(self[0].contents))'} - type: int - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt - scatter: file1 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines5-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines5-wf.cwl deleted file mode 100644 index caeabc42..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines5-wf.cwl +++ /dev/null @@ -1,30 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- default: {class: File, location: hello.txt} - id: file1 - type: File -outputs: -- {id: count_output, outputSource: step1/output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: wc - class: CommandLineTool - inputs: - - id: file1 - inputBinding: {} - type: File - outputs: - - id: output - outputBinding: {glob: output.txt, loadContents: true, outputEval: '$(parseInt(self[0].contents))'} - type: int - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines6-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines6-wf.cwl deleted file mode 100644 index 837840b7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines6-wf.cwl +++ /dev/null @@ -1,40 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: file1 - type: {items: File, type: array} -- id: file2 - type: {items: File, type: array} -outputs: -- id: count_output - outputSource: step1/output - type: {items: int, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - id: file1 - linkMerge: merge_nested - source: [file1, file2] - out: [output] - run: - baseCommand: wc - class: CommandLineTool - inputs: - - id: file1 - inputBinding: {} - type: {items: File, type: array} - outputs: - - id: output - outputBinding: {glob: output.txt, loadContents: true, outputEval: "${\n var\ - \ s = self[0].contents.split(/\\r?\\n/);\n return parseInt(s[s.length-2]);\n\ - }\n"} - type: int - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt - scatter: file1 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines7-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines7-wf.cwl deleted file mode 100644 index a1f680e6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines7-wf.cwl +++ /dev/null @@ -1,36 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: file1 - type: {items: File, type: array} -- id: file2 - type: {items: File, type: array} -outputs: -- {id: count_output, outputSource: step1/output, type: int} -requirements: -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - id: file1 - linkMerge: merge_flattened - source: [file1, file2] - out: [output] - run: - baseCommand: wc - class: CommandLineTool - inputs: - - id: file1 - inputBinding: {} - type: {items: File, type: array} - outputs: - - id: output - outputBinding: {glob: output.txt, loadContents: true, outputEval: "${\n var\ - \ s = self[0].contents.split(/\\r?\\n/);\n return parseInt(s[s.length-2]);\n\ - }\n"} - type: int - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines8-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines8-wf-noET.cwl deleted file mode 100644 index 60714ed4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines8-wf-noET.cwl +++ /dev/null @@ -1,41 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: wc_output, outputSource: step1/wc_output, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: file1, source: file1} - out: [wc_output] - run: - class: Workflow - inputs: - - {id: file1, type: File} - outputs: - - {id: wc_output, outputSource: step1/output, type: File} - requirements: - - {class: SubworkflowFeatureRequirement} - - {class: InlineJavascriptRequirement} - steps: - - id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines8-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines8-wf.cwl deleted file mode 100644 index c152d8d8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines8-wf.cwl +++ /dev/null @@ -1,54 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: count_output, outputSource: step1/count_output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: file1, source: file1} - out: [count_output] - run: - class: Workflow - inputs: - - {id: file1, type: File} - outputs: - - {id: count_output, outputSource: step2/output, type: int} - requirements: - - {class: SubworkflowFeatureRequirement} - - {class: InlineJavascriptRequirement} - steps: - - id: step1 - in: - - {id: file1, source: file1} - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output - - id: step2 - in: - - {id: file1, source: step1/output} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines9-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines9-wf-noET.cwl deleted file mode 100644 index 1e6a1316..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines9-wf-noET.cwl +++ /dev/null @@ -1,27 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: wc_output, outputSource: step1/output, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - default: {class: File, location: whale.txt} - id: file1 - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines9-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines9-wf.cwl deleted file mode 100644 index bddb78b3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_count-lines9-wf.cwl +++ /dev/null @@ -1,40 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: count_output, outputSource: step2/output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - default: {class: File, location: whale.txt} - id: file1 - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output -- id: step2 - in: - - {id: file1, source: step1/output} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cwloutput-nolimit.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cwloutput-nolimit.cwl deleted file mode 100644 index bbc7bda9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_cwloutput-nolimit.cwl +++ /dev/null @@ -1,13 +0,0 @@ -arguments: [python, $(inputs.script)] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- default: {class: File, location: mkfilelist.py} - id: script - type: File -outputs: -- id: filelist - type: {items: string, type: array} -requirements: -- {class: DockerRequirement, dockerPull: python:3-slim} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_default_path.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_default_path.cwl deleted file mode 100644 index 48922545..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_default_path.cwl +++ /dev/null @@ -1,10 +0,0 @@ -arguments: [cat, $(inputs.file1.path)] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- default: {class: File, path: whale.txt} - id: file1 - type: File -outputs: [] -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir.cwl deleted file mode 100644 index d72f4c83..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir.cwl +++ /dev/null @@ -1,20 +0,0 @@ -arguments: -- cd -- $(inputs.indir.path) -- {shellQuote: false, valueFrom: '&&'} -- find -- . -- {shellQuote: false, valueFrom: '|'} -- sort -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: indir, type: Directory} -outputs: -- id: outlist - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir2.cwl deleted file mode 100644 index 0caa3461..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir2.cwl +++ /dev/null @@ -1,22 +0,0 @@ -arguments: -- cd -- $(inputs.indir.path) -- {shellQuote: false, valueFrom: '&&'} -- find -- . -- {shellQuote: false, valueFrom: '|'} -- sort -class: CommandLineTool -cwlVersion: v1.2 -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: -- {id: indir, type: Directory} -outputs: -- id: outlist - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir3.cwl deleted file mode 100644 index dac6ceec..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir3.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: [tar, xvf] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: inf - inputBinding: {position: 1} - type: File -outputs: -- id: outdir - outputBinding: {glob: .} - type: Directory -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir4.cwl deleted file mode 100644 index 62ce54a2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir4.cwl +++ /dev/null @@ -1,20 +0,0 @@ -arguments: -- cd -- $(inputs.inf.dirname)/xtestdir -- {shellQuote: false, valueFrom: '&&'} -- find -- . -- {shellQuote: false, valueFrom: '|'} -- sort -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: inf, type: File} -outputs: -- id: outlist - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir5.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir5.cwl deleted file mode 100644 index fd2c8173..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir5.cwl +++ /dev/null @@ -1,22 +0,0 @@ -arguments: -- find -- -L -- . -- '!' -- -path -- '*.txt' -- {shellQuote: false, valueFrom: '|'} -- sort -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: indir, loadListing: shallow_listing, type: Directory} -outputs: -- id: outlist - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: ShellCommandRequirement} -- {class: InitialWorkDirRequirement, listing: $(inputs.indir.listing)} -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir6.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir6.cwl deleted file mode 100644 index b7d51525..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir6.cwl +++ /dev/null @@ -1,20 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: '&&'} -- find -- . -- {shellQuote: false, valueFrom: '|'} -- sort -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: indir - inputBinding: {position: -1, prefix: cd} - type: Directory -outputs: -- id: outlist - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir7.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir7.cwl deleted file mode 100644 index ffe0cf3a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dir7.cwl +++ /dev/null @@ -1,11 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.2 -expression: "${\nreturn {\"dir\": {\"class\": \"Directory\", \"basename\": \"a_directory\"\ - , \"listing\": inputs.files}};\n}" -inputs: -- id: files - type: {items: File, type: array} -outputs: -- {id: dir, type: Directory} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_docker-array-secondaryfiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_docker-array-secondaryfiles.cwl deleted file mode 100644 index 98126834..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_docker-array-secondaryfiles.cwl +++ /dev/null @@ -1,30 +0,0 @@ -arguments: -- {position: 1, shellQuote: false, valueFrom: '${ var fai_list = ""; for (var i = - 0; i < inputs.fasta_path.length; i ++) { fai_list += " cat " + inputs.fasta_path[i].path - +".fai" + " >> fai.list && " } return fai_list.slice(0,-3) }'} -baseCommand: [] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: fasta_path - secondaryFiles: - - {pattern: .fai, required: true} - - {pattern: .crai, required: false} - - .bai? - - ${ if (inputs.require_dat) {return '.dat'} else {return null} } - - ${ return null; } - - {pattern: .dat2, required: $(inputs.require_dat)} - type: {items: File, type: array} -- id: require_dat - type: ['null', boolean] -outputs: -- id: bai_list - outputBinding: {glob: fai.list} - secondaryFiles: - - .bai? - - {pattern: '${ return null }'} - type: File -requirements: -- {class: DockerRequirement, dockerPull: debian:stretch-slim} -- {class: InlineJavascriptRequirement} -- {class: ShellCommandRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_docker-output-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_docker-output-dir.cwl deleted file mode 100644 index a10d519e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_docker-output-dir.cwl +++ /dev/null @@ -1,11 +0,0 @@ -baseCommand: [touch, /other/thing] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: thing - outputBinding: {glob: thing} - type: File -requirements: -- {class: DockerRequirement, dockerOutputDirectory: /other, dockerPull: debian:stretch-slim} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_docker-run-cmd.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_docker-run-cmd.cwl deleted file mode 100644 index 86fcaab8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_docker-run-cmd.cwl +++ /dev/null @@ -1,11 +0,0 @@ -baseCommand: [-c, echo 'moo' > cow] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: cow - outputBinding: {glob: cow} - type: File -requirements: -- {class: DockerRequirement, dockerPull: bash:4.4.12} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-default.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-default.cwl deleted file mode 100644 index c135f54d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-default.cwl +++ /dev/null @@ -1,14 +0,0 @@ -arguments: [$(runtime.cores)] -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- default: {class: File, location: special_file} - id: special_file - type: File -outputs: -- {id: output, type: stdout} -requirements: -- {class: ResourceRequirement, coresMax: $(inputs.special_file.size), coresMin: $(inputs.special_file.size)} -- {class: InlineJavascriptRequirement} -stdout: cores.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-dir.cwl deleted file mode 100644 index dbfe1bfb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-dir.cwl +++ /dev/null @@ -1,12 +0,0 @@ -arguments: [$(runtime.cores)] -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: dir, type: Directory} -outputs: -- {id: output, type: stdout} -requirements: -- {class: InlineJavascriptRequirement} -- {class: ResourceRequirement, coresMax: '$(inputs.dir.listing[0].size)', coresMin: '$(inputs.dir.listing[0].size)'} -stdout: cores.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-workflow-inputdefault.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-workflow-inputdefault.cwl deleted file mode 100644 index 6b4c4848..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-workflow-inputdefault.cwl +++ /dev/null @@ -1,45 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- default: {class: File, path: special_file} - id: special_file - type: File -outputs: -- {id: cores, outputSource: report/output, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: count - in: - - {id: special_file, source: special_file} - out: [output] - run: - arguments: [$(runtime.cores)] - baseCommand: echo - class: CommandLineTool - inputs: - - {id: special_file, type: File} - outputs: - - {id: output, type: stdout} - requirements: - - {class: ResourceRequirement, coresMax: $(inputs.special_file.size), coresMin: $(inputs.special_file.size)} - - {class: InlineJavascriptRequirement} - stdout: cores.txt -- id: report - in: - - {id: file1, source: count/output} - out: [output] - run: - baseCommand: [cat] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-workflow-stepdefault.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-workflow-stepdefault.cwl deleted file mode 100644 index 58bb876f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-workflow-stepdefault.cwl +++ /dev/null @@ -1,46 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: special_file - type: ['null', File] -outputs: -- {id: cores, outputSource: report/output, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: count - in: - - default: {class: File, location: special_file} - id: special_file - source: special_file - out: [output] - run: - arguments: [$(runtime.cores)] - baseCommand: echo - class: CommandLineTool - inputs: - - {id: special_file, type: File} - outputs: - - {id: output, type: stdout} - requirements: - - {class: ResourceRequirement, coresMax: $(inputs.special_file.size), coresMin: $(inputs.special_file.size)} - - {class: InlineJavascriptRequirement} - stdout: cores.txt -- id: report - in: - - {id: file1, source: count/output} - out: [output] - run: - baseCommand: [cat] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-workflow-tooldefault.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-workflow-tooldefault.cwl deleted file mode 100644 index 991119e3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-workflow-tooldefault.cwl +++ /dev/null @@ -1,46 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: special_file - type: ['null', File] -outputs: -- {id: cores, outputSource: report/output, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: count - in: - - {id: special_file, source: special_file} - out: [output] - run: - arguments: [$(runtime.cores)] - baseCommand: echo - class: CommandLineTool - inputs: - - default: {class: File, location: special_file} - id: special_file - type: File - outputs: - - {id: output, type: stdout} - requirements: - - {class: ResourceRequirement, coresMax: $(inputs.special_file.size), coresMin: $(inputs.special_file.size)} - - {class: InlineJavascriptRequirement} - stdout: cores.txt -- id: report - in: - - {id: file1, source: count/output} - out: [output] - run: - baseCommand: [cat] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-workflow.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-workflow.cwl deleted file mode 100644 index 739e181a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq-workflow.cwl +++ /dev/null @@ -1,43 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: special_file, type: File} -outputs: -- {id: cores, outputSource: report/output, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: count - in: - - {id: special_file, source: special_file} - out: [output] - run: - arguments: [$(runtime.cores)] - baseCommand: echo - class: CommandLineTool - inputs: - - {id: special_file, type: File} - outputs: - - {id: output, type: stdout} - requirements: - - {class: ResourceRequirement, coresMax: $(inputs.special_file.size), coresMin: $(inputs.special_file.size)} - - {class: InlineJavascriptRequirement} - stdout: cores.txt -- id: report - in: - - {id: file1, source: count/output} - out: [output] - run: - baseCommand: [cat] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq.cwl deleted file mode 100644 index 11cfab0f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_dynresreq.cwl +++ /dev/null @@ -1,12 +0,0 @@ -arguments: [$(runtime.cores)] -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: special_file, type: File} -outputs: -- {id: output, type: stdout} -requirements: -- {class: ResourceRequirement, coresMax: $(inputs.special_file.size), coresMin: $(inputs.special_file.size)} -- {class: InlineJavascriptRequirement} -stdout: cores.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-file-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-file-tool.cwl deleted file mode 100644 index a1ca8a42..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-file-tool.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: [echo] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: in - inputBinding: {position: 1} - type: string -- id: name - type: ['null', string] -outputs: -- {id: out, type: stdout} -requirements: -- {class: InlineJavascriptRequirement} -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-position-expr.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-position-expr.cwl deleted file mode 100644 index 24f0cea4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-position-expr.cwl +++ /dev/null @@ -1,20 +0,0 @@ -arguments: -- {position: '${return 2;}', valueFrom: singular} -- {position: '${return null;}', valueFrom: 🕺} -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: one - inputBinding: {position: $(self)} - type: int -- id: two - inputBinding: {position: '${return self+1;}', valueFrom: sensation!} - type: int -outputs: -- id: out - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string -requirements: -- {class: InlineJavascriptRequirement} -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-tool-default.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-tool-default.cwl deleted file mode 100644 index 443665f7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-tool-default.cwl +++ /dev/null @@ -1,15 +0,0 @@ -baseCommand: [echo, -n] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- default: tool_default - id: in - inputBinding: {position: 1} - type: string -outputs: -- id: out - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string -requirements: -- {class: InlineJavascriptRequirement} -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-tool-packed.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-tool-packed.cwl deleted file mode 100644 index 79d20a37..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-tool-packed.cwl +++ /dev/null @@ -1,24 +0,0 @@ -$graph: -- baseCommand: [echo, first] - class: CommandLineTool - id: first - inputs: - in: {type: Any} - outputs: - out: - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - stdout: out.txt -- baseCommand: echo - class: CommandLineTool - id: main - inputs: - in: - inputBinding: {} - type: Any - outputs: - out: - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - stdout: out.txt -cwlVersion: v1.2 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-tool-packed2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-tool-packed2.cwl deleted file mode 100644 index 188989bb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-tool-packed2.cwl +++ /dev/null @@ -1,24 +0,0 @@ -$graph: -- baseCommand: [echo, first] - class: CommandLineTool - id: first - inputs: - in: {type: Any} - outputs: - out: - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - stdout: out.txt -- baseCommand: echo - class: CommandLineTool - id: '#main' - inputs: - in: - inputBinding: {} - type: Any - outputs: - out: - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - stdout: out.txt -cwlVersion: v1.2 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-tool.cwl deleted file mode 100644 index 8a3d6a82..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-tool.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: in - inputBinding: {} - type: Any -outputs: -- id: out - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string -requirements: -- {class: InlineJavascriptRequirement} -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-wf-default.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-wf-default.cwl deleted file mode 100644 index 08ef5988..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_echo-wf-default.cwl +++ /dev/null @@ -1,28 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: default_output, outputSource: step1/out, type: string} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {default: workflow_default, id: in} - out: [out] - run: - baseCommand: [echo, -n] - class: CommandLineTool - inputs: - - default: tool_default - id: in - inputBinding: {position: 1} - type: string - outputs: - - id: out - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_empty-array-input.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_empty-array-input.cwl deleted file mode 100644 index 7dc224b9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_empty-array-input.cwl +++ /dev/null @@ -1,18 +0,0 @@ -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -hints: -- {class: DockerRequirement, dockerPull: python:2-slim} -inputs: -- id: array - inputBinding: {itemSeparator: ',', position: 1, prefix: -I} - type: {items: int, type: array} -- default: {class: File, location: args.py} - id: args.py - inputBinding: {position: -1} - type: File -outputs: -- id: args - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-tool1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-tool1.cwl deleted file mode 100644 index 02d9ff63..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-tool1.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: [/bin/sh, -c, echo $TEST_ENV] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: in, type: string} -outputs: -- id: out - outputBinding: {glob: out} - type: File -requirements: -- class: EnvVarRequirement - envDef: {TEST_ENV: $(inputs.in)} -- {class: InlineJavascriptRequirement} -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-tool2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-tool2.cwl deleted file mode 100644 index 4f1dfa10..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-tool2.cwl +++ /dev/null @@ -1,15 +0,0 @@ -baseCommand: [/bin/sh, -c, echo $TEST_ENV] -class: CommandLineTool -cwlVersion: v1.2 -hints: - EnvVarRequirement: - envDef: {TEST_ENV: $(inputs.in)} -inputs: -- {id: in, type: string} -outputs: -- id: out - outputBinding: {glob: out} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-tool3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-tool3.cwl deleted file mode 100644 index 4ce396ff..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-tool3.cwl +++ /dev/null @@ -1,12 +0,0 @@ -baseCommand: [/bin/bash, -c, echo $TEST_ENV] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: in, type: string} -outputs: -- id: out - outputBinding: {glob: out} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-tool4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-tool4.cwl deleted file mode 100644 index 6264acf7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-tool4.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: [/bin/bash, -c, echo $TEST_ENV] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: in, type: string} -outputs: -- id: out - outputBinding: {glob: out} - type: File -requirements: -- class: EnvVarRequirement - envDef: {TEST_ENV: conflict_original} -- {class: InlineJavascriptRequirement} -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-wf1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-wf1.cwl deleted file mode 100644 index 59628fad..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-wf1.cwl +++ /dev/null @@ -1,30 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: in, type: string} -outputs: -- {id: out, outputSource: step1/out, type: File} -requirements: -- class: EnvVarRequirement - envDef: {TEST_ENV: override} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in, source: in} - out: [out] - run: - baseCommand: [/bin/sh, -c, echo $TEST_ENV] - class: CommandLineTool - inputs: - - {id: in, type: string} - outputs: - - id: out - outputBinding: {glob: out} - type: File - requirements: - - class: EnvVarRequirement - envDef: {TEST_ENV: $(inputs.in)} - - {class: InlineJavascriptRequirement} - stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-wf2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-wf2.cwl deleted file mode 100644 index 850f97b3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-wf2.cwl +++ /dev/null @@ -1,31 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: in, type: string} -outputs: -- {id: out, outputSource: step1/out, type: File} -requirements: -- class: EnvVarRequirement - envDef: {TEST_ENV: override} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in, source: in} - out: [out] - run: - baseCommand: [/bin/sh, -c, echo $TEST_ENV] - class: CommandLineTool - hints: - EnvVarRequirement: - envDef: {TEST_ENV: $(inputs.in)} - inputs: - - {id: in, type: string} - outputs: - - id: out - outputBinding: {glob: out} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-wf3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-wf3.cwl deleted file mode 100644 index 0af20b30..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_env-wf3.cwl +++ /dev/null @@ -1,32 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: in, type: string} -outputs: -- {id: out, outputSource: step1/out, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in, source: in} - out: [out] - requirements: - EnvVarRequirement: - envDef: {TEST_ENV: override} - run: - baseCommand: [/bin/sh, -c, echo $TEST_ENV] - class: CommandLineTool - hints: - EnvVarRequirement: - envDef: {TEST_ENV: $(inputs.in)} - inputs: - - {id: in, type: string} - outputs: - - id: out - outputBinding: {glob: out} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_envvar.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_envvar.cwl deleted file mode 100644 index 193ad2fb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_envvar.cwl +++ /dev/null @@ -1,20 +0,0 @@ -arguments: -- echo -- {shellQuote: false, valueFrom: '"HOME=$HOME"'} -- {shellQuote: false, valueFrom: '"TMPDIR=$TMPDIR"'} -- {shellQuote: false, valueFrom: '&&'} -- test -- {shellQuote: false, valueFrom: '"$HOME"'} -- '=' -- $(runtime.outdir) -- -a -- {shellQuote: false, valueFrom: '"$TMPDIR"'} -- '=' -- $(runtime.tmpdir) -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_envvar2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_envvar2.cwl deleted file mode 100644 index 13f99329..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_envvar2.cwl +++ /dev/null @@ -1,22 +0,0 @@ -arguments: -- echo -- {shellQuote: false, valueFrom: '"HOME=$HOME"'} -- {shellQuote: false, valueFrom: '"TMPDIR=$TMPDIR"'} -- {shellQuote: false, valueFrom: '&&'} -- test -- {shellQuote: false, valueFrom: '"$HOME"'} -- '=' -- $(runtime.outdir) -- -a -- {shellQuote: false, valueFrom: '"$TMPDIR"'} -- '=' -- $(runtime.tmpdir) -class: CommandLineTool -cwlVersion: v1.2 -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: [] -outputs: [] -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_envvar3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_envvar3.cwl deleted file mode 100644 index a13fcdb6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_envvar3.cwl +++ /dev/null @@ -1,16 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: "echo HOME=$HOME TMPDIR=$TMPDIR > log\nif [ \"$HOME\"\ - \ = \"$(runtime.outdir)\" ] && [ \"$TMPDIR\" = \"$(runtime.tmpdir)\" ]\nthen\n\ - \ echo success > results\nelse\n echo failure > results\nfi\n"} -class: CommandLineTool -cwlVersion: v1.2 -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: [] -outputs: -- id: results - outputBinding: {glob: results} - type: File -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_exit-success.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_exit-success.cwl deleted file mode 100644 index 8e376df4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_exit-success.cwl +++ /dev/null @@ -1,10 +0,0 @@ -baseCommand: 'false' -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -permanentFailCodes: [0] -requirements: -- {class: InlineJavascriptRequirement} -successCodes: [1] -temporaryFailCodes: [42] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_exitcode.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_exitcode.cwl deleted file mode 100644 index 560774c4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_exitcode.cwl +++ /dev/null @@ -1,12 +0,0 @@ -arguments: [exit, '7'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: code - outputBinding: {outputEval: $(runtime.exitCode)} - type: int -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} -successCodes: [7] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_fail-unconnected.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_fail-unconnected.cwl deleted file mode 100644 index 9ece9146..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_fail-unconnected.cwl +++ /dev/null @@ -1,28 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {default: hello inp1, id: inp1, type: string} -- {default: hello inp2, id: inp2, type: string} -outputs: -- {id: out, outputSource: step1/out, type: string} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in, source: inp1} - - {id: in2, source: inp2} - out: [out] - run: - arguments: [echo, $(inputs.in), $(inputs.in2)] - class: CommandLineTool - inputs: - - {id: in, type: string} - outputs: - - id: out - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_fail-unspecified-input.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_fail-unspecified-input.cwl deleted file mode 100644 index de4d32bd..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_fail-unspecified-input.cwl +++ /dev/null @@ -1,12 +0,0 @@ -arguments: [echo, $(inputs.in), $(inputs.in2)] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: in, type: string} -outputs: -- id: out - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string -requirements: -- {class: InlineJavascriptRequirement} -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_file-literal-ex.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_file-literal-ex.cwl deleted file mode 100644 index e143fb3a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_file-literal-ex.cwl +++ /dev/null @@ -1,9 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.2 -expression: "${\nreturn {\"lit\": {\"class\": \"File\", \"basename\": \"a_file\",\ - \ \"contents\": \"Hello file literal.\"}};\n}" -inputs: [] -outputs: -- {id: lit, type: File} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_foo.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_foo.cwl deleted file mode 100644 index 04d15926..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_foo.cwl +++ /dev/null @@ -1,11 +0,0 @@ -baseCommand: [echo] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: in1, type: int} -outputs: -- id: out1 - outputBinding: {outputEval: foo $(inputs.in1)} - type: string -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_formattest.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_formattest.cwl deleted file mode 100644 index 841ebc83..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_formattest.cwl +++ /dev/null @@ -1,18 +0,0 @@ -$namespaces: {edam: http://edamontology.org/} -baseCommand: rev -class: CommandLineTool -cwlVersion: v1.2 -doc: Reverse each line using the `rev` command -inputs: -- format: edam:format_2330 - id: input - inputBinding: {} - type: File -outputs: -- format: edam:format_2330 - id: output - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_formattest2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_formattest2.cwl deleted file mode 100644 index 767ddfcb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_formattest2.cwl +++ /dev/null @@ -1,21 +0,0 @@ -$namespaces: {edam: http://edamontology.org/} -$schemas: [EDAM.owl] -baseCommand: rev -class: CommandLineTool -cwlVersion: v1.2 -doc: Reverse each line using the `rev` command -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: -- format: edam:format_2330 - id: input - inputBinding: {} - type: File -outputs: -- format: $(inputs.input.format) - id: output - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_formattest3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_formattest3.cwl deleted file mode 100644 index 19a2a368..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_formattest3.cwl +++ /dev/null @@ -1,21 +0,0 @@ -$namespaces: {edam: http://edamontology.org/, gx: http://galaxyproject.org/formats/} -$schemas: [EDAM.owl, gx_edam.ttl] -baseCommand: rev -class: CommandLineTool -cwlVersion: v1.2 -doc: Reverse each line using the `rev` command -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: -- format: gx:fasta - id: input - inputBinding: {} - type: File -outputs: -- format: $(inputs.input.format) - id: output - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_glob-expr-list.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_glob-expr-list.cwl deleted file mode 100644 index 2c8cb071..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_glob-expr-list.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: touch -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: ids - inputBinding: {position: 1} - type: {items: string, type: array} -outputs: -- id: files - outputBinding: {glob: $(inputs.ids)} - type: {items: File, type: array} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_glob-path-error.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_glob-path-error.cwl deleted file mode 100644 index 3691ade0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_glob-path-error.cwl +++ /dev/null @@ -1,11 +0,0 @@ -baseCommand: [echo] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: OUTPUT - outputBinding: {glob: /etc/passwd} - type: File -requirements: -- {class: DockerRequirement, dockerPull: debian:stretch-slim} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_glob_directory.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_glob_directory.cwl deleted file mode 100644 index 09951884..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_glob_directory.cwl +++ /dev/null @@ -1,10 +0,0 @@ -baseCommand: [mkdir, a_dir, b_dir, c_dir] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: directories - outputBinding: {glob: '[a,b,c]_dir'} - type: {items: Directory, type: array} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_glob_test.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_glob_test.cwl deleted file mode 100644 index b99b1d2d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_glob_test.cwl +++ /dev/null @@ -1,10 +0,0 @@ -baseCommand: [touch, z, y, x, w, c, b, a] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: letters - outputBinding: {glob: '*'} - type: {items: File, type: array} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_import_schema-def.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_import_schema-def.cwl deleted file mode 100644 index 46f8b8f7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_import_schema-def.cwl +++ /dev/null @@ -1,35 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: bam, type: string} -- id: capture_kit - type: - fields: - - {name: bait, type: string} - name: user_type_3 - type: record -outputs: -- {id: output_bam, outputSource: touch_bam/empty_file, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: touch_bam - in: - - {id: name, source: bam} - out: [empty_file] - run: - baseCommand: [touch] - class: CommandLineTool - hints: - DockerRequirement: {dockerPull: debian:stretch-slim} - inputs: - - id: name - inputBinding: {position: 0} - type: string - outputs: - - id: empty_file - outputBinding: {glob: $(inputs.name)} - type: File - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_import_schema-def2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_import_schema-def2.cwl deleted file mode 100644 index df21573d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_import_schema-def2.cwl +++ /dev/null @@ -1,35 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: bam, type: string} -- id: capture_kit[] - type: - fields: - - {name: bait, type: string} - name: user_type_3 - type: record -outputs: -- {id: output_bam, outputSource: touch_bam/empty_file, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: touch_bam - in: - - {id: name, source: bam} - out: [empty_file] - run: - baseCommand: [touch] - class: CommandLineTool - hints: - DockerRequirement: {dockerPull: debian:stretch-slim} - inputs: - - id: name - inputBinding: {position: 0} - type: string - outputs: - - id: empty_file - outputBinding: {glob: $(inputs.name)} - type: File - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_import_schema-def_packed.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_import_schema-def_packed.cwl deleted file mode 100644 index fea27b50..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_import_schema-def_packed.cwl +++ /dev/null @@ -1,35 +0,0 @@ -$graph: -- class: Workflow - id: '#main' - inputs: - - {id: '#main/bam', type: string} - - {id: '#main/capture_kit', type: '#capture_kit.yml/capture_kit'} - outputs: - - {id: '#main/output_bam', outputSource: '#main/touch_bam/empty_file', type: File} - requirements: - - class: SchemaDefRequirement - types: - - fields: - - {name: '#capture_kit.yml/capture_kit/bait', type: string} - name: '#capture_kit.yml/capture_kit' - type: record - steps: - - id: '#main/touch_bam' - in: - - {id: '#main/touch_bam/name', source: '#main/bam'} - out: ['#main/touch_bam/empty_file'] - run: '#touch.cwl' -- baseCommand: [touch] - class: CommandLineTool - hints: - - {class: DockerRequirement, dockerPull: debian:stretch-slim} - id: '#touch.cwl' - inputs: - - id: '#touch.cwl/name' - inputBinding: {position: 0} - type: string - outputs: - - id: '#touch.cwl/empty_file' - outputBinding: {glob: $(inputs.name)} - type: File -cwlVersion: v1.2 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_imported-hint.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_imported-hint.cwl deleted file mode 100644 index 60aa7dd5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_imported-hint.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: [/bin/sh, -c, echo $TEST_ENV] -class: CommandLineTool -cwlVersion: v1.2 -hints: -- class: EnvVarRequirement - envDef: - - {envName: TEST_ENV, envValue: hello test env} -inputs: [] -outputs: -- {id: out, type: stdout} -requirements: -- {class: InlineJavascriptRequirement} -stdout: out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_initialwork-path.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_initialwork-path.cwl deleted file mode 100644 index 3dfef130..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_initialwork-path.cwl +++ /dev/null @@ -1,14 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: "test \"$(inputs.file1.path)\" = \"$(runtime.outdir)/bob.txt\"\ - \n"} -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: [] -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.file1), entryname: bob.txt} -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_initialworkdir-glob-fullpath.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_initialworkdir-glob-fullpath.cwl deleted file mode 100644 index adb3089c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_initialworkdir-glob-fullpath.cwl +++ /dev/null @@ -1,16 +0,0 @@ -arguments: -- {position: 0, valueFrom: $(inputs.INPUT.basename).fai} -baseCommand: [touch] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: INPUT, type: File} -outputs: -- id: OUTPUT - outputBinding: {glob: $(runtime.outdir)/$(inputs.INPUT.basename)} - secondaryFiles: [.fai] - type: File -requirements: -- class: InitialWorkDirRequirement - listing: [$(inputs.INPUT)] -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_initialworkdirrequirement-docker-out.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_initialworkdirrequirement-docker-out.cwl deleted file mode 100644 index be4805c7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_initialworkdirrequirement-docker-out.cwl +++ /dev/null @@ -1,17 +0,0 @@ -arguments: -- {position: 0, valueFrom: $(inputs.INPUT.basename).fai} -baseCommand: [touch] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: INPUT, type: File} -outputs: -- id: OUTPUT - outputBinding: {glob: $(inputs.INPUT.basename)} - secondaryFiles: [.fai] - type: File -requirements: -- {class: DockerRequirement, dockerPull: debian:stretch-slim} -- class: InitialWorkDirRequirement - listing: [$(inputs.INPUT)] -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_inline-js.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_inline-js.cwl deleted file mode 100644 index 8ae4f0ff..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_inline-js.cwl +++ /dev/null @@ -1,22 +0,0 @@ -arguments: -- {prefix: -A, valueFrom: $(1+1)} -- {prefix: -B, valueFrom: "$(\"/foo/bar/baz\".split('/').slice(-1)[0])"} -- {prefix: -C, valueFrom: "${\n var r = [];\n for (var i = 10; i >= 1; i--) {\n\ - \ r.push(i);\n }\n return r;\n}\n"} -- {prefix: -D, valueFrom: $(true)} -- {prefix: -E, valueFrom: $(false)} -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -hints: -- {class: DockerRequirement, dockerPull: python:2-slim} -inputs: -- default: {class: File, location: args.py} - id: args.py - inputBinding: {position: -1} - type: File -outputs: -- id: args - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_inp_update_wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_inp_update_wf.cwl deleted file mode 100644 index e8d6b0e4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_inp_update_wf.cwl +++ /dev/null @@ -1,79 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: a, outputSource: step3/output, type: int} -- {id: b, outputSource: step4/output, type: int} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {default: '3', id: in} - out: [out] - run: - baseCommand: [echo] - class: CommandLineTool - inputs: - - id: in - inputBinding: {position: 1} - type: string - - id: name - type: ['null', string] - outputs: - - {id: out, type: stdout} - requirements: - - {class: InlineJavascriptRequirement} - stdout: out.txt -- id: step2 - in: - - {id: r, source: step1/out} - out: [out] - run: - arguments: [python, $(inputs.script), $(inputs.r.basename)] - class: CommandLineTool - hints: - DockerRequirement: {dockerPull: python:2.7.15-alpine3.7} - inputs: - - {id: r, type: File} - - default: {class: File, location: updateval.py} - id: script - type: File - outputs: - - id: out - outputBinding: {glob: $(inputs.r.basename)} - type: File - requirements: - - class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.r), writable: true} - - {class: InplaceUpdateRequirement, inplaceUpdate: true} - - {class: InlineJavascriptRequirement} -- id: step3 - in: - - {id: file1, source: step1/out} - - {id: wait, source: step2/out} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} -- id: step4 - in: - - {id: file1, source: step2/out} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_inpdir_update_wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_inpdir_update_wf.cwl deleted file mode 100644 index 668e8c1f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_inpdir_update_wf.cwl +++ /dev/null @@ -1,66 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: [] -outputs: -- id: a - outputSource: step3/d1out - type: {items: File, type: array} -- id: b - outputSource: step3/d2out - type: {items: File, type: array} -requirements: -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {default: step1dir, id: dirname} - out: [out] - run: - arguments: [mkdir, $(inputs.dirname)] - class: CommandLineTool - inputs: - - {id: dirname, type: string} - outputs: - - id: out - outputBinding: {glob: $(inputs.dirname)} - type: Directory - requirements: - - {class: InlineJavascriptRequirement} -- id: step2 - in: - - {id: r, source: step1/out} - out: [out] - run: - arguments: [touch, inp/blurb] - class: CommandLineTool - inputs: - - {id: r, type: Directory} - outputs: - - id: out - outputBinding: {glob: inp} - type: Directory - requirements: - - class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.r), entryname: inp, writable: true} - - {class: InplaceUpdateRequirement, inplaceUpdate: true} - - {class: InlineJavascriptRequirement} -- id: step3 - in: - - {id: d1, source: step1/out} - - {id: d2, source: step2/out} - out: [d1out, d2out] - run: - class: ExpressionTool - expression: '$({d1out: inputs.d1.listing, d2out: inputs.d2.listing})' - inputs: - - {id: d1, loadListing: shallow_listing, type: Directory} - - {id: d2, loadListing: shallow_listing, type: Directory} - outputs: - - id: d1out - type: {items: File, type: array} - - id: d2out - type: {items: File, type: array} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-any-1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-any-1.cwl deleted file mode 100644 index ee889c81..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-any-1.cwl +++ /dev/null @@ -1,11 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: bar, type: Any} -outputs: -- id: t1 - outputBinding: {outputEval: $(inputs.bar.class || inputs.bar)} - type: Any -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-any-wf-1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-any-wf-1.cwl deleted file mode 100644 index 7a61cfc5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-any-wf-1.cwl +++ /dev/null @@ -1,25 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: bar, type: Any} -outputs: -- {id: t1, outputSource: step1/t1, type: Any} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: bar, source: bar} - out: [t1] - run: - baseCommand: 'true' - class: CommandLineTool - inputs: - - {id: bar, type: Any} - outputs: - - id: t1 - outputBinding: {outputEval: $(inputs.bar.class || inputs.bar)} - type: Any - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-file-default-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-file-default-wf.cwl deleted file mode 100644 index 6fbb0247..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-file-default-wf.cwl +++ /dev/null @@ -1,28 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- default: {class: File, path: whale.txt} - id: file1 - type: File -outputs: -- {id: o, outputSource: step1/o, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: catfile1, source: file1} - out: [o] - run: - arguments: [cat, $(inputs.catfile1.path)] - class: CommandLineTool - inputs: - - {id: catfile1, type: File} - outputs: - - id: o - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-file-or-files.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-file-or-files.cwl deleted file mode 100644 index ad39546a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-file-or-files.cwl +++ /dev/null @@ -1,22 +0,0 @@ -arguments: -- {valueFrom: "${\n var cmd = [];\n if (inputs.input === null) {\n cmd.push('echo');\n\ - \ cmd.push('no_inputs');\n } else {\n cmd.push('cat');\n if (Array.isArray(inputs.input))\ - \ {\n for (var i = 0; i < inputs.input.length; i++) {\n cmd.push(inputs.input[i].path);\n\ - \ }\n } else {\n cmd.push(inputs.input.path);\n }\n }\n return\ - \ cmd;\n}\n"} -baseCommand: [] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: input - type: - - 'null' - - File - - {items: File, type: array} -outputs: -- id: output_file - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-int-default-tool-and-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-int-default-tool-and-wf.cwl deleted file mode 100644 index ac9507c2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-int-default-tool-and-wf.cwl +++ /dev/null @@ -1,37 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {default: 4, id: i, type: int} -outputs: -- {id: o, outputSource: step2/o, type: int} -requirements: -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: i, source: i} - out: [o] - run: - class: ExpressionTool - expression: "${return {'o': (inputs.i || 2)};}\n" - inputs: - - {id: i, type: int} - outputs: - - {id: o, type: int} - requirements: - - {class: InlineJavascriptRequirement} -- id: step2 - in: - - {id: i, source: step1/o} - out: [o] - run: - class: ExpressionTool - expression: "${return {'o': inputs.i * 2 + inputs.i2};}\n" - inputs: - - {id: i, type: int} - - {default: 5, id: i2, type: int} - outputs: - - {id: o, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-int-default-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-int-default-wf.cwl deleted file mode 100644 index fe067b7b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-int-default-wf.cwl +++ /dev/null @@ -1,23 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {default: 4, id: i, type: int} -outputs: -- {id: o, outputSource: step1/o, type: int} -requirements: -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: i, source: i} - out: [o] - run: - class: ExpressionTool - expression: "${return {'o': (inputs.i || 2) * 2};}\n" - inputs: - - {id: i, type: int} - outputs: - - {id: o, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-int-optional-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-int-optional-wf.cwl deleted file mode 100644 index bd9f064c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-int-optional-wf.cwl +++ /dev/null @@ -1,25 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: i - type: ['null', int] -outputs: -- {id: o, outputSource: step1/o, type: int} -requirements: -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: i, source: i} - out: [o] - run: - class: ExpressionTool - expression: "${return {'o': (inputs.i || 2) * 2};}\n" - inputs: - - id: i - type: ['null', int] - outputs: - - {id: o, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-int-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-int-wf.cwl deleted file mode 100644 index 4582b3dd..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-int-wf.cwl +++ /dev/null @@ -1,23 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: i, type: int} -outputs: -- {id: o, outputSource: step1/o, type: int} -requirements: -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: i, source: i} - out: [o] - run: - class: ExpressionTool - expression: "${return {'o': inputs.i * 2};}\n" - inputs: - - {id: i, type: int} - outputs: - - {id: o, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-union-input-default-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-union-input-default-wf.cwl deleted file mode 100644 index e6d40da7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_io-union-input-default-wf.cwl +++ /dev/null @@ -1,26 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- default: the default value - id: bar - type: [File, 'null', string] -outputs: -- {id: o, outputSource: step1/o, type: string} -requirements: -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: i, source: bar} - out: [o] - run: - class: ExpressionTool - expression: "${return {'o': (inputs.i.class || inputs.i)};}\n" - inputs: - - id: i - type: [File, 'null', string] - outputs: - - {id: o, type: string} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-container-entryname1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-container-entryname1.cwl deleted file mode 100644 index 2cb5c530..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-container-entryname1.cwl +++ /dev/null @@ -1,19 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt} -class: CommandLineTool -cwlVersion: v1.2 -doc: "When executing in a container, entryname can have an absolute path\nto a mount\ - \ location inside the container.\n" -inputs: -- {id: filelist, type: File} -outputs: -- id: head - outputBinding: {glob: head.txt} - type: File -requirements: -- {class: DockerRequirement, dockerOutputDirectory: /output, dockerPull: debian:10} -- class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.filelist), entryname: /tmp2j3y7rpb/input/stuff.txt} -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-container-entryname2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-container-entryname2.cwl deleted file mode 100644 index 90ef1bb5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-container-entryname2.cwl +++ /dev/null @@ -1,18 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt} -class: CommandLineTool -cwlVersion: v1.2 -doc: "Must fail if entryname is an absolute path and DockerRequirement is\nnot in\ - \ the 'requirements' section.\n" -inputs: -- {id: filelist, type: File} -outputs: -- id: head - outputBinding: {glob: head.txt} - type: File -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.filelist), entryname: /tmp2j3y7rpb/input/stuff.txt} -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-container-entryname3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-container-entryname3.cwl deleted file mode 100644 index 5f4ff265..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-container-entryname3.cwl +++ /dev/null @@ -1,20 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt} -class: CommandLineTool -cwlVersion: v1.2 -doc: "Must fail if entryname is an absolute path and DockerRequirement is\nnot in\ - \ the 'requirements' section.\n" -hints: - DockerRequirement: {dockerOutputDirectory: /output, dockerPull: debian:10} -inputs: -- {id: filelist, type: File} -outputs: -- id: head - outputBinding: {glob: head.txt} - type: File -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.filelist), entryname: /tmp2j3y7rpb/input/stuff.txt} -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-container-entryname4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-container-entryname4.cwl deleted file mode 100644 index 66b65ac2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-container-entryname4.cwl +++ /dev/null @@ -1,17 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: head -n10 ../input/stuff.txt > head.txt} -class: CommandLineTool -cwlVersion: v1.2 -doc: "Must fail if entryname starts with ../\n" -inputs: -- {id: filelist, type: File} -outputs: -- id: head - outputBinding: {glob: head.txt} - type: File -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.filelist), entryname: ../input/stuff.txt} -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-fileobjs1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-fileobjs1.cwl deleted file mode 100644 index a58ebf55..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-fileobjs1.cwl +++ /dev/null @@ -1,18 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -doc: Can have a file declared directly in InitialWorkDir -inputs: [] -outputs: -- id: filelist - outputBinding: {glob: inp-filelist.txt} - type: File -- id: testdir - outputBinding: {glob: testdir} - type: Directory -requirements: -- class: InitialWorkDirRequirement - listing: - - {class: File, location: inp-filelist.txt} - - {class: Directory, location: testdir} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-fileobjs2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-fileobjs2.cwl deleted file mode 100644 index 0a063861..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-fileobjs2.cwl +++ /dev/null @@ -1,18 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -doc: Can have a file declared directly in InitialWorkDir -inputs: [] -outputs: -- id: filelist - outputBinding: {glob: inp-filelist.txt} - type: File -- id: testdir - outputBinding: {glob: testdir} - type: Directory -requirements: -- class: InitialWorkDirRequirement - listing: - - - {class: File, location: ../loadContents/inp-filelist.txt} - - {class: Directory, location: ../testdir} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump1-nl.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump1-nl.cwl deleted file mode 100644 index 65209f51..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump1-nl.cwl +++ /dev/null @@ -1,14 +0,0 @@ -arguments: ['true'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: filelist - outputBinding: {glob: out-filelist.json} - type: File -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "${\n var ls = [];\n for (var i = 1; i < 10000; i++) {\n ls.push(\"\ - example_input_file\"+i+\".txt\");\n }\n return ls;\n}\n", entryname: out-filelist.json} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump1.cwl deleted file mode 100644 index 4bb22be6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump1.cwl +++ /dev/null @@ -1,14 +0,0 @@ -arguments: ['true'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: filelist - outputBinding: {glob: out-filelist.json} - type: File -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "${\n var ls = [];\n for (var i = 1; i < 10000; i++) {\n ls.push(\"\ - example_input_file\"+i+\".txt\");\n }\n return ls;\n}", entryname: out-filelist.json} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump2-nl.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump2-nl.cwl deleted file mode 100644 index fa60784d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump2-nl.cwl +++ /dev/null @@ -1,15 +0,0 @@ -arguments: ['true'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: filelist - outputBinding: {glob: out-filelist.json} - type: File -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "${\n var ls = [];\n for (var i = 1; i < 10000; i++) {\n ls.push(\"\ - example_input_file\"+i+\".txt\");\n }\n return {\"filelist\": ls};\n}\n", - entryname: out-filelist.json} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump2.cwl deleted file mode 100644 index ed630006..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump2.cwl +++ /dev/null @@ -1,14 +0,0 @@ -arguments: ['true'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: filelist - outputBinding: {glob: out-filelist.json} - type: File -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "${\n var ls = [];\n for (var i = 1; i < 10000; i++) {\n ls.push(\"\ - example_input_file\"+i+\".txt\");\n }\n return {\"filelist\": ls};\n}", entryname: out-filelist.json} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump3-nl.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump3-nl.cwl deleted file mode 100644 index 10733776..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump3-nl.cwl +++ /dev/null @@ -1,13 +0,0 @@ -arguments: ['true'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: filelist - outputBinding: {glob: out-number.json} - type: File -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "${\n return 44.4;\n}\n", entryname: out-number.json} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump3.cwl deleted file mode 100644 index f6dbb1ef..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-jsondump3.cwl +++ /dev/null @@ -1,13 +0,0 @@ -arguments: ['true'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: filelist - outputBinding: {glob: out-number.json} - type: File -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "${\n return 44.4;\n}", entryname: out-number.json} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-nolimit.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-nolimit.cwl deleted file mode 100644 index 701a500b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-nolimit.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: filelist - outputBinding: {glob: out-filelist.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "${\n var ls = \"\";\n for (var i = 1; i < 10000; i++) {\n ls +=\ - \ \"example_input_file\"+i+\".txt\\n\";\n }\n return ls;\n}", entryname: out-filelist.txt} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-passthrough1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-passthrough1.cwl deleted file mode 100644 index 6fefb45e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-passthrough1.cwl +++ /dev/null @@ -1,17 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -doc: "YAML |- syntax does not add trailing newline so in the listing entry\nbelow\ - \ there is no whitespace surrounding the value\n$(inputs.filelist), so it is evaluated\ - \ as a File object. Compare to\niwd-passthrough2.cwl\n" -inputs: -- {id: filelist, type: File} -outputs: -- id: filelist - outputBinding: {glob: renamed-filelist.txt} - type: File -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.filelist), entryname: renamed-filelist.txt} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-passthrough2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-passthrough2.cwl deleted file mode 100644 index 56e3c807..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-passthrough2.cwl +++ /dev/null @@ -1,20 +0,0 @@ -arguments: [python3, $(inputs.script), renamed-filelist.txt] -class: CommandLineTool -cwlVersion: v1.2 -doc: "YAML | syntax adds a trailing newline, so in the listing entry\nbelow, it becomes\ - \ a string interpolation -- it evaluates to a string\nconsisting of $(inputs.filelist)\ - \ serialized to JSON and then adding\na newline. Compare to iwd-passthrough1.cwl\n" -inputs: -- {id: filelist, type: File} -- default: {class: File, location: loadit.py} - id: script - type: File -outputs: -- {id: out, type: stdout} -requirements: -- {class: DockerRequirement, dockerPull: python:3-slim} -- class: InitialWorkDirRequirement - listing: - - {entry: "$(inputs.filelist)\n", entryname: renamed-filelist.txt} -- {class: InlineJavascriptRequirement} -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-passthrough3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-passthrough3.cwl deleted file mode 100644 index 61fb8d25..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-passthrough3.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: filelist, type: File} -outputs: -- id: filelist - outputBinding: {glob: renamed-filelist.txt} - type: File -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.filelist), entryname: renamed-filelist.txt} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-passthrough4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-passthrough4.cwl deleted file mode 100644 index 74ba0383..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwd-passthrough4.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: filelist, type: File} -outputs: -- id: filelist - outputBinding: {glob: $(inputs.filelist.basename)} - type: File -requirements: -- class: InitialWorkDirRequirement - listing: [$(inputs.filelist)] -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwdr-entry.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwdr-entry.cwl deleted file mode 100644 index 254ab442..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwdr-entry.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: [cat, example.conf] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: message, type: string} -outputs: -- id: out - outputBinding: {glob: example.conf} - type: File -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: "CONFIGVAR=$(inputs.message)\n", entryname: example.conf} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwdr_dir_literal_real_file.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwdr_dir_literal_real_file.cwl deleted file mode 100644 index fbd71cc3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwdr_dir_literal_real_file.cwl +++ /dev/null @@ -1,15 +0,0 @@ -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: filelist, type: File} -outputs: -- id: same - outputBinding: {glob: subdir/$(inputs.filelist.basename)} - type: File -requirements: -- {class: DockerRequirement, dockerPull: debian:stable-slim} -- {class: InlineJavascriptRequirement} -- {class: InitialWorkDirRequirement, listing: "${\n return [{\"class\": \"Directory\"\ - ,\n \"basename\": \"subdir\",\n \"listing\": [ inputs.filelist\ - \ ]\n }]}\n"} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwdr_with_nested_dirs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwdr_with_nested_dirs.cwl deleted file mode 100644 index 5a076416..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_iwdr_with_nested_dirs.cwl +++ /dev/null @@ -1,40 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: ya_empty, outputSource: second/ya, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: first - in: [] - out: [deep_dir] - run: - baseCommand: [mkdir, -p, deeply/nested/dir/structure] - class: CommandLineTool - inputs: [] - outputs: - - id: deep_dir - outputBinding: {glob: deeply} - type: Directory - requirements: - - {class: InlineJavascriptRequirement} -- id: second - in: - - {id: dir, source: first/deep_dir} - out: [ya] - run: - baseCommand: [touch, deeply/nested/dir/structure/ya] - class: CommandLineTool - inputs: - - {id: dir, type: Directory} - outputs: - - id: ya - outputBinding: {glob: deeply/nested/dir/structure/ya} - type: File - requirements: - - class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.dir), writable: true} - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_js-input-record.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_js-input-record.cwl deleted file mode 100644 index 673eb842..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_js-input-record.cwl +++ /dev/null @@ -1,22 +0,0 @@ -baseCommand: [echo] -class: CommandLineTool -cwlVersion: v1.0 -inputs: -- id: message - type: - fields: - - inputBinding: {position: 1} - name: text - type: string - - inputBinding: {position: 0, prefix: -n} - name: newlines - type: ['null', boolean] - name: message_object - type: record -outputs: -- id: out - outputBinding: {glob: output.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_js-quote.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_js-quote.cwl deleted file mode 100644 index adb5c9a3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_js-quote.cwl +++ /dev/null @@ -1,18 +0,0 @@ -arguments: [] -baseCommand: [echo] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {default: Hello, id: quote, type: string} -label: Check for a JS quoting bug -outputs: -- id: out - outputBinding: {glob: file.txt} - type: File -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: "${return 'quote \"' + inputs.quote + '\"'}\n", entryname: file.txt} - - {entry: "set -xe\ncat file.txt\n", entryname: script.sh} -- {class: InlineJavascriptRequirement} -- {class: ResourceRequirement, coresMin: 2, ramMin: 1000} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_linkfile.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_linkfile.cwl deleted file mode 100644 index 44e13780..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_linkfile.cwl +++ /dev/null @@ -1,15 +0,0 @@ -baseCommand: touch -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: src - inputBinding: {position: 1, valueFrom: $(self.nameroot).class} - type: File -outputs: -- id: classfile - outputBinding: {glob: '*.class'} - type: File -requirements: -- class: InitialWorkDirRequirement - listing: [$(inputs.src)] -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_deep1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_deep1.cwl deleted file mode 100644 index 45b511c0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_deep1.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: d, type: Directory} -outputs: -- id: out - outputBinding: {outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing.length - === 1)'} - type: boolean -requirements: -- {class: LoadListingRequirement, loadListing: deep_listing} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_deep2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_deep2.cwl deleted file mode 100644 index 94bfa33b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_deep2.cwl +++ /dev/null @@ -1,12 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: d, loadListing: deep_listing, type: Directory} -outputs: -- id: out - outputBinding: {outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing.length - === 1)'} - type: boolean -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_none1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_none1.cwl deleted file mode 100644 index 24ff658b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_none1.cwl +++ /dev/null @@ -1,11 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: d, type: Directory} -outputs: -- id: out - outputBinding: {outputEval: $(inputs.d.listing === undefined)} - type: boolean -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_none2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_none2.cwl deleted file mode 100644 index 18b6061e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_none2.cwl +++ /dev/null @@ -1,12 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: d, type: Directory} -outputs: -- id: out - outputBinding: {outputEval: $(inputs.d.listing === undefined)} - type: boolean -requirements: -- {class: LoadListingRequirement, loadListing: no_listing} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_none3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_none3.cwl deleted file mode 100644 index f23c1d7f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_none3.cwl +++ /dev/null @@ -1,11 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: d, loadListing: no_listing, type: Directory} -outputs: -- id: out - outputBinding: {outputEval: $(inputs.d.listing === undefined)} - type: boolean -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_shallow1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_shallow1.cwl deleted file mode 100644 index b8493602..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_shallow1.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: d, type: Directory} -outputs: -- id: out - outputBinding: {outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing - === undefined)'} - type: boolean -requirements: -- {class: LoadListingRequirement, loadListing: shallow_listing} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_shallow2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_shallow2.cwl deleted file mode 100644 index f5027d50..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_listing_shallow2.cwl +++ /dev/null @@ -1,12 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: d, loadListing: shallow_listing, type: Directory} -outputs: -- id: out - outputBinding: {outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing - === undefined)'} - type: boolean -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_loadContents-limit.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_loadContents-limit.cwl deleted file mode 100644 index ec2318c0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_loadContents-limit.cwl +++ /dev/null @@ -1,8 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: filelist, loadContents: true, type: File} -outputs: [] -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_metadata.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_metadata.cwl deleted file mode 100644 index f44a38d3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_metadata.cwl +++ /dev/null @@ -1,20 +0,0 @@ -$namespaces: {dct: http://purl.org/dc/terms/, foaf: http://xmlns.com/foaf/0.1/} -$schemas: [foaf.rdf, dcterms.rdf] -baseCommand: cat -class: CommandLineTool -cwlVersion: v1.2 -dct:creator: {class: foaf:Person, foaf:mbox: mailto:peter.amstutz@curoverse.com, foaf:name: Peter - Amstutz, id: http://orcid.org/0000-0003-3566-7705} -doc: Print the contents of a file to stdout using 'cat' running in a docker container. -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: -- id: file1 - inputBinding: {position: 1} - type: File -- id: numbering - inputBinding: {position: 0, prefix: -n} - type: ['null', boolean] -outputs: [] -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_mkdir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_mkdir.cwl deleted file mode 100644 index f3dbc744..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_mkdir.cwl +++ /dev/null @@ -1,11 +0,0 @@ -arguments: [mkdir, $(inputs.dirname)] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: dirname, type: string} -outputs: -- id: out - outputBinding: {glob: $(inputs.dirname)} - type: Directory -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_multiple_input_feature_requirement.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_multiple_input_feature_requirement.cwl deleted file mode 100644 index 5f8fca0b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_multiple_input_feature_requirement.cwl +++ /dev/null @@ -1,46 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: [] -outputs: -- id: hello_world_in_two_lines - outputSource: [step1/out, step2/out] - type: {items: string, type: array} -requirements: -- {class: MultipleInputFeatureRequirement} -steps: -- id: step1 - in: - - {default: hello, id: in} - out: [out] - run: - baseCommand: echo - class: CommandLineTool - cwlVersion: v1.2 - inputs: - - id: in - inputBinding: {} - type: Any - outputs: - - id: out - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: [] - stdout: out.txt -- id: step2 - in: - - {default: world, id: in} - out: [out] - run: - baseCommand: echo - class: CommandLineTool - cwlVersion: v1.2 - inputs: - - id: in - inputBinding: {} - type: Any - outputs: - - id: out - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: [] - stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_nameroot.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_nameroot.cwl deleted file mode 100644 index 2726347c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_nameroot.cwl +++ /dev/null @@ -1,11 +0,0 @@ -arguments: [echo, $(inputs.file1.basename), $(inputs.file1.nameroot), $(inputs.file1.nameext)] -baseCommand: [] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: b, type: stdout} -requirements: -- {class: InlineJavascriptRequirement} -stdout: $(inputs.file1.nameroot).xtx diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_nested-array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_nested-array.cwl deleted file mode 100644 index ee32caf5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_nested-array.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: letters - inputBinding: {position: 1} - type: - items: {items: string, type: array} - type: array -outputs: -- {id: echo, type: stdout} -requirements: -- {class: InlineJavascriptRequirement} -stdout: echo.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_networkaccess.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_networkaccess.cwl deleted file mode 100644 index 39ebf6e3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_networkaccess.cwl +++ /dev/null @@ -1,13 +0,0 @@ -arguments: -- -c -- {valueFrom: "import urllib.request\nassert(urllib.request.urlopen(\"http://commonwl.org\"\ - ).code == 200)"} -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: -- {class: DockerRequirement, dockerPull: python:3} -- {class: NetworkAccess, networkAccess: true} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_networkaccess2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_networkaccess2.cwl deleted file mode 100644 index 5df27510..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_networkaccess2.cwl +++ /dev/null @@ -1,12 +0,0 @@ -arguments: -- -c -- {valueFrom: "import urllib.request\nassert(urllib.request.urlopen(\"http://commonwl.org\"\ - ).code == 200)"} -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: -- {class: DockerRequirement, dockerPull: python:3} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_no-inputs-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_no-inputs-tool.cwl deleted file mode 100644 index f60aef86..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_no-inputs-tool.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: [echo, cwl] -class: CommandLineTool -cwlVersion: v1.2 -doc: CommandLineTool without inputs. -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: [] -outputs: -- id: output - outputBinding: {glob: output} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_no-inputs-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_no-inputs-wf.cwl deleted file mode 100644 index b78bad2a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_no-inputs-wf.cwl +++ /dev/null @@ -1,27 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -doc: Workflow without inputs. -inputs: [] -outputs: -- {id: output, outputSource: step0/output, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step0 - in: [] - out: [output] - run: - baseCommand: [echo, cwl] - class: CommandLineTool - doc: CommandLineTool without inputs. - hints: - DockerRequirement: {dockerPull: debian:stretch-slim} - inputs: [] - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_no-outputs-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_no-outputs-tool.cwl deleted file mode 100644 index f5b5bc46..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_no-outputs-tool.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -doc: CommandLineTool without outputs. -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: -- id: file1 - inputBinding: {position: 1} - label: Input File - type: File -outputs: [] -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_no-outputs-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_no-outputs-wf.cwl deleted file mode 100644 index b822c3b8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_no-outputs-wf.cwl +++ /dev/null @@ -1,28 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -doc: Workflow without outputs. -inputs: -- {id: file1, type: File} -outputs: [] -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step0 - in: - - {id: file1, source: file1} - out: [] - run: - baseCommand: echo - class: CommandLineTool - doc: CommandLineTool without outputs. - hints: - DockerRequirement: {dockerPull: debian:stretch-slim} - inputs: - - id: file1 - inputBinding: {position: 1} - label: Input File - type: File - outputs: [] - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_null-defined.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_null-defined.cwl deleted file mode 100644 index 8a198ea3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_null-defined.cwl +++ /dev/null @@ -1,13 +0,0 @@ -arguments: [echo, '$(inputs.file1 === null ? "t" : "f")'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: file1 - type: ['null', File] -outputs: -- id: out - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string -requirements: -- {class: InlineJavascriptRequirement} -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_null-expression1-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_null-expression1-tool.cwl deleted file mode 100644 index 5b6afac9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_null-expression1-tool.cwl +++ /dev/null @@ -1,9 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.2 -expression: "$({'output': (inputs.i1 == 'the-default' ? 1 : 2)})" -inputs: -- {default: the-default, id: i1, type: Any} -outputs: -- {id: output, type: int} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_null-expression2-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_null-expression2-tool.cwl deleted file mode 100644 index f82f474e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_null-expression2-tool.cwl +++ /dev/null @@ -1,9 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.2 -expression: "$({'output': (inputs.i1 == 'the-default' ? 1 : 2)})" -inputs: -- {id: i1, type: Any} -outputs: -- {id: output, type: int} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_null-expression3-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_null-expression3-tool.cwl deleted file mode 100644 index 0babf75b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_null-expression3-tool.cwl +++ /dev/null @@ -1,8 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.2 -expression: "$({'output': null })" -inputs: [] -outputs: -- {id: output, type: Any} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_operation.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_operation.cwl deleted file mode 100644 index 99e34104..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_operation.cwl +++ /dev/null @@ -1,10 +0,0 @@ -class: Operation -cwlVersion: v1.2 -doc: Reverse each line -id: reverse -inputs: -- {id: input, type: File} -outputs: -- {id: output, type: File} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_optional-numerical-output-0.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_optional-numerical-output-0.cwl deleted file mode 100644 index 8982721c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_optional-numerical-output-0.cwl +++ /dev/null @@ -1,12 +0,0 @@ -baseCommand: [echo, '0'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: out - outputBinding: {glob: a.txt, loadContents: true, outputEval: "${\n return parseFloat(self[0].contents);\n\ - }"} - type: ['null', float] -requirements: -- {class: InlineJavascriptRequirement} -stdout: a.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_optional-output.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_optional-output.cwl deleted file mode 100644 index 06e16a85..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_optional-output.cwl +++ /dev/null @@ -1,23 +0,0 @@ -baseCommand: cat -class: CommandLineTool -cwlVersion: v1.2 -doc: Print the contents of a file to stdout using 'cat' running in a docker container. -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: -- doc: The file that will be copied using 'cat' - id: file1 - inputBinding: {position: 1} - label: Input File - type: File -outputs: -- id: output_file - outputBinding: {glob: output.txt} - secondaryFiles: [.idx] - type: File -- id: optional_file - outputBinding: {glob: bumble.txt} - type: ['null', File] -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_output-arrays-file-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_output-arrays-file-wf.cwl deleted file mode 100644 index 03e164bc..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_output-arrays-file-wf.cwl +++ /dev/null @@ -1,43 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: i, type: File} -outputs: -- id: o - outputSource: step2/o - type: {items: File, type: array} -requirements: -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: i, source: i} - out: [o] - run: - class: ExpressionTool - expression: "${return {'o': inputs.i.contents.split(\" \")};}\n" - inputs: - - {id: i, loadContents: true, type: File} - outputs: - - id: o - type: {items: string, type: array} - requirements: - - {class: InlineJavascriptRequirement} -- id: step2 - in: - - {id: i, source: step1/o} - out: [o] - run: - baseCommand: touch - class: CommandLineTool - inputs: - - id: i - inputBinding: {position: 1} - type: {items: string, type: array} - outputs: - - id: o - outputBinding: {glob: $(inputs.i)} - type: {items: File, type: array} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_output-arrays-int-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_output-arrays-int-wf.cwl deleted file mode 100644 index 5a45335f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_output-arrays-int-wf.cwl +++ /dev/null @@ -1,54 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: i, type: int} -outputs: -- {id: o, outputSource: step3/o, type: int} -requirements: -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: i, source: i} - out: [o] - run: - class: ExpressionTool - expression: "${return {'o': Array.apply(null, {length: inputs.i}).map(Number.call,\ - \ Number)};}\n" - inputs: - - {id: i, type: int} - outputs: - - id: o - type: {items: int, type: array} - requirements: - - {class: InlineJavascriptRequirement} -- id: step2 - in: - - {id: i, source: step1/o} - out: [o] - run: - class: ExpressionTool - expression: "${return {'o': inputs.i.map(function(x) { return (x + 1) * 2; })};}\n" - inputs: - - id: i - type: {items: int, type: array} - outputs: - - id: o - type: {items: int, type: array} - requirements: - - {class: InlineJavascriptRequirement} -- id: step3 - in: - - {id: i, source: step2/o} - out: [o] - run: - class: ExpressionTool - expression: "${return {'o': inputs.i.reduce(function(a, b) { return a + b; })};}\n" - inputs: - - id: i - type: {items: int, type: array} - outputs: - - {id: o, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_output-arrays-int.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_output-arrays-int.cwl deleted file mode 100644 index 3e402641..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_output-arrays-int.cwl +++ /dev/null @@ -1,11 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.2 -expression: "${return {'o': Array.apply(null, {length: inputs.i}).map(Number.call,\ - \ Number)};}\n" -inputs: -- {id: i, type: int} -outputs: -- id: o - type: {items: int, type: array} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_output_reference_workflow_input.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_output_reference_workflow_input.cwl deleted file mode 100644 index 61ca2e23..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_output_reference_workflow_input.cwl +++ /dev/null @@ -1,8 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {default: me, id: first, type: string} -outputs: -- {id: last, outputSource: first, type: string} -requirements: [] -steps: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_params.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_params.cwl deleted file mode 100644 index e7048bd2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_params.cwl +++ /dev/null @@ -1,99 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- default: - b az: 2 - b"az: null - b'az: true - baz: zab1 - buz: [a, b, c] - id: bar - type: Any -outputs: -- id: t1 - outputBinding: {outputEval: $(inputs)} - type: Any -- id: t2 - outputBinding: {outputEval: $(inputs.bar)} - type: Any -- id: t3 - outputBinding: {outputEval: "$(inputs['bar'])"} - type: Any -- id: t4 - outputBinding: {outputEval: '$(inputs["bar"])'} - type: Any -- id: t5 - outputBinding: {outputEval: $(inputs.bar.baz)} - type: Any -- id: t6 - outputBinding: {outputEval: "$(inputs['bar'].baz)"} - type: Any -- id: t7 - outputBinding: {outputEval: "$(inputs['bar'][\"baz\"])"} - type: Any -- id: t8 - outputBinding: {outputEval: "$(inputs.bar['baz'])"} - type: Any -- id: t9 - outputBinding: {outputEval: "$(inputs.bar['b az'])"} - type: Any -- id: t10 - outputBinding: {outputEval: "$(inputs.bar['b\\'az'])"} - type: Any -- id: t11 - outputBinding: {outputEval: "$(inputs.bar[\"b'az\"])"} - type: Any -- id: t12 - outputBinding: {outputEval: "$(inputs.bar['b\"az'])"} - type: 'null' -- id: t13 - outputBinding: {outputEval: -$(inputs.bar.baz)} - type: Any -- id: t14 - outputBinding: {outputEval: "-$(inputs['bar'].baz)"} - type: Any -- id: t15 - outputBinding: {outputEval: "-$(inputs['bar'][\"baz\"])"} - type: Any -- id: t16 - outputBinding: {outputEval: "-$(inputs.bar['baz'])"} - type: Any -- id: t17 - outputBinding: {outputEval: $(inputs.bar.baz) $(inputs.bar.baz)} - type: Any -- id: t18 - outputBinding: {outputEval: "$(inputs['bar'].baz) $(inputs['bar'].baz)"} - type: Any -- id: t19 - outputBinding: {outputEval: "$(inputs['bar'][\"baz\"]) $(inputs['bar'][\"baz\"])"} - type: Any -- id: t20 - outputBinding: {outputEval: "$(inputs.bar['baz']) $(inputs.bar['baz'])"} - type: Any -- id: t21 - outputBinding: {outputEval: "$(inputs.bar['b az']) $(inputs.bar['b az'])"} - type: Any -- id: t22 - outputBinding: {outputEval: "$(inputs.bar['b\\'az']) $(inputs.bar['b\\'az'])"} - type: Any -- id: t23 - outputBinding: {outputEval: "$(inputs.bar[\"b'az\"]) $(inputs.bar[\"b'az\"])"} - type: Any -- id: t24 - outputBinding: {outputEval: "$(inputs.bar['b\"az']) $(inputs.bar['b\"az'])"} - type: Any -- id: t25 - outputBinding: {outputEval: '$(inputs.bar.buz[1])'} - type: Any -- id: t26 - outputBinding: {outputEval: '$(inputs.bar.buz[1]) $(inputs.bar.buz[1])'} - type: Any -- id: t27 - outputBinding: {outputEval: $(null)} - type: 'null' -- id: t28 - outputBinding: {outputEval: $(inputs.bar.buz.length)} - type: int -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_params2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_params2.cwl deleted file mode 100644 index e7048bd2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_params2.cwl +++ /dev/null @@ -1,99 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- default: - b az: 2 - b"az: null - b'az: true - baz: zab1 - buz: [a, b, c] - id: bar - type: Any -outputs: -- id: t1 - outputBinding: {outputEval: $(inputs)} - type: Any -- id: t2 - outputBinding: {outputEval: $(inputs.bar)} - type: Any -- id: t3 - outputBinding: {outputEval: "$(inputs['bar'])"} - type: Any -- id: t4 - outputBinding: {outputEval: '$(inputs["bar"])'} - type: Any -- id: t5 - outputBinding: {outputEval: $(inputs.bar.baz)} - type: Any -- id: t6 - outputBinding: {outputEval: "$(inputs['bar'].baz)"} - type: Any -- id: t7 - outputBinding: {outputEval: "$(inputs['bar'][\"baz\"])"} - type: Any -- id: t8 - outputBinding: {outputEval: "$(inputs.bar['baz'])"} - type: Any -- id: t9 - outputBinding: {outputEval: "$(inputs.bar['b az'])"} - type: Any -- id: t10 - outputBinding: {outputEval: "$(inputs.bar['b\\'az'])"} - type: Any -- id: t11 - outputBinding: {outputEval: "$(inputs.bar[\"b'az\"])"} - type: Any -- id: t12 - outputBinding: {outputEval: "$(inputs.bar['b\"az'])"} - type: 'null' -- id: t13 - outputBinding: {outputEval: -$(inputs.bar.baz)} - type: Any -- id: t14 - outputBinding: {outputEval: "-$(inputs['bar'].baz)"} - type: Any -- id: t15 - outputBinding: {outputEval: "-$(inputs['bar'][\"baz\"])"} - type: Any -- id: t16 - outputBinding: {outputEval: "-$(inputs.bar['baz'])"} - type: Any -- id: t17 - outputBinding: {outputEval: $(inputs.bar.baz) $(inputs.bar.baz)} - type: Any -- id: t18 - outputBinding: {outputEval: "$(inputs['bar'].baz) $(inputs['bar'].baz)"} - type: Any -- id: t19 - outputBinding: {outputEval: "$(inputs['bar'][\"baz\"]) $(inputs['bar'][\"baz\"])"} - type: Any -- id: t20 - outputBinding: {outputEval: "$(inputs.bar['baz']) $(inputs.bar['baz'])"} - type: Any -- id: t21 - outputBinding: {outputEval: "$(inputs.bar['b az']) $(inputs.bar['b az'])"} - type: Any -- id: t22 - outputBinding: {outputEval: "$(inputs.bar['b\\'az']) $(inputs.bar['b\\'az'])"} - type: Any -- id: t23 - outputBinding: {outputEval: "$(inputs.bar[\"b'az\"]) $(inputs.bar[\"b'az\"])"} - type: Any -- id: t24 - outputBinding: {outputEval: "$(inputs.bar['b\"az']) $(inputs.bar['b\"az'])"} - type: Any -- id: t25 - outputBinding: {outputEval: '$(inputs.bar.buz[1])'} - type: Any -- id: t26 - outputBinding: {outputEval: '$(inputs.bar.buz[1]) $(inputs.bar.buz[1])'} - type: Any -- id: t27 - outputBinding: {outputEval: $(null)} - type: 'null' -- id: t28 - outputBinding: {outputEval: $(inputs.bar.buz.length)} - type: int -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_params_input_length_non_array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_params_input_length_non_array.cwl deleted file mode 100644 index 48591415..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_params_input_length_non_array.cwl +++ /dev/null @@ -1,33 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {default: 1, id: length, type: int} -- id: bar - type: - fields: - - {name: length, type: int} - name: bar_record - type: record -- id: baz - type: - fields: - - name: length - type: - fields: - - {name: bap, type: int} - name: length_record - type: record - name: baz_record - type: record -outputs: -- id: output1 - outputBinding: {outputEval: $(inputs.length)} - type: int -- id: output2 - outputBinding: {outputEval: $(inputs.bar.length)} - type: int -- id: output3 - outputBinding: {outputEval: $(inputs.baz.length.bap)} - type: int -requirements: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_parseInt-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_parseInt-tool.cwl deleted file mode 100644 index 71a6067d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_parseInt-tool.cwl +++ /dev/null @@ -1,9 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.2 -expression: "$({'output': parseInt(inputs.file1.contents)})" -inputs: -- {id: file1, loadContents: true, type: File} -outputs: -- {id: output, type: int} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_pass-unconnected.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_pass-unconnected.cwl deleted file mode 100644 index 8fe43725..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_pass-unconnected.cwl +++ /dev/null @@ -1,30 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {default: hello inp1, id: inp1, type: string} -- {default: hello inp2, id: inp2, type: string} -outputs: -- {id: out, outputSource: step1/out, type: string} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: in, source: inp1} - - {id: in2, source: inp2} - out: [out] - run: - baseCommand: echo - class: CommandLineTool - inputs: - - id: in - inputBinding: {} - type: Any - outputs: - - id: out - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-in-format.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-in-format.cwl deleted file mode 100644 index 6ae76986..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-in-format.cwl +++ /dev/null @@ -1,16 +0,0 @@ -arguments: ['true'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {format: http://example.com/format1, id: regular_input, type: File} -- id: record_input - type: - fields: - - {format: http://example.com/format1, name: f1, type: File} - - format: http://example.com/format2 - name: f2 - type: {items: File, type: array} - type: record -outputs: [] -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-in-secondaryFiles-missing-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-in-secondaryFiles-missing-wf.cwl deleted file mode 100644 index 7a32efd7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-in-secondaryFiles-missing-wf.cwl +++ /dev/null @@ -1,36 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: record_input - type: - fields: - - {name: f1, type: File} - - name: f2 - type: {items: File, type: array} - type: record -outputs: [] -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: record_input, source: record_input} - out: [] - run: - arguments: [-f, $(inputs.record_input.f1.path).s2, -a, -f, '$(inputs.record_input.f2[0].path).s3', - -a, -f, '$(inputs.record_input.f2[1].path).s3'] - baseCommand: test - class: CommandLineTool - inputs: - - id: record_input - type: - fields: - - {name: f1, secondaryFiles: .s2, type: File} - - name: f2 - secondaryFiles: .s3 - type: {items: File, type: array} - type: record - outputs: [] - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-in-secondaryFiles-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-in-secondaryFiles-wf.cwl deleted file mode 100644 index c65b974c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-in-secondaryFiles-wf.cwl +++ /dev/null @@ -1,37 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: record_input - type: - fields: - - {name: f1, secondaryFiles: .s2, type: File} - - name: f2 - secondaryFiles: .s3 - type: {items: File, type: array} - type: record -outputs: [] -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: record_input, source: record_input} - out: [] - run: - arguments: [-f, $(inputs.record_input.f1.path).s2, -a, -f, '$(inputs.record_input.f2[0].path).s3', - -a, -f, '$(inputs.record_input.f2[1].path).s3'] - baseCommand: test - class: CommandLineTool - inputs: - - id: record_input - type: - fields: - - {name: f1, secondaryFiles: .s2, type: File} - - name: f2 - secondaryFiles: .s3 - type: {items: File, type: array} - type: record - outputs: [] - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-in-secondaryFiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-in-secondaryFiles.cwl deleted file mode 100644 index 3d0828ac..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-in-secondaryFiles.cwl +++ /dev/null @@ -1,17 +0,0 @@ -arguments: [-f, $(inputs.record_input.f1.path).s2, -a, -f, '$(inputs.record_input.f2[0].path).s3', - -a, -f, '$(inputs.record_input.f2[1].path).s3'] -baseCommand: test -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: record_input - type: - fields: - - {name: f1, secondaryFiles: .s2, type: File} - - name: f2 - secondaryFiles: .s3 - type: {items: File, type: array} - type: record -outputs: [] -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-order.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-order.cwl deleted file mode 100644 index fd8a7580..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-order.cwl +++ /dev/null @@ -1,36 +0,0 @@ -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -hints: -- {class: DockerRequirement, dockerPull: 'docker.io/python:3-slim'} -inputs: -- default: {class: File, location: args.py} - id: args.py - inputBinding: {position: -1} - type: File -- id: a - inputBinding: {position: 5, prefix: -a} - type: - fields: - - inputBinding: {position: 1, prefix: -b} - name: b - type: int - - inputBinding: {position: 3, prefix: -c} - name: c - type: int - type: record -- id: d - inputBinding: {position: 6, prefix: -d} - type: - fields: - - inputBinding: {position: 2, prefix: -e} - name: e - type: int - - inputBinding: {position: 4, prefix: -f} - name: f - type: int - type: record -outputs: -- id: args - type: {items: string, type: array} -requirements: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-out-format.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-out-format.cwl deleted file mode 100644 index 1842b6b0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-out-format.cwl +++ /dev/null @@ -1,26 +0,0 @@ -arguments: ['true'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: record_input - type: - fields: - - {name: f1, type: File} - - name: f2 - type: {items: File, type: array} - type: record -outputs: -- format: http://example.com/format1 - id: f1out - outputBinding: {outputEval: $(inputs.record_input.f1)} - type: File -- id: record_output - type: - fields: - - format: http://example.com/format2 - name: f2out - outputBinding: {outputEval: '$(inputs.record_input.f2[0])'} - type: File - type: record -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-out-secondaryFiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-out-secondaryFiles.cwl deleted file mode 100644 index 2f1eab44..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-out-secondaryFiles.cwl +++ /dev/null @@ -1,21 +0,0 @@ -arguments: [A, A.s2, B, B.s3, C, C.s3] -baseCommand: touch -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: record_output - type: - fields: - - name: f1 - outputBinding: {glob: A} - secondaryFiles: .s2 - type: File - - name: f2 - outputBinding: - glob: [B, C] - secondaryFiles: .s3 - type: {items: File, type: array} - type: record -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-output-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-output-wf.cwl deleted file mode 100644 index 95ebf782..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-output-wf.cwl +++ /dev/null @@ -1,62 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: irec - type: - fields: - - {name: ifoo, type: File} - - {name: ibar, type: File} - name: irec - type: record -outputs: -- id: orec - outputSource: step1/orec - type: - fields: - - {name: ofoo, type: File} - - {name: obar, type: File} - name: orec - type: record -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: irec, source: irec} - out: [orec] - run: - arguments: - - {position: 1, valueFrom: cat} - - {position: 3, shellQuote: false, valueFrom: '> foo'} - - {position: 4, shellQuote: false, valueFrom: '&&'} - - {position: 5, valueFrom: cat} - - {position: 7, shellQuote: false, valueFrom: '> bar'} - class: CommandLineTool - inputs: - - id: irec - type: - fields: - - inputBinding: {position: 2} - name: ifoo - type: File - - inputBinding: {position: 6} - name: ibar - type: File - name: irec - type: record - outputs: - - id: orec - type: - fields: - - name: ofoo - outputBinding: {glob: foo} - type: File - - name: obar - outputBinding: {glob: bar} - type: File - name: orec - type: record - requirements: - - {class: ShellCommandRequirement} - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-output.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-output.cwl deleted file mode 100644 index 3638838c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-output.cwl +++ /dev/null @@ -1,35 +0,0 @@ -arguments: -- {position: 1, valueFrom: cat} -- {position: 3, shellQuote: false, valueFrom: '> foo'} -- {position: 4, shellQuote: false, valueFrom: '&&'} -- {position: 5, valueFrom: cat} -- {position: 7, shellQuote: false, valueFrom: '> bar'} -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: irec - type: - fields: - - inputBinding: {position: 2} - name: ifoo - type: File - - inputBinding: {position: 6} - name: ibar - type: File - name: irec - type: record -outputs: -- id: orec - type: - fields: - - name: ofoo - outputBinding: {glob: foo} - type: File - - name: obar - outputBinding: {glob: bar} - type: File - name: orec - type: record -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-sd-secondaryFiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-sd-secondaryFiles.cwl deleted file mode 100644 index f8058ad0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record-sd-secondaryFiles.cwl +++ /dev/null @@ -1,19 +0,0 @@ -arguments: [-f, $(inputs.record_input.f1.path).s2, -a, -f, '$(inputs.record_input.f2[0].path).s3', - -a, -f, '$(inputs.record_input.f2[1].path).s3'] -baseCommand: test -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: record_input - type: - doc: Type test record - fields: - - {name: f1, secondaryFiles: .s2, type: File} - - name: f2 - secondaryFiles: .s3 - type: {items: File, type: array} - name: user_type_2 - type: record -outputs: [] -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record_outputeval.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record_outputeval.cwl deleted file mode 100644 index 48f36946..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record_outputeval.cwl +++ /dev/null @@ -1,22 +0,0 @@ -arguments: [touch GRC$(inputs.organism_prefix)38.primary_assembly.genome.fa ; touch gencode.v$(inputs.gtf_version).primary_assembly.annotation.gtf] -baseCommand: [bash, -c] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {default: M21, id: gtf_version, type: string} -- {default: mouse, id: organism, type: string} -- {default: m, id: organism_prefix, type: string} -outputs: -- id: references - outputBinding: {outputEval: '$({ "genome_fa": { "class": "File", "path": runtime.outdir+"/"+"GRC" - + inputs.organism_prefix + "38.primary_assembly.genome.fa" }, "annotation_gtf": - { "class": "File", "path": runtime.outdir+"/"+"gencode.v" + inputs.gtf_version - + ".primary_assembly.annotation.gtf" } })'} - type: - fields: - - {name: genome_fa, type: File} - - {name: annotation_gtf, type: File} - name: References - type: record -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record_outputeval_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record_outputeval_nojs.cwl deleted file mode 100644 index 248c5174..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_record_outputeval_nojs.cwl +++ /dev/null @@ -1,22 +0,0 @@ -arguments: [$(inputs.ref.genome_fa) $(inputs.ref.annotation_gtf)] -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- default: {annotation_gtf: gencode.vM21.primary_assembly.annotation.gtf, genome_fa: GRCm38.primary_assembly.genome.fa} - id: ref - type: - fields: - - {name: genome_fa, type: string} - - {name: annotation_gtf, type: string} - type: record -outputs: -- id: references - outputBinding: {outputEval: $(inputs.ref)} - type: - fields: - - {name: genome_fa, type: string} - - {name: annotation_gtf, type: string} - type: record -- {id: summary, type: stdout} -requirements: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_recursive-input-directory.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_recursive-input-directory.cwl deleted file mode 100644 index c2aad04c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_recursive-input-directory.cwl +++ /dev/null @@ -1,26 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: "touch work_dir/e;\nif [ ! -w work_dir ]; then echo\ - \ work_dir not writable; fi;\nif [ -L work_dir ]; then echo work_dir is a symlink;\ - \ fi;\nif [ ! -w work_dir/a ]; then echo work_dir/a not writable; fi;\nif [ -L\ - \ work_dir/a ]; then echo work_dir/a is a symlink; fi;\nif [ ! -w work_dir/c ];\ - \ then echo work_dir/c not writable; fi;\nif [ -L work_dir/c ]; then echo work_dir/c\ - \ is a symlink; fi;\nif [ ! -w work_dir/c/d ]; then echo work_dir/c/d not writable;\ - \ fi;\nif [ -L work_dir/c/d ]; then echo work_dir/c/d is a symlink; fi;\nif [\ - \ ! -w work_dir/e ]; then echo work_dir/e not writable; fi;\nif [ -L work_dir/e\ - \ ]; then echo work_dir/e is a symlink ; fi;\n"} -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: input_dir, type: Directory} -outputs: -- id: output_dir - outputBinding: {glob: work_dir} - type: Directory -- {id: test_result, type: stdout} -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.input_dir), entryname: work_dir, writable: true} -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_rename-inputs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_rename-inputs.cwl deleted file mode 100644 index 97a7c9b5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_rename-inputs.cwl +++ /dev/null @@ -1,34 +0,0 @@ -arguments: -- {position: 0, shellQuote: false, valueFrom: '|'} -- {position: 1, valueFrom: grep} -- {position: 2, valueFrom: secondary} -baseCommand: [ls] -class: CommandLineTool -cwlVersion: v1.2 -doc: "Simple test to confirm the implementation of expressions returning a File within\ - \ a CommandInputParameter.secondaryFile field.\n\nUse GREP to filter the result\ - \ from ls to ensure we only get the secondary files in there.\n\nRelated links:\n\ - - Issue: https://github.com/common-workflow-language/cwltool/issues/1232\n- PR:\ - \ https://github.com/common-workflow-language/cwltool/pull/1233\n- Discourse: https://cwl.discourse.group/t/ask-cwl-to-rename-a-secondary-file/72\n" -id: InputSecondaryFileConformanceTest -inputs: -- doc: "This input will with a secondary file `.accessory`. You could create these\ - \ files (and its accessory) with:\n```bash\ntouch secondary_file_test.txt\ntouch\ - \ secondary_file_test.txt.accessory\n```\n" - id: inputWithSecondary - secondaryFiles: [.accessory, "${\n function resolveSecondary(base, secPattern)\ - \ {\n if (secPattern[0] == '^') {\n var spl = base.split('.');\n \ - \ var endIndex = spl.length > 1 ? spl.length - 1 : 1;\n return resolveSecondary(spl.slice(undefined,\ - \ endIndex).join(\".\"), secPattern.slice(1));\n }\n return base + secPattern;\n\ - \ }\n return [{\n \"class\": \"File\",\n \"location\": self.secondaryFiles[0].location,\n\ - \ \"basename\": resolveSecondary(self.basename, '^.accessory')\n }];\n\ - }\n"] - type: File -outputs: -- {id: output_file, type: stdout} -requirements: -- {class: InlineJavascriptRequirement} -- {class: ShellCommandRequirement} -- class: InitialWorkDirRequirement - listing: [$(inputs.inputWithSecondary)] -stdout: result diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_rename-outputs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_rename-outputs.cwl deleted file mode 100644 index 5e2a1bf7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_rename-outputs.cwl +++ /dev/null @@ -1,28 +0,0 @@ -baseCommand: [ls] -class: CommandLineTool -cwlVersion: v1.2 -doc: "Simple test to confirm the implementation of expressions returning a File within\ - \ a CommandOutputParameter.secondaryFile field.\n\nRelated links:\n- Issue: https://github.com/common-workflow-language/cwltool/issues/1232\n\ - - PR: https://github.com/common-workflow-language/cwltool/pull/1233\n- Discourse:\ - \ https://cwl.discourse.group/t/ask-cwl-to-rename-a-secondary-file/72\n" -id: OutputSecondaryFileConformanceTest -inputs: [] -outputs: -- id: output_file - label: out - outputBinding: {glob: '*.txt'} - secondaryFiles: "${\n function resolveSecondary(base, secPattern) {\n \ - \ if (secPattern[0] == \"^\") {\n var spl = base.split(\".\");\n \ - \ var endIndex = spl.length > 1 ? spl.length - 1 : 1;\n return resolveSecondary(spl.slice(undefined,\ - \ endIndex).join(\".\"), secPattern.slice(1));\n }\n return base +\ - \ secPattern;\n }\n return [\n {\n \"class\": \"File\",\n\ - \ \"path\": resolveSecondary(self.path, \"^.accessory\"),\n \"\ - basename\": resolveSecondary(self.basename, \".accessory\")\n }\n ];\n\ - }\n" - type: File -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: '', entryname: secondary_file_test.txt, writable: true} - - {entry: '', entryname: secondary_file_test.accessory, writable: true} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_rename.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_rename.cwl deleted file mode 100644 index 493b3756..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_rename.cwl +++ /dev/null @@ -1,15 +0,0 @@ -baseCommand: 'true' -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: srcfile, type: File} -- {id: newname, type: string} -outputs: -- id: outfile - outputBinding: {glob: $(inputs.newname)} - type: File -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.srcfile), entryname: $(inputs.newname)} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_revsort-abstract.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_revsort-abstract.cwl deleted file mode 100644 index abe2effa..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_revsort-abstract.cwl +++ /dev/null @@ -1,48 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -doc: Reverse the lines in a document, then sort those lines. -inputs: -- {doc: The input file to be processed., id: input, type: File} -- {default: true, doc: 'If true, reverse (decending) sort', id: reverse_sort, type: boolean} -outputs: -- {doc: The output with the lines reversed and sorted., id: output, outputSource: sort/sorted, - type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: rev - in: - - {id: input, source: input} - out: [output] - run: - baseCommand: rev - class: CommandLineTool - doc: Reverse each line using the `rev` command - inputs: - - id: input - inputBinding: {} - type: File - outputs: - - id: output - outputBinding: {glob: output.txt} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt -- id: sort - in: - - {id: input, source: rev/output} - - {id: reverse, source: reverse_sort} - out: [sorted] - run: - class: Operation - doc: Sort the lines of the file - id: sort - inputs: - - {doc: The input file to be sorted., id: input, type: File} - - {default: true, doc: 'If true, reverse (decending) sort', id: reverse, type: boolean} - outputs: - - {doc: The sorted file, id: sorted, type: File} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_revsort-packed.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_revsort-packed.cwl deleted file mode 100644 index 82ae021a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_revsort-packed.cwl +++ /dev/null @@ -1,55 +0,0 @@ -$graph: -- class: Workflow - doc: Reverse the lines in a document, then sort those lines. - hints: - - {class: DockerRequirement, dockerPull: debian:stretch-slim} - id: '#main' - inputs: - - {doc: The input file to be processed., id: '#main/input', type: File} - - {default: true, doc: 'If true, reverse (decending) sort', id: '#main/reverse_sort', - type: boolean} - outputs: - - {doc: The output with the lines reversed and sorted., id: '#main/output', outputSource: '#main/sorted/output', - type: File} - steps: - - id: '#main/rev' - in: - - {id: '#main/rev/input', source: '#main/input'} - out: ['#main/rev/output'] - run: '#revtool.cwl' - - id: '#main/sorted' - in: - - {id: '#main/sorted/input', source: '#main/rev/output'} - - {id: '#main/sorted/reverse', source: '#main/reverse_sort'} - out: ['#main/sorted/output'] - run: '#sorttool.cwl' -- baseCommand: rev - class: CommandLineTool - doc: Reverse each line using the `rev` command - id: '#revtool.cwl' - inputs: - - id: '#revtool.cwl/input' - inputBinding: {} - type: File - outputs: - - id: '#revtool.cwl/output' - outputBinding: {glob: output.txt} - type: File - stdout: output.txt -- baseCommand: sort - class: CommandLineTool - doc: Sort lines using the `sort` command - id: '#sorttool.cwl' - inputs: - - id: '#sorttool.cwl/reverse' - inputBinding: {position: 1, prefix: -r} - type: boolean - - id: '#sorttool.cwl/input' - inputBinding: {position: 2} - type: File - outputs: - - id: '#sorttool.cwl/output' - outputBinding: {glob: output.txt} - type: File - stdout: output.txt -cwlVersion: v1.2 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_revsort.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_revsort.cwl deleted file mode 100644 index a2160365..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_revsort.cwl +++ /dev/null @@ -1,57 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -doc: Reverse the lines in a document, then sort those lines. -hints: -- {class: DockerRequirement, dockerPull: debian:stretch-slim} -inputs: -- {doc: The input file to be processed., id: input, type: File} -- {default: true, doc: 'If true, reverse (decending) sort', id: reverse_sort, type: boolean} -outputs: -- {doc: The output with the lines reversed and sorted., id: output, outputSource: sorted/output, - type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: rev - in: - - {id: input, source: input} - out: [output] - run: - baseCommand: rev - class: CommandLineTool - doc: Reverse each line using the `rev` command - inputs: - - id: input - inputBinding: {} - type: File - outputs: - - id: output - outputBinding: {glob: output.txt} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt -- id: sorted - in: - - {id: input, source: rev/output} - - {id: reverse, source: reverse_sort} - out: [output] - run: - baseCommand: sort - class: CommandLineTool - doc: Sort lines using the `sort` command - inputs: - - id: reverse - inputBinding: {position: 1, prefix: -r} - type: boolean - - id: input - inputBinding: {position: 2} - type: File - outputs: - - id: output - outputBinding: {glob: output.txt} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_revtool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_revtool.cwl deleted file mode 100644 index e84cb22d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_revtool.cwl +++ /dev/null @@ -1,15 +0,0 @@ -baseCommand: rev -class: CommandLineTool -cwlVersion: v1.2 -doc: Reverse each line using the `rev` command -inputs: -- id: input - inputBinding: {} - type: File -outputs: -- id: output - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_runtime-outdir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_runtime-outdir.cwl deleted file mode 100644 index a26a8fb9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_runtime-outdir.cwl +++ /dev/null @@ -1,16 +0,0 @@ -arguments: ['mkdir -p foo - - touch baz.txt - - touch foo/bar.txt - - '] -baseCommand: [bash, -c] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: stuff - outputBinding: {glob: $(runtime.outdir)} - type: Directory -requirements: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_runtime-paths-distinct.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_runtime-paths-distinct.cwl deleted file mode 100644 index 24bf6d0b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_runtime-paths-distinct.cwl +++ /dev/null @@ -1,12 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: "echo \"cow\" > \"$(runtime.outdir)/foo\" &&\necho\ - \ \"moo\" > \"$(runtime.tmpdir)/foo\" &&\necho '{\"foo\": {\"path\": \"$(runtime.outdir)/foo\"\ - , \"class\": \"File\"} }' > cwl.output.json\n"} -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: foo, type: File} -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valueFrom-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valueFrom-tool.cwl deleted file mode 100644 index 2f841b84..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valueFrom-tool.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: scattered_message - inputBinding: {position: 2} - type: string -- id: message - inputBinding: {position: 1} - type: string -outputs: -- {id: out_message, type: stdout} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-inputs-wf1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-inputs-wf1.cwl deleted file mode 100644 index 58400422..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-inputs-wf1.cwl +++ /dev/null @@ -1,47 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: inp - type: - items: - fields: - - {name: instr, type: string} - name: instr - type: record - type: array -outputs: -- id: out - outputSource: step1/echo_out - type: {items: string, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: StepInputExpressionRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: echo_unused, source: inp} - - {id: echo_in, valueFrom: $(inputs.echo_unused.instr)} - - {id: first, source: inp, valueFrom: '$(self[0].instr)'} - out: [echo_out] - run: - arguments: [-n, foo] - baseCommand: echo - class: CommandLineTool - inputs: - - id: first - inputBinding: {position: 1} - type: string - - id: echo_in - inputBinding: {position: 2} - type: string - - {id: echo_unused, type: Any} - outputs: - - id: echo_out - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: step1_out - scatter: echo_unused diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf1.cwl deleted file mode 100644 index f961fd00..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf1.cwl +++ /dev/null @@ -1,45 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: inp - type: - items: - fields: - - {name: instr, type: string} - name: instr - type: record - type: array -outputs: -- id: out - outputSource: step1/echo_out - type: {items: string, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: StepInputExpressionRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: echo_in, source: inp, valueFrom: $(self.instr)} - - {id: first, source: inp, valueFrom: '$(self[0].instr)'} - out: [echo_out] - run: - arguments: [-n, foo] - baseCommand: echo - class: CommandLineTool - inputs: - - id: first - inputBinding: {position: 1} - type: string - - id: echo_in - inputBinding: {position: 2} - type: string - outputs: - - id: echo_out - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: step1_out - scatter: echo_in diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf2.cwl deleted file mode 100644 index e9ff3263..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf2.cwl +++ /dev/null @@ -1,55 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: inp1 - type: - items: - fields: - - {name: instr, type: string} - name: instr - type: record - type: array -- id: inp2 - type: {items: string, type: array} -outputs: -- id: out - outputSource: step1/echo_out - type: - items: {items: string, type: array} - type: array -requirements: -- {class: ScatterFeatureRequirement} -- {class: StepInputExpressionRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: echo_in1, source: inp1, valueFrom: $(self.instr)} - - {id: echo_in2, source: inp2} - - {id: first, source: inp1, valueFrom: '$(self[0].instr)'} - out: [echo_out] - run: - arguments: [-n, foo] - baseCommand: echo - class: CommandLineTool - id: step1command - inputs: - - id: first - inputBinding: {position: 1} - type: string - - id: echo_in1 - inputBinding: {position: 2} - type: string - - id: echo_in2 - inputBinding: {position: 3} - type: string - outputs: - - id: echo_out - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: step1_out - scatter: [echo_in1, echo_in2] - scatterMethod: nested_crossproduct diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf3.cwl deleted file mode 100644 index e78ab151..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf3.cwl +++ /dev/null @@ -1,51 +0,0 @@ -$graph: -- arguments: [-n, foo] - baseCommand: echo - class: CommandLineTool - id: echo - inputs: - echo_in1: - inputBinding: {position: 2} - type: string - echo_in2: - inputBinding: {position: 3} - type: string - first: - inputBinding: {position: 1} - type: string - outputs: - echo_out: - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - stdout: step1_out -- class: Workflow - id: main - inputs: - inp1: - type: - items: - fields: - - {name: instr, type: string} - name: instr - type: record - type: array - inp2: - type: {items: string, type: array} - outputs: - out: - outputSource: step1/echo_out - type: {items: string, type: array} - requirements: - - {class: ScatterFeatureRequirement} - - {class: StepInputExpressionRequirement} - steps: - step1: - in: - echo_in1: {source: inp1, valueFrom: $(self.instr)} - echo_in2: inp2 - first: {source: inp1, valueFrom: '$(self[0].instr)'} - out: [echo_out] - run: '#echo' - scatter: [echo_in1, echo_in2] - scatterMethod: flat_crossproduct -cwlVersion: v1.2 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf4.cwl deleted file mode 100644 index 17a9b80d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf4.cwl +++ /dev/null @@ -1,51 +0,0 @@ -$graph: -- arguments: [-n, foo] - baseCommand: echo - class: CommandLineTool - id: echo - inputs: - echo_in1: - inputBinding: {position: 2} - type: string - echo_in2: - inputBinding: {position: 3} - type: string - first: - inputBinding: {position: 1} - type: string - outputs: - echo_out: - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - stdout: step1_out -- class: Workflow - id: main - inputs: - inp1: - type: - items: - fields: - - {name: instr, type: string} - name: instr - type: record - type: array - inp2: - type: {items: string, type: array} - outputs: - out: - outputSource: step1/echo_out - type: {items: string, type: array} - requirements: - - {class: ScatterFeatureRequirement} - - {class: StepInputExpressionRequirement} - steps: - step1: - in: - echo_in1: {source: inp1, valueFrom: $(self.instr)} - echo_in2: inp2 - first: {source: inp1, valueFrom: '$(self[0].instr)'} - out: [echo_out] - run: '#echo' - scatter: [echo_in1, echo_in2] - scatterMethod: dotproduct -cwlVersion: v1.2 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf5.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf5.cwl deleted file mode 100644 index 1ad6fe42..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf5.cwl +++ /dev/null @@ -1,45 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: inp - type: - items: - fields: - - {name: instr, type: string} - name: instr - type: record - type: array -outputs: -- id: out - outputSource: step1/echo_out - type: {items: string, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: StepInputExpressionRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: echo_in, source: inp, valueFrom: $(self.instr)} - - {id: first, source: inp, valueFrom: $(inputs.echo_in.instr)} - out: [echo_out] - run: - arguments: [-n, foo] - baseCommand: echo - class: CommandLineTool - inputs: - - id: first - inputBinding: {position: 1} - type: string - - id: echo_in - inputBinding: {position: 2} - type: string - outputs: - - id: echo_out - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: step1_out - scatter: echo_in diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf6.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf6.cwl deleted file mode 100644 index 27c1b3b9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-valuefrom-wf6.cwl +++ /dev/null @@ -1,36 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: scattered_messages - type: {items: string, type: array} -outputs: -- id: out_message - outputSource: step1/out_message - type: {items: File, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: StepInputExpressionRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: scattered_message, source: scattered_messages} - - {id: message, valueFrom: Hello} - out: [out_message] - run: - baseCommand: echo - class: CommandLineTool - inputs: - - id: scattered_message - inputBinding: {position: 2} - type: string - - id: message - inputBinding: {position: 1} - type: string - outputs: - - {id: out_message, type: stdout} - requirements: - - {class: InlineJavascriptRequirement} - scatter: [scattered_message] - scatterMethod: dotproduct diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-wf1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-wf1.cwl deleted file mode 100644 index c3b2e9cf..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-wf1.cwl +++ /dev/null @@ -1,34 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: inp - type: {items: string, type: array} -outputs: -- id: out - outputSource: step1/echo_out - type: {items: string, type: array} -requirements: -- {class: ScatterFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: echo_in, source: inp} - out: [echo_out] - run: - arguments: [-n, foo] - baseCommand: echo - class: CommandLineTool - inputs: - - id: echo_in - inputBinding: {} - type: string - outputs: - - id: echo_out - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: step1_out - scatter: echo_in diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-wf2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-wf2.cwl deleted file mode 100644 index df9913cf..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-wf2.cwl +++ /dev/null @@ -1,44 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: inp1 - type: {items: string, type: array} -- id: inp2 - type: {items: string, type: array} -outputs: -- id: out - outputSource: step1/echo_out - type: - items: {items: string, type: array} - type: array -requirements: -- {class: ScatterFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: echo_in1, source: inp1} - - {id: echo_in2, source: inp2} - out: [echo_out] - run: - arguments: [-n, foo] - baseCommand: echo - class: CommandLineTool - id: step1command - inputs: - - id: echo_in1 - inputBinding: {} - type: string - - id: echo_in2 - inputBinding: {} - type: string - outputs: - - id: echo_out - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: step1_out - scatter: [echo_in1, echo_in2] - scatterMethod: nested_crossproduct diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-wf3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-wf3.cwl deleted file mode 100644 index 323fb3b9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-wf3.cwl +++ /dev/null @@ -1,34 +0,0 @@ -$graph: -- arguments: [-n, foo] - baseCommand: echo - class: CommandLineTool - id: echo - inputs: - echo_in1: - inputBinding: {} - type: string - echo_in2: - inputBinding: {} - type: string - outputs: - echo_out: - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - stdout: step1_out -- class: Workflow - id: main - inputs: {inp1: 'string[]', inp2: 'string[]'} - outputs: - out: - outputSource: step1/echo_out - type: {items: string, type: array} - requirements: - - {class: ScatterFeatureRequirement} - steps: - step1: - in: {echo_in1: inp1, echo_in2: inp2} - out: [echo_out] - run: '#echo' - scatter: [echo_in1, echo_in2] - scatterMethod: flat_crossproduct -cwlVersion: v1.2 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-wf4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-wf4.cwl deleted file mode 100644 index 61ba7ba8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_scatter-wf4.cwl +++ /dev/null @@ -1,34 +0,0 @@ -$graph: -- arguments: [-n, foo] - baseCommand: echo - class: CommandLineTool - id: echo - inputs: - echo_in1: - inputBinding: {} - type: string - echo_in2: - inputBinding: {} - type: string - outputs: - echo_out: - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - stdout: step1_out -- class: Workflow - id: main - inputs: {inp1: 'string[]', inp2: 'string[]'} - outputs: - - id: out - outputSource: step1/echo_out - type: {items: string, type: array} - requirements: - - {class: ScatterFeatureRequirement} - steps: - step1: - in: {echo_in1: inp1, echo_in2: inp2} - out: [echo_out] - run: '#echo' - scatter: [echo_in1, echo_in2] - scatterMethod: dotproduct -cwlVersion: v1.2 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_schemadef-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_schemadef-tool.cwl deleted file mode 100644 index 22e1028b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_schemadef-tool.cwl +++ /dev/null @@ -1,19 +0,0 @@ -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: hello - inputBinding: {valueFrom: $(self.a)/$(self.b)} - type: - fields: - - {name: a, type: string} - - {name: b, type: string} - name: user_type_2 - type: record -outputs: -- id: output - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_schemadef-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_schemadef-wf.cwl deleted file mode 100644 index e86a8100..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_schemadef-wf.cwl +++ /dev/null @@ -1,39 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: hello - type: - fields: - - {name: a, type: string} - - {name: b, type: string} - name: user_type_2 - type: record -outputs: -- {id: output, outputSource: step1/output, type: File} -requirements: -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: hello, source: hello} - out: [output] - run: - baseCommand: echo - class: CommandLineTool - inputs: - - id: hello - inputBinding: {valueFrom: $(self.a)/$(self.b)} - type: - fields: - - {name: a, type: string} - - {name: b, type: string} - name: user_type_8 - type: record - outputs: - - id: output - outputBinding: {glob: output.txt} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_schemadef_types_with_import-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_schemadef_types_with_import-wf.cwl deleted file mode 100644 index 44ea1ce9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_schemadef_types_with_import-wf.cwl +++ /dev/null @@ -1,64 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: readgroups_bam - type: - fields: - - {name: bam, type: File} - - name: readgroup_meta_list - type: - items: - fields: - - {name: CN, type: string} - - {name: DT, type: string} - - {name: ID, type: string} - - {name: LB, type: string} - - {name: PI, type: string} - - {name: PL, type: string} - - {name: SM, type: string} - name: readgroup_meta - type: record - type: array - name: readgroups_bam_file - type: record -outputs: -- {id: out, outputSource: step1/out, type: string} -requirements: [] -steps: -- id: step1 - in: - - {id: message, source: readgroups_bam} - out: [out] - run: - baseCommand: echo - class: CommandLineTool - cwlVersion: v1.2 - inputs: - - id: message - inputBinding: {valueFrom: '$(self.readgroup_meta_list[0][''DT''])'} - type: - fields: - - {name: bam, type: File} - - name: readgroup_meta_list - type: - items: - fields: - - {name: CN, type: string} - - {name: DT, type: string} - - {name: ID, type: string} - - {name: LB, type: string} - - {name: PI, type: string} - - {name: PL, type: string} - - {name: SM, type: string} - name: readgroup_meta_23 - type: record - type: array - name: readgroups_bam_file_18 - type: record - outputs: - - id: out - outputBinding: {glob: output.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_search.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_search.cwl deleted file mode 100644 index 3f23c266..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_search.cwl +++ /dev/null @@ -1,69 +0,0 @@ -$graph: -- arguments: - - {position: 1, valueFrom: input.txt} - baseCommand: python - class: CommandLineTool - hints: - - {class: DockerRequirement, dockerPull: python:2-slim} - id: index - inputs: - file: File - index.py: - default: {class: File, location: index.py} - inputBinding: {position: 0} - type: File - secondfile: File - outputs: - result: - outputBinding: {glob: input.txt} - secondaryFiles: [.idx1, ^.idx2, $(self.basename).idx3, '${ return self.basename+".idx4"; - }', '$({"path": self.path+".idx5", "class": "File"})', $(self.nameroot).idx6$(self.nameext), - '${ return [self.basename+".idx7", inputs.secondfile]; }', _idx8] - type: File - requirements: - - class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.file), entryname: input.txt} - - {class: InlineJavascriptRequirement} -- baseCommand: python - class: CommandLineTool - hints: - - {class: DockerRequirement, dockerPull: python:2-slim} - id: search - inputs: - file: - inputBinding: {position: 1} - secondaryFiles: [.idx1, ^.idx2, $(self.basename).idx3, '${ return self.basename+".idx4"; - }', $(self.nameroot).idx6$(self.nameext), '${ return [self.basename+".idx7"]; - }', _idx8] - type: File - search.py: - default: {class: File, location: search.py} - inputBinding: {position: 0} - type: File - term: - inputBinding: {position: 2} - type: string - outputs: - result: - outputBinding: {glob: result.txt} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdout: result.txt -- class: Workflow - id: main - inputs: {infile: File, secondfile: File, term: string} - outputs: - indexedfile: {outputSource: index/result, type: File} - outfile: {outputSource: search/result, type: File} - steps: - index: - in: {file: infile, secondfile: secondfile} - out: [result] - run: '#index' - search: - in: {file: index/result, term: term} - out: [result] - run: '#search' -cwlVersion: v1.2 diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_shellchar.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_shellchar.cwl deleted file mode 100644 index c9a89a9b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_shellchar.cwl +++ /dev/null @@ -1,14 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: foo 1>&2} -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -doc: "Ensure that arguments containing shell directives are not interpreted and\n\ - that `shellQuote: false` has no effect when ShellCommandRequirement is not in\n\ - effect.\n" -inputs: [] -outputs: -- {id: stdout_file, type: stdout} -- {id: stderr_file, type: stderr} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_shellchar2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_shellchar2.cwl deleted file mode 100644 index 057988a6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_shellchar2.cwl +++ /dev/null @@ -1,13 +0,0 @@ -arguments: [foo 1>&2] -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -doc: "Ensure that `shellQuote: true` is the default behavior when\nShellCommandRequirement\ - \ is in effect.\n" -inputs: [] -outputs: -- {id: stdout_file, type: stdout} -- {id: stderr_file, type: stderr} -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_size-expression-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_size-expression-tool.cwl deleted file mode 100644 index 2c78f7fd..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_size-expression-tool.cwl +++ /dev/null @@ -1,20 +0,0 @@ -arguments: -- {valueFrom: "${\n var cmd = [\"echo\"];\n if (inputs.input.length == 0) {\n \ - \ cmd.push('no_inputs');\n }\n else {\n for (var i = 0; i < inputs.input.length;\ - \ i++) {\n var filesize = inputs.input[i].size;\n if (filesize == 0)\ - \ {\n cmd.push(\"empty_file\");\n } else if (filesize <= 16) {\n \ - \ cmd.push(\"small_file\");\n } else {\n cmd.push(\"big_file\"\ - )\n }\n }\n }\n return cmd;\n}\n"} -baseCommand: [] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: input - type: {items: File, type: array} -outputs: -- id: output_file - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_sorttool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_sorttool.cwl deleted file mode 100644 index 3ff4cc38..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_sorttool.cwl +++ /dev/null @@ -1,18 +0,0 @@ -baseCommand: sort -class: CommandLineTool -cwlVersion: v1.2 -doc: Sort lines using the `sort` command -inputs: -- id: reverse - inputBinding: {position: 1, prefix: -r} - type: boolean -- id: input - inputBinding: {position: 2} - type: File -outputs: -- id: output - outputBinding: {glob: output.txt} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage-array-dirs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage-array-dirs.cwl deleted file mode 100644 index 000273cf..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage-array-dirs.cwl +++ /dev/null @@ -1,17 +0,0 @@ -baseCommand: [ls] -class: CommandLineTool -cwlVersion: v1.2 -id: stage_array_dirs -inputs: -- id: input_list - type: {items: Directory, type: array} -label: stage-array-dirs.cwl -outputs: -- id: output - outputBinding: - glob: [testdir/a, rec/B] - type: {items: File, type: array} -requirements: -- class: InitialWorkDirRequirement - listing: [$(inputs.input_list)] -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage-array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage-array.cwl deleted file mode 100644 index 3208d82e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage-array.cwl +++ /dev/null @@ -1,28 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: ls | grep -v lsout} -class: CommandLineTool -cwlVersion: v1.2 -id: stage_array -inputs: -- {id: input_file, type: File} -- id: optional_file - type: ['null', File] -- id: input_list - secondaryFiles: [^.tar] - type: {items: File, type: array} -label: stage-array.cwl -outputs: -- id: output - outputBinding: {glob: lsout} - type: ['null', File] -requirements: -- class: InitialWorkDirRequirement - listing: - - $(inputs.input_file) - - $(inputs.optional_file) - - {entry: $(inputs.input_list)} - - {entry: $(null)} - - {entry: b, entryname: a} -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} -stdout: lsout diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage-unprovided-file.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage-unprovided-file.cwl deleted file mode 100644 index cc429ee0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage-unprovided-file.cwl +++ /dev/null @@ -1,18 +0,0 @@ -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -hints: -- {class: DockerRequirement, dockerPull: python:2-slim} -inputs: -- id: infile - inputBinding: {prefix: -cfg, valueFrom: $(self.basename)} - type: ['null', File] -- default: {class: File, location: args.py} - id: args.py - inputBinding: {position: -1} - type: File -outputs: -- id: args - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage_file_array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage_file_array.cwl deleted file mode 100644 index 024511ca..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage_file_array.cwl +++ /dev/null @@ -1,18 +0,0 @@ -arguments: [ls] -class: CommandLineTool -cwlVersion: v1.2 -id: stage_file_array -inputs: -- id: input_list - secondaryFiles: [.sec] - type: {items: File, type: array} -label: Stage File Array -outputs: -- id: output - outputBinding: {glob: input_dir/*} - type: {items: File, type: array} -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "${ return {class: 'Directory', listing: inputs.input_list} }", entryname: input_dir} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage_file_array_basename.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage_file_array_basename.cwl deleted file mode 100644 index 8f305709..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage_file_array_basename.cwl +++ /dev/null @@ -1,19 +0,0 @@ -arguments: [ls] -class: CommandLineTool -cwlVersion: v1.2 -id: stage_file_array_basename -inputs: -- id: input_list - secondaryFiles: [.sec] - type: {items: File, type: array} -label: Stage File Array (with Directory Basename) -outputs: -- id: output - outputBinding: {glob: input_dir/*} - type: {items: File, type: array} -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "${ return {class: 'Directory', basename: 'input_dir', listing: inputs.input_list}\ - \ }"} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage_file_array_basename_and_entryname.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage_file_array_basename_and_entryname.cwl deleted file mode 100644 index cbae3af6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stage_file_array_basename_and_entryname.cwl +++ /dev/null @@ -1,19 +0,0 @@ -arguments: [ls] -class: CommandLineTool -cwlVersion: v1.2 -id: stage_file_array_basename_and_entryname -inputs: -- id: input_list - secondaryFiles: [.sec] - type: {items: File, type: array} -label: Stage File Array (with Directory Basename AND entryname) -outputs: -- id: output - outputBinding: {glob: input_dir/*} - type: {items: File, type: array} -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "${ return {class: 'Directory', basename: 'not_input_dir', listing: inputs.input_list}\ - \ }", entryname: input_dir} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stagefile.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stagefile.cwl deleted file mode 100644 index 3015d0e0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stagefile.cwl +++ /dev/null @@ -1,18 +0,0 @@ -arguments: [-c, "f = open(\"bob.txt\", \"r+\")\nf.seek(8)\nf.write(\"Bob. \")\n\ - f.close()\n"] -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -hints: -- {class: DockerRequirement, dockerPull: python:2-slim} -inputs: -- {id: infile, type: File} -outputs: -- id: outfile - outputBinding: {glob: bob.txt} - type: File -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.infile), entryname: bob.txt, writable: true} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stderr-mediumcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stderr-mediumcut.cwl deleted file mode 100644 index 068e5e10..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stderr-mediumcut.cwl +++ /dev/null @@ -1,12 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: echo foo 1>&2} -class: CommandLineTool -cwlVersion: v1.2 -doc: Test of capturing stderr output in a docker container. -inputs: [] -outputs: -- {id: output_file, type: stderr} -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} -stderr: std.err diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stderr-shortcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stderr-shortcut.cwl deleted file mode 100644 index 6446a2da..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stderr-shortcut.cwl +++ /dev/null @@ -1,11 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: echo foo 1>&2} -class: CommandLineTool -cwlVersion: v1.2 -doc: Test of capturing stderr output. -inputs: [] -outputs: -- {id: output_file, type: stderr} -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stderr.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stderr.cwl deleted file mode 100644 index 9ecb39c2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stderr.cwl +++ /dev/null @@ -1,14 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: echo foo 1>&2} -class: CommandLineTool -cwlVersion: v1.2 -doc: Test of capturing stderr output. -inputs: [] -outputs: -- id: output_file - outputBinding: {glob: error.txt} - type: File -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} -stderr: error.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stdout_chained_commands.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stdout_chained_commands.cwl deleted file mode 100644 index 20517441..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_stdout_chained_commands.cwl +++ /dev/null @@ -1,16 +0,0 @@ -arguments: -- echo -- a -- {shellQuote: false, valueFrom: '&&'} -- echo -- b -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: out - outputBinding: {glob: out.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string -requirements: -- {class: ShellCommandRequirement} -stdout: out.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom-wf.cwl deleted file mode 100644 index 982eb685..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom-wf.cwl +++ /dev/null @@ -1,46 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: in - type: - fields: - - {name: file1, type: File} - name: in - type: record -outputs: -- {id: count_output, outputSource: step2/output, type: int} -requirements: -- {class: StepInputExpressionRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: file1, source: in, valueFrom: $(self.file1)} - out: [output] - run: - baseCommand: [wc, -l] - class: CommandLineTool - inputs: - - {id: file1, type: File} - outputs: - - id: output - outputBinding: {glob: output} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdin: $(inputs.file1.path) - stdout: output -- id: step2 - in: - - {id: file1, source: step1/output} - out: [output] - run: - class: ExpressionTool - expression: "$({'output': parseInt(inputs.file1.contents)})" - inputs: - - {id: file1, loadContents: true, type: File} - outputs: - - {id: output, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom2-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom2-wf.cwl deleted file mode 100644 index 01cb7d60..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom2-wf.cwl +++ /dev/null @@ -1,34 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: a, type: int} -- {id: b, type: int} -outputs: -- {id: val, outputSource: step1/echo_out, type: string} -requirements: -- {class: StepInputExpressionRequirement} -- {class: InlineJavascriptRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - id: c - source: [a, b] - valueFrom: $(self[0] + self[1]) - out: [echo_out] - run: - baseCommand: echo - class: CommandLineTool - id: echo - inputs: - - id: c - inputBinding: {} - type: int - outputs: - - id: echo_out - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: step1_out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom3-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom3-wf.cwl deleted file mode 100644 index ad1a4bc8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom3-wf.cwl +++ /dev/null @@ -1,33 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: a, type: int} -- {id: b, type: int} -outputs: -- {id: val, outputSource: step1/echo_out, type: string} -requirements: -- {class: StepInputExpressionRequirement} -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: a, source: a} - - {id: b, source: b} - - {id: c, valueFrom: $(inputs.a + inputs.b)} - out: [echo_out] - run: - baseCommand: echo - class: CommandLineTool - id: echo - inputs: - - id: c - inputBinding: {} - type: int - outputs: - - id: echo_out - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: step1_out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom4-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom4-wf.cwl deleted file mode 100644 index 5abbf3d3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom4-wf.cwl +++ /dev/null @@ -1,29 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: val, outputSource: step1/echo_out, type: string} -requirements: -- {class: StepInputExpressionRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: a, valueFrom: moocow} - out: [echo_out] - run: - baseCommand: echo - class: CommandLineTool - id: echo - inputs: - - id: a - inputBinding: {} - type: string - outputs: - - id: echo_out - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: step1_out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom5-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom5-wf.cwl deleted file mode 100644 index 5af6c11a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_step-valuefrom5-wf.cwl +++ /dev/null @@ -1,51 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- {id: val1, outputSource: step1/echo_out, type: string} -- {id: val2, outputSource: step2/echo_out, type: string} -requirements: -- {class: StepInputExpressionRequirement} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: - - {id: name, source: file1, valueFrom: $(self.basename)} - out: [echo_out, echo_out_file] - run: - baseCommand: echo - class: CommandLineTool - inputs: - - id: name - inputBinding: {} - type: string - outputs: - - id: echo_out - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - - id: echo_out_file - outputBinding: {glob: step1_out} - type: File - requirements: - - {class: InlineJavascriptRequirement} - stdout: step1_out -- id: step2 - in: - - {id: name, source: step1/echo_out_file, valueFrom: $(self.basename)} - out: [echo_out] - run: - baseCommand: echo - class: CommandLineTool - inputs: - - id: name - inputBinding: {} - type: string - outputs: - - id: echo_out - outputBinding: {glob: step1_out, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: step1_out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_steplevel-resreq.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_steplevel-resreq.cwl deleted file mode 100644 index ece59dd0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_steplevel-resreq.cwl +++ /dev/null @@ -1,25 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: out, outputSource: step1/output, type: File} -requirements: -- {class: ResourceRequirement, coresMax: 4, coresMin: 4} -- {class: SubworkflowFeatureRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: step1 - in: [] - out: [output] - requirements: - ResourceRequirement: {coresMax: 1, coresMin: 1} - run: - arguments: [$(runtime.cores)] - baseCommand: echo - class: CommandLineTool - inputs: [] - outputs: - - {id: output, type: stdout} - requirements: - - {class: InlineJavascriptRequirement} - stdout: cores.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_storage_float.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_storage_float.cwl deleted file mode 100644 index 6850fca5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_storage_float.cwl +++ /dev/null @@ -1,12 +0,0 @@ -arguments: [$(runtime.ram), $(runtime.tmpdirSize), $(runtime.outdirSize)] -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- {id: output, type: stdout} -requirements: -- {class: ResourceRequirement, outdirMax: 256.9, outdirMin: 256.1, ramMax: 254.9, - ramMin: 254.1, tmpdirMax: 255.9, tmpdirMin: 255.1} -- {class: InlineJavascriptRequirement} -stdout: values.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_sum-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_sum-wf-noET.cwl deleted file mode 100644 index 981f024d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_sum-wf-noET.cwl +++ /dev/null @@ -1,34 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: int_1 - type: [int, string] -- id: int_2 - type: [int, string] -outputs: -- {id: result, outputSource: sum/result, type: File} -requirements: -- {class: StepInputExpressionRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: sum - in: - - id: data - source: [int_1, int_2] - valueFrom: "${\n var sum = 0;\n for (var i = 0; i < self.length; i++){\n \ - \ sum += self[i];\n };\n return sum;\n}\n" - out: [result] - run: - baseCommand: echo - class: CommandLineTool - inputs: - - id: data - inputBinding: {} - type: int - outputs: - - {id: result, type: stdout} - requirements: - - {class: InlineJavascriptRequirement} - stdout: result.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_sum-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_sum-wf.cwl deleted file mode 100644 index 1dc35d8a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_sum-wf.cwl +++ /dev/null @@ -1,31 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: int_1 - type: [int, string] -- id: int_2 - type: [int, string] -outputs: -- {id: result, outputSource: sum/result, type: int} -requirements: -- {class: StepInputExpressionRequirement} -- {class: MultipleInputFeatureRequirement} -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: sum - in: - - id: data - source: [int_1, int_2] - valueFrom: "${\n var sum = 0;\n for (var i = 0; i < self.length; i++){\n \ - \ sum += self[i];\n };\n return sum;\n}\n" - out: [result] - run: - class: ExpressionTool - expression: "${\n return {\"result\": inputs.data};\n}\n" - inputs: - - {id: data, type: int} - outputs: - - {id: result, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_symlink-illegal.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_symlink-illegal.cwl deleted file mode 100644 index 13bc146f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_symlink-illegal.cwl +++ /dev/null @@ -1,23 +0,0 @@ -arguments: -- echo -- Who's gonna drive you home -- {shellQuote: false, valueFrom: '> /tmp/original.txt'} -- {shellQuote: false, valueFrom: ' && '} -- ln -- -s -- /tmp/original.txt -- symlink.txt -class: CommandLineTool -cwlVersion: v1.2 -doc: Create a file under /tmp, symlink it to working directory and glob symlink. The - executor should NOT resolve this symlink -hints: - DockerRequirement: {dockerPull: alpine} -inputs: [] -outputs: -- id: output_file - outputBinding: {glob: symlink.txt} - type: File -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_symlink-legal.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_symlink-legal.cwl deleted file mode 100644 index 2c224943..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_symlink-legal.cwl +++ /dev/null @@ -1,26 +0,0 @@ -arguments: -- mkdir -- adir -- {shellQuote: false, valueFrom: ' && '} -- echo -- Who's gonna drive you home -- {shellQuote: false, valueFrom: '> adir/original.txt'} -- {shellQuote: false, valueFrom: ' && '} -- ln -- -s -- adir/original.txt -- symlink.txt -class: CommandLineTool -cwlVersion: v1.2 -doc: Create a file under adir/, symlink it to working directory (./) and glob symlink. - The executor should resolve this symlink -hints: - DockerRequirement: {dockerPull: alpine} -inputs: [] -outputs: -- id: output_file - outputBinding: {glob: symlink.txt} - type: File -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_synth-file.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_synth-file.cwl deleted file mode 100644 index 4aa8468f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_synth-file.cwl +++ /dev/null @@ -1,10 +0,0 @@ -baseCommand: [cat] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: names - inputBinding: {position: 1} - type: File -outputs: -- {id: sequence, type: stdout} -requirements: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_template-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_template-tool.cwl deleted file mode 100644 index abe87eef..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_template-tool.cwl +++ /dev/null @@ -1,646 +0,0 @@ -baseCommand: [cat, foo.txt] -class: CommandLineTool -cwlVersion: v1.2 -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: -- {id: file1, type: File} -outputs: -- id: foo - outputBinding: {glob: foo.txt} - type: File -requirements: -- class: InlineJavascriptRequirement - expressionLib: ["// Underscore.js 1.7.0\n// http://underscorejs.org\n//\ - \ (c) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters\ - \ & Editors\n// Underscore may be freely distributed under the MIT license.\n\ - \n(function() {\n\n // Baseline setup\n // --------------\n\n // Establish\ - \ the root object, `window` in the browser, or `exports` on the server.\n var\ - \ root = this;\n\n // Save the previous value of the `_` variable.\n //var\ - \ previousUnderscore = root._;\n\n // Save bytes in the minified (but not gzipped)\ - \ version:\n var ArrayProto = Array.prototype, ObjProto = Object.prototype,\ - \ FuncProto = Function.prototype;\n\n // Create quick reference variables for\ - \ speed access to core prototypes.\n var\n push = ArrayProto.push,\n\ - \ slice = ArrayProto.slice,\n concat = ArrayProto.concat,\n\ - \ toString = ObjProto.toString,\n hasOwnProperty = ObjProto.hasOwnProperty;\n\ - \n // All **ECMAScript 5** native function implementations that we hope to\ - \ use\n // are declared here.\n var\n nativeIsArray = Array.isArray,\n\ - \ nativeKeys = Object.keys,\n nativeBind = FuncProto.bind;\n\ - \n // Create a safe reference to the Underscore object for use below.\n var\ - \ _ = function(obj) {\n if (obj instanceof _) return obj;\n if (!(this\ - \ instanceof _)) return new _(obj);\n this._wrapped = obj;\n };\n\n //\ - \ Export the Underscore object for **Node.js**, with\n // backwards-compatibility\ - \ for the old `require()` API. If we're in\n // the browser, add `_` as a global\ - \ object.\n if (typeof exports !== 'undefined') {\n if (typeof module !==\ - \ 'undefined' && module.exports) {\n exports = module.exports = _;\n \ - \ }\n exports._ = _;\n } else {\n root._ = _;\n }\n\n // Current version.\n\ - \ _.VERSION = '1.7.0';\n\n // Internal function that returns an efficient\ - \ (for current engines) version\n // of the passed-in callback, to be repeatedly\ - \ applied in other Underscore\n // functions.\n var createCallback = function(func,\ - \ context, argCount) {\n if (context === void 0) return func;\n switch\ - \ (argCount == null ? 3 : argCount) {\n case 1: return function(value)\ - \ {\n return func.call(context, value);\n };\n case 2: return\ - \ function(value, other) {\n return func.call(context, value, other);\n\ - \ };\n case 3: return function(value, index, collection) {\n \ - \ return func.call(context, value, index, collection);\n };\n case\ - \ 4: return function(accumulator, value, index, collection) {\n return\ - \ func.call(context, accumulator, value, index, collection);\n };\n \ - \ }\n return function() {\n return func.apply(context, arguments);\n\ - \ };\n };\n\n // A mostly-internal function to generate callbacks that\ - \ can be applied\n // to each element in a collection, returning the desired\ - \ result — either\n // identity, an arbitrary callback, a property matcher,\ - \ or a property accessor.\n _.iteratee = function(value, context, argCount)\ - \ {\n if (value == null) return _.identity;\n if (_.isFunction(value))\ - \ return createCallback(value, context, argCount);\n if (_.isObject(value))\ - \ return _.matches(value);\n return _.property(value);\n };\n\n // Collection\ - \ Functions\n // --------------------\n\n // The cornerstone, an `each` implementation,\ - \ aka `forEach`.\n // Handles raw objects in addition to array-likes. Treats\ - \ all\n // sparse array-likes as if they were dense.\n _.each = _.forEach\ - \ = function(obj, iteratee, context) {\n if (obj == null) return obj;\n \ - \ iteratee = createCallback(iteratee, context);\n var i, length = obj.length;\n\ - \ if (length === +length) {\n for (i = 0; i < length; i++) {\n \ - \ iteratee(obj[i], i, obj);\n }\n } else {\n var keys = _.keys(obj);\n\ - \ for (i = 0, length = keys.length; i < length; i++) {\n iteratee(obj[keys[i]],\ - \ keys[i], obj);\n }\n }\n return obj;\n };\n\n // Return the results\ - \ of applying the iteratee to each element.\n _.map = _.collect = function(obj,\ - \ iteratee, context) {\n if (obj == null) return [];\n iteratee = _.iteratee(iteratee,\ - \ context);\n var keys = obj.length !== +obj.length && _.keys(obj),\n \ - \ length = (keys || obj).length,\n results = Array(length),\n \ - \ currentKey;\n for (var index = 0; index < length; index++) {\n \ - \ currentKey = keys ? keys[index] : index;\n results[index] = iteratee(obj[currentKey],\ - \ currentKey, obj);\n }\n return results;\n };\n\n var reduceError =\ - \ 'Reduce of empty array with no initial value';\n\n // **Reduce** builds up\ - \ a single result from a list of values, aka `inject`,\n // or `foldl`.\n \ - \ _.reduce = _.foldl = _.inject = function(obj, iteratee, memo, context) {\n\ - \ if (obj == null) obj = [];\n iteratee = createCallback(iteratee, context,\ - \ 4);\n var keys = obj.length !== +obj.length && _.keys(obj),\n length\ - \ = (keys || obj).length,\n index = 0, currentKey;\n if (arguments.length\ - \ < 3) {\n if (!length) throw new TypeError(reduceError);\n memo =\ - \ obj[keys ? keys[index++] : index++];\n }\n for (; index < length; index++)\ - \ {\n currentKey = keys ? keys[index] : index;\n memo = iteratee(memo,\ - \ obj[currentKey], currentKey, obj);\n }\n return memo;\n };\n\n //\ - \ The right-associative version of reduce, also known as `foldr`.\n _.reduceRight\ - \ = _.foldr = function(obj, iteratee, memo, context) {\n if (obj == null)\ - \ obj = [];\n iteratee = createCallback(iteratee, context, 4);\n var keys\ - \ = obj.length !== + obj.length && _.keys(obj),\n index = (keys || obj).length,\n\ - \ currentKey;\n if (arguments.length < 3) {\n if (!index) throw\ - \ new TypeError(reduceError);\n memo = obj[keys ? keys[--index] : --index];\n\ - \ }\n while (index--) {\n currentKey = keys ? keys[index] : index;\n\ - \ memo = iteratee(memo, obj[currentKey], currentKey, obj);\n }\n \ - \ return memo;\n };\n\n // Return the first value which passes a truth test.\ - \ Aliased as `detect`.\n _.find = _.detect = function(obj, predicate, context)\ - \ {\n var result;\n predicate = _.iteratee(predicate, context);\n _.some(obj,\ - \ function(value, index, list) {\n if (predicate(value, index, list)) {\n\ - \ result = value;\n return true;\n }\n });\n return\ - \ result;\n };\n\n // Return all the elements that pass a truth test.\n //\ - \ Aliased as `select`.\n _.filter = _.select = function(obj, predicate, context)\ - \ {\n var results = [];\n if (obj == null) return results;\n predicate\ - \ = _.iteratee(predicate, context);\n _.each(obj, function(value, index,\ - \ list) {\n if (predicate(value, index, list)) results.push(value);\n \ - \ });\n return results;\n };\n\n // Return all the elements for which\ - \ a truth test fails.\n _.reject = function(obj, predicate, context) {\n \ - \ return _.filter(obj, _.negate(_.iteratee(predicate)), context);\n };\n\n\ - \ // Determine whether all of the elements match a truth test.\n // Aliased\ - \ as `all`.\n _.every = _.all = function(obj, predicate, context) {\n if\ - \ (obj == null) return true;\n predicate = _.iteratee(predicate, context);\n\ - \ var keys = obj.length !== +obj.length && _.keys(obj),\n length =\ - \ (keys || obj).length,\n index, currentKey;\n for (index = 0; index\ - \ < length; index++) {\n currentKey = keys ? keys[index] : index;\n \ - \ if (!predicate(obj[currentKey], currentKey, obj)) return false;\n }\n\ - \ return true;\n };\n\n // Determine if at least one element in the object\ - \ matches a truth test.\n // Aliased as `any`.\n _.some = _.any = function(obj,\ - \ predicate, context) {\n if (obj == null) return false;\n predicate =\ - \ _.iteratee(predicate, context);\n var keys = obj.length !== +obj.length\ - \ && _.keys(obj),\n length = (keys || obj).length,\n index, currentKey;\n\ - \ for (index = 0; index < length; index++) {\n currentKey = keys ? keys[index]\ - \ : index;\n if (predicate(obj[currentKey], currentKey, obj)) return true;\n\ - \ }\n return false;\n };\n\n // Determine if the array or object contains\ - \ a given value (using `===`).\n // Aliased as `include`.\n _.contains = _.include\ - \ = function(obj, target) {\n if (obj == null) return false;\n if (obj.length\ - \ !== +obj.length) obj = _.values(obj);\n return _.indexOf(obj, target) >=\ - \ 0;\n };\n\n // Invoke a method (with arguments) on every item in a collection.\n\ - \ _.invoke = function(obj, method) {\n var args = slice.call(arguments,\ - \ 2);\n var isFunc = _.isFunction(method);\n return _.map(obj, function(value)\ - \ {\n return (isFunc ? method : value[method]).apply(value, args);\n \ - \ });\n };\n\n // Convenience version of a common use case of `map`: fetching\ - \ a property.\n _.pluck = function(obj, key) {\n return _.map(obj, _.property(key));\n\ - \ };\n\n // Convenience version of a common use case of `filter`: selecting\ - \ only objects\n // containing specific `key:value` pairs.\n _.where = function(obj,\ - \ attrs) {\n return _.filter(obj, _.matches(attrs));\n };\n\n // Convenience\ - \ version of a common use case of `find`: getting the first object\n // containing\ - \ specific `key:value` pairs.\n _.findWhere = function(obj, attrs) {\n return\ - \ _.find(obj, _.matches(attrs));\n };\n\n // Return the maximum element (or\ - \ element-based computation).\n _.max = function(obj, iteratee, context) {\n\ - \ var result = -Infinity, lastComputed = -Infinity,\n value, computed;\n\ - \ if (iteratee == null && obj != null) {\n obj = obj.length === +obj.length\ - \ ? obj : _.values(obj);\n for (var i = 0, length = obj.length; i < length;\ - \ i++) {\n value = obj[i];\n if (value > result) {\n \ - \ result = value;\n }\n }\n } else {\n iteratee = _.iteratee(iteratee,\ - \ context);\n _.each(obj, function(value, index, list) {\n computed\ - \ = iteratee(value, index, list);\n if (computed > lastComputed || computed\ - \ === -Infinity && result === -Infinity) {\n result = value;\n \ - \ lastComputed = computed;\n }\n });\n }\n return result;\n\ - \ };\n\n // Return the minimum element (or element-based computation).\n \ - \ _.min = function(obj, iteratee, context) {\n var result = Infinity, lastComputed\ - \ = Infinity,\n value, computed;\n if (iteratee == null && obj !=\ - \ null) {\n obj = obj.length === +obj.length ? obj : _.values(obj);\n \ - \ for (var i = 0, length = obj.length; i < length; i++) {\n value\ - \ = obj[i];\n if (value < result) {\n result = value;\n \ - \ }\n }\n } else {\n iteratee = _.iteratee(iteratee, context);\n\ - \ _.each(obj, function(value, index, list) {\n computed = iteratee(value,\ - \ index, list);\n if (computed < lastComputed || computed === Infinity\ - \ && result === Infinity) {\n result = value;\n lastComputed\ - \ = computed;\n }\n });\n }\n return result;\n };\n\n //\ - \ Shuffle a collection, using the modern version of the\n // [Fisher-Yates\ - \ shuffle](http://en.wikipedia.org/wiki/Fisher–Yates_shuffle).\n _.shuffle\ - \ = function(obj) {\n var set = obj && obj.length === +obj.length ? obj :\ - \ _.values(obj);\n var length = set.length;\n var shuffled = Array(length);\n\ - \ for (var index = 0, rand; index < length; index++) {\n rand = _.random(0,\ - \ index);\n if (rand !== index) shuffled[index] = shuffled[rand];\n \ - \ shuffled[rand] = set[index];\n }\n return shuffled;\n };\n\n //\ - \ Sample **n** random values from a collection.\n // If **n** is not specified,\ - \ returns a single random element.\n // The internal `guard` argument allows\ - \ it to work with `map`.\n _.sample = function(obj, n, guard) {\n if (n\ - \ == null || guard) {\n if (obj.length !== +obj.length) obj = _.values(obj);\n\ - \ return obj[_.random(obj.length - 1)];\n }\n return _.shuffle(obj).slice(0,\ - \ Math.max(0, n));\n };\n\n // Sort the object's values by a criterion produced\ - \ by an iteratee.\n _.sortBy = function(obj, iteratee, context) {\n iteratee\ - \ = _.iteratee(iteratee, context);\n return _.pluck(_.map(obj, function(value,\ - \ index, list) {\n return {\n value: value,\n index: index,\n\ - \ criteria: iteratee(value, index, list)\n };\n }).sort(function(left,\ - \ right) {\n var a = left.criteria;\n var b = right.criteria;\n \ - \ if (a !== b) {\n if (a > b || a === void 0) return 1;\n if\ - \ (a < b || b === void 0) return -1;\n }\n return left.index - right.index;\n\ - \ }), 'value');\n };\n\n // An internal function used for aggregate \"\ - group by\" operations.\n var group = function(behavior) {\n return function(obj,\ - \ iteratee, context) {\n var result = {};\n iteratee = _.iteratee(iteratee,\ - \ context);\n _.each(obj, function(value, index) {\n var key = iteratee(value,\ - \ index, obj);\n behavior(result, value, key);\n });\n return\ - \ result;\n };\n };\n\n // Groups the object's values by a criterion. Pass\ - \ either a string attribute\n // to group by, or a function that returns the\ - \ criterion.\n _.groupBy = group(function(result, value, key) {\n if (_.has(result,\ - \ key)) result[key].push(value); else result[key] = [value];\n });\n\n //\ - \ Indexes the object's values by a criterion, similar to `groupBy`, but for\n\ - \ // when you know that your index values will be unique.\n _.indexBy = group(function(result,\ - \ value, key) {\n result[key] = value;\n });\n\n // Counts instances of\ - \ an object that group by a certain criterion. Pass\n // either a string attribute\ - \ to count by, or a function that returns the\n // criterion.\n _.countBy\ - \ = group(function(result, value, key) {\n if (_.has(result, key)) result[key]++;\ - \ else result[key] = 1;\n });\n\n // Use a comparator function to figure out\ - \ the smallest index at which\n // an object should be inserted so as to maintain\ - \ order. Uses binary search.\n _.sortedIndex = function(array, obj, iteratee,\ - \ context) {\n iteratee = _.iteratee(iteratee, context, 1);\n var value\ - \ = iteratee(obj);\n var low = 0, high = array.length;\n while (low <\ - \ high) {\n var mid = low + high >>> 1;\n if (iteratee(array[mid])\ - \ < value) low = mid + 1; else high = mid;\n }\n return low;\n };\n\n\ - \ // Safely create a real, live array from anything iterable.\n _.toArray\ - \ = function(obj) {\n if (!obj) return [];\n if (_.isArray(obj)) return\ - \ slice.call(obj);\n if (obj.length === +obj.length) return _.map(obj, _.identity);\n\ - \ return _.values(obj);\n };\n\n // Return the number of elements in an\ - \ object.\n _.size = function(obj) {\n if (obj == null) return 0;\n return\ - \ obj.length === +obj.length ? obj.length : _.keys(obj).length;\n };\n\n //\ - \ Split a collection into two arrays: one whose elements all satisfy the given\n\ - \ // predicate, and one whose elements all do not satisfy the predicate.\n\ - \ _.partition = function(obj, predicate, context) {\n predicate = _.iteratee(predicate,\ - \ context);\n var pass = [], fail = [];\n _.each(obj, function(value,\ - \ key, obj) {\n (predicate(value, key, obj) ? pass : fail).push(value);\n\ - \ });\n return [pass, fail];\n };\n\n // Array Functions\n // ---------------\n\ - \n // Get the first element of an array. Passing **n** will return the first\ - \ N\n // values in the array. Aliased as `head` and `take`. The **guard** check\n\ - \ // allows it to work with `_.map`.\n _.first = _.head = _.take = function(array,\ - \ n, guard) {\n if (array == null) return void 0;\n if (n == null || guard)\ - \ return array[0];\n if (n < 0) return [];\n return slice.call(array,\ - \ 0, n);\n };\n\n // Returns everything but the last entry of the array. Especially\ - \ useful on\n // the arguments object. Passing **n** will return all the values\ - \ in\n // the array, excluding the last N. The **guard** check allows it to\ - \ work with\n // `_.map`.\n _.initial = function(array, n, guard) {\n return\ - \ slice.call(array, 0, Math.max(0, array.length - (n == null || guard ? 1 :\ - \ n)));\n };\n\n // Get the last element of an array. Passing **n** will return\ - \ the last N\n // values in the array. The **guard** check allows it to work\ - \ with `_.map`.\n _.last = function(array, n, guard) {\n if (array == null)\ - \ return void 0;\n if (n == null || guard) return array[array.length - 1];\n\ - \ return slice.call(array, Math.max(array.length - n, 0));\n };\n\n //\ - \ Returns everything but the first entry of the array. Aliased as `tail` and\ - \ `drop`.\n // Especially useful on the arguments object. Passing an **n**\ - \ will return\n // the rest N values in the array. The **guard**\n // check\ - \ allows it to work with `_.map`.\n _.rest = _.tail = _.drop = function(array,\ - \ n, guard) {\n return slice.call(array, n == null || guard ? 1 : n);\n \ - \ };\n\n // Trim out all falsy values from an array.\n _.compact = function(array)\ - \ {\n return _.filter(array, _.identity);\n };\n\n // Internal implementation\ - \ of a recursive `flatten` function.\n var flatten = function(input, shallow,\ - \ strict, output) {\n if (shallow && _.every(input, _.isArray)) {\n \ - \ return concat.apply(output, input);\n }\n for (var i = 0, length = input.length;\ - \ i < length; i++) {\n var value = input[i];\n if (!_.isArray(value)\ - \ && !_.isArguments(value)) {\n if (!strict) output.push(value);\n \ - \ } else if (shallow) {\n push.apply(output, value);\n } else\ - \ {\n flatten(value, shallow, strict, output);\n }\n }\n return\ - \ output;\n };\n\n // Flatten out an array, either recursively (by default),\ - \ or just one level.\n _.flatten = function(array, shallow) {\n return flatten(array,\ - \ shallow, false, []);\n };\n\n // Return a version of the array that does\ - \ not contain the specified value(s).\n _.without = function(array) {\n \ - \ return _.difference(array, slice.call(arguments, 1));\n };\n\n // Produce\ - \ a duplicate-free version of the array. If the array has already\n // been\ - \ sorted, you have the option of using a faster algorithm.\n // Aliased as\ - \ `unique`.\n _.uniq = _.unique = function(array, isSorted, iteratee, context)\ - \ {\n if (array == null) return [];\n if (!_.isBoolean(isSorted)) {\n\ - \ context = iteratee;\n iteratee = isSorted;\n isSorted = false;\n\ - \ }\n if (iteratee != null) iteratee = _.iteratee(iteratee, context);\n\ - \ var result = [];\n var seen = [];\n for (var i = 0, length = array.length;\ - \ i < length; i++) {\n var value = array[i];\n if (isSorted) {\n \ - \ if (!i || seen !== value) result.push(value);\n seen = value;\n\ - \ } else if (iteratee) {\n var computed = iteratee(value, i, array);\n\ - \ if (_.indexOf(seen, computed) < 0) {\n seen.push(computed);\n\ - \ result.push(value);\n }\n } else if (_.indexOf(result,\ - \ value) < 0) {\n result.push(value);\n }\n }\n return result;\n\ - \ };\n\n // Produce an array that contains the union: each distinct element\ - \ from all of\n // the passed-in arrays.\n _.union = function() {\n return\ - \ _.uniq(flatten(arguments, true, true, []));\n };\n\n // Produce an array\ - \ that contains every item shared between all the\n // passed-in arrays.\n\ - \ _.intersection = function(array) {\n if (array == null) return [];\n \ - \ var result = [];\n var argsLength = arguments.length;\n for (var i\ - \ = 0, length = array.length; i < length; i++) {\n var item = array[i];\n\ - \ if (_.contains(result, item)) continue;\n for (var j = 1; j < argsLength;\ - \ j++) {\n if (!_.contains(arguments[j], item)) break;\n }\n \ - \ if (j === argsLength) result.push(item);\n }\n return result;\n };\n\ - \n // Take the difference between one array and a number of other arrays.\n\ - \ // Only the elements present in just the first array will remain.\n _.difference\ - \ = function(array) {\n var rest = flatten(slice.call(arguments, 1), true,\ - \ true, []);\n return _.filter(array, function(value){\n return !_.contains(rest,\ - \ value);\n });\n };\n\n // Zip together multiple lists into a single array\ - \ -- elements that share\n // an index go together.\n _.zip = function(array)\ - \ {\n if (array == null) return [];\n var length = _.max(arguments, 'length').length;\n\ - \ var results = Array(length);\n for (var i = 0; i < length; i++) {\n\ - \ results[i] = _.pluck(arguments, i);\n }\n return results;\n };\n\ - \n // Converts lists into objects. Pass either a single array of `[key, value]`\n\ - \ // pairs, or two parallel arrays of the same length -- one of keys, and one\ - \ of\n // the corresponding values.\n _.object = function(list, values) {\n\ - \ if (list == null) return {};\n var result = {};\n for (var i = 0,\ - \ length = list.length; i < length; i++) {\n if (values) {\n result[list[i]]\ - \ = values[i];\n } else {\n result[list[i][0]] = list[i][1];\n \ - \ }\n }\n return result;\n };\n\n // Return the position of the\ - \ first occurrence of an item in an array,\n // or -1 if the item is not included\ - \ in the array.\n // If the array is large and already in sort order, pass\ - \ `true`\n // for **isSorted** to use binary search.\n _.indexOf = function(array,\ - \ item, isSorted) {\n if (array == null) return -1;\n var i = 0, length\ - \ = array.length;\n if (isSorted) {\n if (typeof isSorted == 'number')\ - \ {\n i = isSorted < 0 ? Math.max(0, length + isSorted) : isSorted;\n\ - \ } else {\n i = _.sortedIndex(array, item);\n return array[i]\ - \ === item ? i : -1;\n }\n }\n for (; i < length; i++) if (array[i]\ - \ === item) return i;\n return -1;\n };\n\n _.lastIndexOf = function(array,\ - \ item, from) {\n if (array == null) return -1;\n var idx = array.length;\n\ - \ if (typeof from == 'number') {\n idx = from < 0 ? idx + from + 1 :\ - \ Math.min(idx, from + 1);\n }\n while (--idx >= 0) if (array[idx] ===\ - \ item) return idx;\n return -1;\n };\n\n // Generate an integer Array\ - \ containing an arithmetic progression. A port of\n // the native Python `range()`\ - \ function. See\n // [the Python documentation](http://docs.python.org/library/functions.html#range).\n\ - \ _.range = function(start, stop, step) {\n if (arguments.length <= 1) {\n\ - \ stop = start || 0;\n start = 0;\n }\n step = step || 1;\n\n\ - \ var length = Math.max(Math.ceil((stop - start) / step), 0);\n var range\ - \ = Array(length);\n\n for (var idx = 0; idx < length; idx++, start += step)\ - \ {\n range[idx] = start;\n }\n\n return range;\n };\n\n // Function\ - \ (ahem) Functions\n // ------------------\n\n // Reusable constructor function\ - \ for prototype setting.\n var Ctor = function(){};\n\n // Create a function\ - \ bound to a given object (assigning `this`, and arguments,\n // optionally).\ - \ Delegates to **ECMAScript 5**'s native `Function.bind` if\n // available.\n\ - \ _.bind = function(func, context) {\n var args, bound;\n if (nativeBind\ - \ && func.bind === nativeBind) return nativeBind.apply(func, slice.call(arguments,\ - \ 1));\n if (!_.isFunction(func)) throw new TypeError('Bind must be called\ - \ on a function');\n args = slice.call(arguments, 2);\n bound = function()\ - \ {\n if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments)));\n\ - \ Ctor.prototype = func.prototype;\n var self = new Ctor;\n Ctor.prototype\ - \ = null;\n var result = func.apply(self, args.concat(slice.call(arguments)));\n\ - \ if (_.isObject(result)) return result;\n return self;\n };\n\ - \ return bound;\n };\n\n // Partially apply a function by creating a version\ - \ that has had some of its\n // arguments pre-filled, without changing its\ - \ dynamic `this` context. _ acts\n // as a placeholder, allowing any combination\ - \ of arguments to be pre-filled.\n _.partial = function(func) {\n var boundArgs\ - \ = slice.call(arguments, 1);\n return function() {\n var position =\ - \ 0;\n var args = boundArgs.slice();\n for (var i = 0, length = args.length;\ - \ i < length; i++) {\n if (args[i] === _) args[i] = arguments[position++];\n\ - \ }\n while (position < arguments.length) args.push(arguments[position++]);\n\ - \ return func.apply(this, args);\n };\n };\n\n // Bind a number of\ - \ an object's methods to that object. Remaining arguments\n // are the method\ - \ names to be bound. Useful for ensuring that all callbacks\n // defined on\ - \ an object belong to it.\n _.bindAll = function(obj) {\n var i, length\ - \ = arguments.length, key;\n if (length <= 1) throw new Error('bindAll must\ - \ be passed function names');\n for (i = 1; i < length; i++) {\n key\ - \ = arguments[i];\n obj[key] = _.bind(obj[key], obj);\n }\n return\ - \ obj;\n };\n\n // Memoize an expensive function by storing its results.\n\ - \ _.memoize = function(func, hasher) {\n var memoize = function(key) {\n\ - \ var cache = memoize.cache;\n var address = hasher ? hasher.apply(this,\ - \ arguments) : key;\n if (!_.has(cache, address)) cache[address] = func.apply(this,\ - \ arguments);\n return cache[address];\n };\n memoize.cache = {};\n\ - \ return memoize;\n };\n\n // Delays a function for the given number of\ - \ milliseconds, and then calls\n // it with the arguments supplied.\n _.delay\ - \ = function(func, wait) {\n var args = slice.call(arguments, 2);\n return\ - \ setTimeout(function(){\n return func.apply(null, args);\n }, wait);\n\ - \ };\n\n // Defers a function, scheduling it to run after the current call\ - \ stack has\n // cleared.\n _.defer = function(func) {\n return _.delay.apply(_,\ - \ [func, 1].concat(slice.call(arguments, 1)));\n };\n\n // Returns a function,\ - \ that, when invoked, will only be triggered at most once\n // during a given\ - \ window of time. Normally, the throttled function will run\n // as much as\ - \ it can, without ever going more than once per `wait` duration;\n // but if\ - \ you'd like to disable the execution on the leading edge, pass\n // `{leading:\ - \ false}`. To disable execution on the trailing edge, ditto.\n _.throttle =\ - \ function(func, wait, options) {\n var context, args, result;\n var timeout\ - \ = null;\n var previous = 0;\n if (!options) options = {};\n var later\ - \ = function() {\n previous = options.leading === false ? 0 : _.now();\n\ - \ timeout = null;\n result = func.apply(context, args);\n if\ - \ (!timeout) context = args = null;\n };\n return function() {\n \ - \ var now = _.now();\n if (!previous && options.leading === false) previous\ - \ = now;\n var remaining = wait - (now - previous);\n context = this;\n\ - \ args = arguments;\n if (remaining <= 0 || remaining > wait) {\n\ - \ clearTimeout(timeout);\n timeout = null;\n previous =\ - \ now;\n result = func.apply(context, args);\n if (!timeout) context\ - \ = args = null;\n } else if (!timeout && options.trailing !== false) {\n\ - \ timeout = setTimeout(later, remaining);\n }\n return result;\n\ - \ };\n };\n\n // Returns a function, that, as long as it continues to be\ - \ invoked, will not\n // be triggered. The function will be called after it\ - \ stops being called for\n // N milliseconds. If `immediate` is passed, trigger\ - \ the function on the\n // leading edge, instead of the trailing.\n _.debounce\ - \ = function(func, wait, immediate) {\n var timeout, args, context, timestamp,\ - \ result;\n\n var later = function() {\n var last = _.now() - timestamp;\n\ - \n if (last < wait && last > 0) {\n timeout = setTimeout(later,\ - \ wait - last);\n } else {\n timeout = null;\n if (!immediate)\ - \ {\n result = func.apply(context, args);\n if (!timeout)\ - \ context = args = null;\n }\n }\n };\n\n return function()\ - \ {\n context = this;\n args = arguments;\n timestamp = _.now();\n\ - \ var callNow = immediate && !timeout;\n if (!timeout) timeout = setTimeout(later,\ - \ wait);\n if (callNow) {\n result = func.apply(context, args);\n\ - \ context = args = null;\n }\n\n return result;\n };\n \ - \ };\n\n // Returns the first function passed as an argument to the second,\n\ - \ // allowing you to adjust arguments, run code before and after, and\n //\ - \ conditionally execute the original function.\n _.wrap = function(func, wrapper)\ - \ {\n return _.partial(wrapper, func);\n };\n\n // Returns a negated version\ - \ of the passed-in predicate.\n _.negate = function(predicate) {\n return\ - \ function() {\n return !predicate.apply(this, arguments);\n };\n };\n\ - \n // Returns a function that is the composition of a list of functions, each\n\ - \ // consuming the return value of the function that follows.\n _.compose\ - \ = function() {\n var args = arguments;\n var start = args.length - 1;\n\ - \ return function() {\n var i = start;\n var result = args[start].apply(this,\ - \ arguments);\n while (i--) result = args[i].call(this, result);\n \ - \ return result;\n };\n };\n\n // Returns a function that will only be\ - \ executed after being called N times.\n _.after = function(times, func) {\n\ - \ return function() {\n if (--times < 1) {\n return func.apply(this,\ - \ arguments);\n }\n };\n };\n\n // Returns a function that will only\ - \ be executed before being called N times.\n _.before = function(times, func)\ - \ {\n var memo;\n return function() {\n if (--times > 0) {\n \ - \ memo = func.apply(this, arguments);\n } else {\n func = null;\n\ - \ }\n return memo;\n };\n };\n\n // Returns a function that will\ - \ be executed at most one time, no matter how\n // often you call it. Useful\ - \ for lazy initialization.\n _.once = _.partial(_.before, 2);\n\n // Object\ - \ Functions\n // ----------------\n\n // Retrieve the names of an object's\ - \ properties.\n // Delegates to **ECMAScript 5**'s native `Object.keys`\n \ - \ _.keys = function(obj) {\n if (!_.isObject(obj)) return [];\n if (nativeKeys)\ - \ return nativeKeys(obj);\n var keys = [];\n for (var key in obj) if (_.has(obj,\ - \ key)) keys.push(key);\n return keys;\n };\n\n // Retrieve the values\ - \ of an object's properties.\n _.values = function(obj) {\n var keys = _.keys(obj);\n\ - \ var length = keys.length;\n var values = Array(length);\n for (var\ - \ i = 0; i < length; i++) {\n values[i] = obj[keys[i]];\n }\n return\ - \ values;\n };\n\n // Convert an object into a list of `[key, value]` pairs.\n\ - \ _.pairs = function(obj) {\n var keys = _.keys(obj);\n var length =\ - \ keys.length;\n var pairs = Array(length);\n for (var i = 0; i < length;\ - \ i++) {\n pairs[i] = [keys[i], obj[keys[i]]];\n }\n return pairs;\n\ - \ };\n\n // Invert the keys and values of an object. The values must be serializable.\n\ - \ _.invert = function(obj) {\n var result = {};\n var keys = _.keys(obj);\n\ - \ for (var i = 0, length = keys.length; i < length; i++) {\n result[obj[keys[i]]]\ - \ = keys[i];\n }\n return result;\n };\n\n // Return a sorted list of\ - \ the function names available on the object.\n // Aliased as `methods`\n \ - \ _.functions = _.methods = function(obj) {\n var names = [];\n for (var\ - \ key in obj) {\n if (_.isFunction(obj[key])) names.push(key);\n }\n\ - \ return names.sort();\n };\n\n // Extend a given object with all the properties\ - \ in passed-in object(s).\n _.extend = function(obj) {\n if (!_.isObject(obj))\ - \ return obj;\n var source, prop;\n for (var i = 1, length = arguments.length;\ - \ i < length; i++) {\n source = arguments[i];\n for (prop in source)\ - \ {\n if (hasOwnProperty.call(source, prop)) {\n obj[prop]\ - \ = source[prop];\n }\n }\n }\n return obj;\n };\n\n //\ - \ Return a copy of the object only containing the whitelisted properties.\n\ - \ _.pick = function(obj, iteratee, context) {\n var result = {}, key;\n\ - \ if (obj == null) return result;\n if (_.isFunction(iteratee)) {\n \ - \ iteratee = createCallback(iteratee, context);\n for (key in obj) {\n\ - \ var value = obj[key];\n if (iteratee(value, key, obj)) result[key]\ - \ = value;\n }\n } else {\n var keys = concat.apply([], slice.call(arguments,\ - \ 1));\n obj = new Object(obj);\n for (var i = 0, length = keys.length;\ - \ i < length; i++) {\n key = keys[i];\n if (key in obj) result[key]\ - \ = obj[key];\n }\n }\n return result;\n };\n\n // Return a copy\ - \ of the object without the blacklisted properties.\n _.omit = function(obj,\ - \ iteratee, context) {\n if (_.isFunction(iteratee)) {\n iteratee =\ - \ _.negate(iteratee);\n } else {\n var keys = _.map(concat.apply([],\ - \ slice.call(arguments, 1)), String);\n iteratee = function(value, key)\ - \ {\n return !_.contains(keys, key);\n };\n }\n return _.pick(obj,\ - \ iteratee, context);\n };\n\n // Fill in a given object with default properties.\n\ - \ _.defaults = function(obj) {\n if (!_.isObject(obj)) return obj;\n \ - \ for (var i = 1, length = arguments.length; i < length; i++) {\n var source\ - \ = arguments[i];\n for (var prop in source) {\n if (obj[prop] ===\ - \ void 0) obj[prop] = source[prop];\n }\n }\n return obj;\n };\n\ - \n // Create a (shallow-cloned) duplicate of an object.\n _.clone = function(obj)\ - \ {\n if (!_.isObject(obj)) return obj;\n return _.isArray(obj) ? obj.slice()\ - \ : _.extend({}, obj);\n };\n\n // Invokes interceptor with the obj, and then\ - \ returns obj.\n // The primary purpose of this method is to \"tap into\" a\ - \ method chain, in\n // order to perform operations on intermediate results\ - \ within the chain.\n _.tap = function(obj, interceptor) {\n interceptor(obj);\n\ - \ return obj;\n };\n\n // Internal recursive comparison function for `isEqual`.\n\ - \ var eq = function(a, b, aStack, bStack) {\n // Identical objects are equal.\ - \ `0 === -0`, but they aren't identical.\n // See the [Harmony `egal` proposal](http://wiki.ecmascript.org/doku.php?id=harmony:egal).\n\ - \ if (a === b) return a !== 0 || 1 / a === 1 / b;\n // A strict comparison\ - \ is necessary because `null == undefined`.\n if (a == null || b == null)\ - \ return a === b;\n // Unwrap any wrapped objects.\n if (a instanceof\ - \ _) a = a._wrapped;\n if (b instanceof _) b = b._wrapped;\n // Compare\ - \ `[[Class]]` names.\n var className = toString.call(a);\n if (className\ - \ !== toString.call(b)) return false;\n switch (className) {\n // Strings,\ - \ numbers, regular expressions, dates, and booleans are compared by value.\n\ - \ case '[object RegExp]':\n // RegExps are coerced to strings for\ - \ comparison (Note: '' + /a/i === '/a/i')\n case '[object String]':\n \ - \ // Primitives and their corresponding object wrappers are equivalent;\ - \ thus, `\"5\"` is\n // equivalent to `new String(\"5\")`.\n return\ - \ '' + a === '' + b;\n case '[object Number]':\n // `NaN`s are equivalent,\ - \ but non-reflexive.\n // Object(NaN) is equivalent to NaN\n if\ - \ (+a !== +a) return +b !== +b;\n // An `egal` comparison is performed\ - \ for other numeric values.\n return +a === 0 ? 1 / +a === 1 / b : +a\ - \ === +b;\n case '[object Date]':\n case '[object Boolean]':\n \ - \ // Coerce dates and booleans to numeric primitive values. Dates are compared\ - \ by their\n // millisecond representations. Note that invalid dates\ - \ with millisecond representations\n // of `NaN` are not equivalent.\n\ - \ return +a === +b;\n }\n if (typeof a != 'object' || typeof b\ - \ != 'object') return false;\n // Assume equality for cyclic structures.\ - \ The algorithm for detecting cyclic\n // structures is adapted from ES 5.1\ - \ section 15.12.3, abstract operation `JO`.\n var length = aStack.length;\n\ - \ while (length--) {\n // Linear search. Performance is inversely proportional\ - \ to the number of\n // unique nested structures.\n if (aStack[length]\ - \ === a) return bStack[length] === b;\n }\n // Objects with different\ - \ constructors are not equivalent, but `Object`s\n // from different frames\ - \ are.\n var aCtor = a.constructor, bCtor = b.constructor;\n if (\n \ - \ aCtor !== bCtor &&\n // Handle Object.create(x) cases\n 'constructor'\ - \ in a && 'constructor' in b &&\n !(_.isFunction(aCtor) && aCtor instanceof\ - \ aCtor &&\n _.isFunction(bCtor) && bCtor instanceof bCtor)\n ) {\n\ - \ return false;\n }\n // Add the first object to the stack of traversed\ - \ objects.\n aStack.push(a);\n bStack.push(b);\n var size, result;\n\ - \ // Recursively compare objects and arrays.\n if (className === '[object\ - \ Array]') {\n // Compare array lengths to determine if a deep comparison\ - \ is necessary.\n size = a.length;\n result = size === b.length;\n\ - \ if (result) {\n // Deep compare the contents, ignoring non-numeric\ - \ properties.\n while (size--) {\n if (!(result = eq(a[size],\ - \ b[size], aStack, bStack))) break;\n }\n }\n } else {\n \ - \ // Deep compare objects.\n var keys = _.keys(a), key;\n size =\ - \ keys.length;\n // Ensure that both objects contain the same number of\ - \ properties before comparing deep equality.\n result = _.keys(b).length\ - \ === size;\n if (result) {\n while (size--) {\n // Deep\ - \ compare each member\n key = keys[size];\n if (!(result =\ - \ _.has(b, key) && eq(a[key], b[key], aStack, bStack))) break;\n }\n\ - \ }\n }\n // Remove the first object from the stack of traversed\ - \ objects.\n aStack.pop();\n bStack.pop();\n return result;\n };\n\ - \n // Perform a deep comparison to check if two objects are equal.\n _.isEqual\ - \ = function(a, b) {\n return eq(a, b, [], []);\n };\n\n // Is a given\ - \ array, string, or object empty?\n // An \"empty\" object has no enumerable\ - \ own-properties.\n _.isEmpty = function(obj) {\n if (obj == null) return\ - \ true;\n if (_.isArray(obj) || _.isString(obj) || _.isArguments(obj)) return\ - \ obj.length === 0;\n for (var key in obj) if (_.has(obj, key)) return false;\n\ - \ return true;\n };\n\n // Is a given value a DOM element?\n _.isElement\ - \ = function(obj) {\n return !!(obj && obj.nodeType === 1);\n };\n\n //\ - \ Is a given value an array?\n // Delegates to ECMA5's native Array.isArray\n\ - \ _.isArray = nativeIsArray || function(obj) {\n return toString.call(obj)\ - \ === '[object Array]';\n };\n\n // Is a given variable an object?\n _.isObject\ - \ = function(obj) {\n var type = typeof obj;\n return type === 'function'\ - \ || type === 'object' && !!obj;\n };\n\n // Add some isType methods: isArguments,\ - \ isFunction, isString, isNumber, isDate, isRegExp.\n _.each(['Arguments',\ - \ 'Function', 'String', 'Number', 'Date', 'RegExp'], function(name) {\n _['is'\ - \ + name] = function(obj) {\n return toString.call(obj) === '[object '\ - \ + name + ']';\n };\n });\n\n // Define a fallback version of the method\ - \ in browsers (ahem, IE), where\n // there isn't any inspectable \"Arguments\"\ - \ type.\n if (!_.isArguments(arguments)) {\n _.isArguments = function(obj)\ - \ {\n return _.has(obj, 'callee');\n };\n }\n\n // Optimize `isFunction`\ - \ if appropriate. Work around an IE 11 bug.\n if (typeof /./ !== 'function')\ - \ {\n _.isFunction = function(obj) {\n return typeof obj == 'function'\ - \ || false;\n };\n }\n\n // Is a given object a finite number?\n _.isFinite\ - \ = function(obj) {\n return isFinite(obj) && !isNaN(parseFloat(obj));\n\ - \ };\n\n // Is the given value `NaN`? (NaN is the only number which does not\ - \ equal itself).\n _.isNaN = function(obj) {\n return _.isNumber(obj) &&\ - \ obj !== +obj;\n };\n\n // Is a given value a boolean?\n _.isBoolean = function(obj)\ - \ {\n return obj === true || obj === false || toString.call(obj) === '[object\ - \ Boolean]';\n };\n\n // Is a given value equal to null?\n _.isNull = function(obj)\ - \ {\n return obj === null;\n };\n\n // Is a given variable undefined?\n\ - \ _.isUndefined = function(obj) {\n return obj === void 0;\n };\n\n //\ - \ Shortcut function for checking if an object has a given property directly\n\ - \ // on itself (in other words, not on a prototype).\n _.has = function(obj,\ - \ key) {\n return obj != null && hasOwnProperty.call(obj, key);\n };\n\n\ - \ // Utility Functions\n // -----------------\n\n // Run Underscore.js in\ - \ *noConflict* mode, returning the `_` variable to its\n // previous owner.\ - \ Returns a reference to the Underscore object.\n _.noConflict = function()\ - \ {\n root._ = previousUnderscore;\n return this;\n };\n\n // Keep the\ - \ identity function around for default iteratees.\n _.identity = function(value)\ - \ {\n return value;\n };\n\n // Predicate-generating functions. Often useful\ - \ outside of Underscore.\n _.constant = function(value) {\n return function()\ - \ {\n return value;\n };\n };\n\n _.noop = function(){};\n\n _.property\ - \ = function(key) {\n return function(obj) {\n return obj[key];\n \ - \ };\n };\n\n // Returns a predicate for checking whether an object has a\ - \ given set of `key:value` pairs.\n _.matches = function(attrs) {\n var\ - \ pairs = _.pairs(attrs), length = pairs.length;\n return function(obj) {\n\ - \ if (obj == null) return !length;\n obj = new Object(obj);\n \ - \ for (var i = 0; i < length; i++) {\n var pair = pairs[i], key = pair[0];\n\ - \ if (pair[1] !== obj[key] || !(key in obj)) return false;\n }\n\ - \ return true;\n };\n };\n\n // Run a function **n** times.\n _.times\ - \ = function(n, iteratee, context) {\n var accum = Array(Math.max(0, n));\n\ - \ iteratee = createCallback(iteratee, context, 1);\n for (var i = 0; i\ - \ < n; i++) accum[i] = iteratee(i);\n return accum;\n };\n\n // Return\ - \ a random integer between min and max (inclusive).\n _.random = function(min,\ - \ max) {\n if (max == null) {\n max = min;\n min = 0;\n }\n\ - \ return min + Math.floor(Math.random() * (max - min + 1));\n };\n\n //\ - \ A (possibly faster) way to get the current timestamp as an integer.\n _.now\ - \ = Date.now || function() {\n return new Date().getTime();\n };\n\n //\ - \ List of HTML entities for escaping.\n var escapeMap = {\n '&': '&',\n\ - \ '<': '<',\n '>': '>',\n '\"': '"',\n \"'\": ''',\n\ - \ '`': '`'\n };\n var unescapeMap = _.invert(escapeMap);\n\n // Functions\ - \ for escaping and unescaping strings to/from HTML interpolation.\n var createEscaper\ - \ = function(map) {\n var escaper = function(match) {\n return map[match];\n\ - \ };\n // Regexes for identifying a key that needs to be escaped\n \ - \ var source = '(?:' + _.keys(map).join('|') + ')';\n var testRegexp = RegExp(source);\n\ - \ var replaceRegexp = RegExp(source, 'g');\n return function(string) {\n\ - \ string = string == null ? '' : '' + string;\n return testRegexp.test(string)\ - \ ? string.replace(replaceRegexp, escaper) : string;\n };\n };\n _.escape\ - \ = createEscaper(escapeMap);\n _.unescape = createEscaper(unescapeMap);\n\n\ - \ // If the value of the named `property` is a function then invoke it with\ - \ the\n // `object` as context; otherwise, return it.\n _.result = function(object,\ - \ property) {\n if (object == null) return void 0;\n var value = object[property];\n\ - \ return _.isFunction(value) ? object[property]() : value;\n };\n\n //\ - \ Generate a unique integer id (unique within the entire client session).\n\ - \ // Useful for temporary DOM ids.\n var idCounter = 0;\n _.uniqueId = function(prefix)\ - \ {\n var id = ++idCounter + '';\n return prefix ? prefix + id : id;\n\ - \ };\n\n // By default, Underscore uses ERB-style template delimiters, change\ - \ the\n // following template settings to use alternative delimiters.\n _.templateSettings\ - \ = {\n evaluate : /<%([\\s\\S]+?)%>/g,\n interpolate : /<%=([\\s\\\ - S]+?)%>/g,\n escape : /<%-([\\s\\S]+?)%>/g\n };\n\n // When customizing\ - \ `templateSettings`, if you don't want to define an\n // interpolation, evaluation\ - \ or escaping regex, we need one that is\n // guaranteed not to match.\n var\ - \ noMatch = /(.)^/;\n\n // Certain characters need to be escaped so that they\ - \ can be put into a\n // string literal.\n var escapes = {\n \"'\": \ - \ \"'\",\n '\\\\': '\\\\',\n '\\r': 'r',\n '\\n': 'n',\n\ - \ '\\u2028': 'u2028',\n '\\u2029': 'u2029'\n };\n\n var escaper = /\\\ - \\|'|\\r|\\n|\\u2028|\\u2029/g;\n\n var escapeChar = function(match) {\n \ - \ return '\\\\' + escapes[match];\n };\n\n // JavaScript micro-templating,\ - \ similar to John Resig's implementation.\n // Underscore templating handles\ - \ arbitrary delimiters, preserves whitespace,\n // and correctly escapes quotes\ - \ within interpolated code.\n // NB: `oldSettings` only exists for backwards\ - \ compatibility.\n _.template = function(text, settings, oldSettings) {\n \ - \ if (!settings && oldSettings) settings = oldSettings;\n settings = _.defaults({},\ - \ settings, _.templateSettings);\n\n // Combine delimiters into one regular\ - \ expression via alternation.\n var matcher = RegExp([\n (settings.escape\ - \ || noMatch).source,\n (settings.interpolate || noMatch).source,\n \ - \ (settings.evaluate || noMatch).source\n ].join('|') + '|$', 'g');\n\n\ - \ // Compile the template source, escaping string literals appropriately.\n\ - \ var index = 0;\n var source = \"__p+='\";\n text.replace(matcher,\ - \ function(match, escape, interpolate, evaluate, offset) {\n source +=\ - \ text.slice(index, offset).replace(escaper, escapeChar);\n index = offset\ - \ + match.length;\n\n if (escape) {\n source += \"'+\\n((__t=(\"\ - \ + escape + \"))==null?'':_.escape(__t))+\\n'\";\n } else if (interpolate)\ - \ {\n source += \"'+\\n((__t=(\" + interpolate + \"))==null?'':__t)+\\\ - n'\";\n } else if (evaluate) {\n source += \"';\\n\" + evaluate\ - \ + \"\\n__p+='\";\n }\n\n // Adobe VMs need the match returned to\ - \ produce the correct offest.\n return match;\n });\n source += \"\ - ';\\n\";\n\n // If a variable is not specified, place data values in local\ - \ scope.\n if (!settings.variable) source = 'with(obj||{}){\\n' + source\ - \ + '}\\n';\n\n source = \"var __t,__p='',__j=Array.prototype.join,\" +\n\ - \ \"print=function(){__p+=__j.call(arguments,'');};\\n\" +\n source\ - \ + 'return __p;\\n';\n\n try {\n var render = new Function(settings.variable\ - \ || 'obj', '_', source);\n } catch (e) {\n e.source = source;\n \ - \ throw e;\n }\n\n var template = function(data) {\n return render.call(this,\ - \ data, _);\n };\n\n // Provide the compiled source as a convenience for\ - \ precompilation.\n var argument = settings.variable || 'obj';\n template.source\ - \ = 'function(' + argument + '){\\n' + source + '}';\n\n return template;\n\ - \ };\n\n // Add a \"chain\" function. Start chaining a wrapped Underscore\ - \ object.\n _.chain = function(obj) {\n var instance = _(obj);\n instance._chain\ - \ = true;\n return instance;\n };\n\n // OOP\n // ---------------\n //\ - \ If Underscore is called as a function, it returns a wrapped object that\n\ - \ // can be used OO-style. This wrapper holds altered versions of all the\n\ - \ // underscore functions. Wrapped objects may be chained.\n\n // Helper function\ - \ to continue chaining intermediate results.\n var result = function(obj) {\n\ - \ return this._chain ? _(obj).chain() : obj;\n };\n\n // Add your own custom\ - \ functions to the Underscore object.\n _.mixin = function(obj) {\n _.each(_.functions(obj),\ - \ function(name) {\n var func = _[name] = obj[name];\n _.prototype[name]\ - \ = function() {\n var args = [this._wrapped];\n push.apply(args,\ - \ arguments);\n return result.call(this, func.apply(_, args));\n \ - \ };\n });\n };\n\n // Add all of the Underscore functions to the wrapper\ - \ object.\n _.mixin(_);\n\n // Add all mutator Array functions to the wrapper.\n\ - \ _.each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'],\ - \ function(name) {\n var method = ArrayProto[name];\n _.prototype[name]\ - \ = function() {\n var obj = this._wrapped;\n method.apply(obj, arguments);\n\ - \ if ((name === 'shift' || name === 'splice') && obj.length === 0) delete\ - \ obj[0];\n return result.call(this, obj);\n };\n });\n\n // Add all\ - \ accessor Array functions to the wrapper.\n _.each(['concat', 'join', 'slice'],\ - \ function(name) {\n var method = ArrayProto[name];\n _.prototype[name]\ - \ = function() {\n return result.call(this, method.apply(this._wrapped,\ - \ arguments));\n };\n });\n\n // Extracts the result from a wrapped and\ - \ chained object.\n _.prototype.value = function() {\n return this._wrapped;\n\ - \ };\n\n // AMD registration happens at the end for compatibility with AMD\ - \ loaders\n // that may not enforce next-turn semantics on modules. Even though\ - \ general\n // practice for AMD registration is to be anonymous, underscore\ - \ registers\n // as a named module because, like jQuery, it is a base library\ - \ that is\n // popular enough to be bundled in a third party lib, but not be\ - \ part of\n // an AMD load request. Those cases could generate an error when\ - \ an\n // anonymous define() is called outside of a loader request.\n if (typeof\ - \ define === 'function' && define.amd) {\n define('underscore', [], function()\ - \ {\n return _;\n });\n }\n}.call(this));\n", "var t = function(s)\ - \ { return _.template(s, {variable: 'data'})({'inputs': inputs}); };"] -- class: InitialWorkDirRequirement - listing: - - {entry: "$(t(\"The file is <%= data.inputs.file1.path.split('/').slice(-1)[0]\ - \ %>\\n\"))", entryname: foo.txt} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_test-cwl-out.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_test-cwl-out.cwl deleted file mode 100644 index 352d5aaa..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_test-cwl-out.cwl +++ /dev/null @@ -1,13 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: "echo foo > foo && echo '{\"foo\": {\"path\": \"\ - $(runtime.outdir)/foo\", \"class\": \"File\"} }' > cwl.output.json\n"} -class: CommandLineTool -cwlVersion: v1.2 -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: [] -outputs: -- {id: foo, type: File} -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_test-cwl-out2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_test-cwl-out2.cwl deleted file mode 100644 index 69380f6b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_test-cwl-out2.cwl +++ /dev/null @@ -1,13 +0,0 @@ -arguments: -- {shellQuote: false, valueFrom: "echo foo > foo && echo '{\"foo\": {\"location\"\ - : \"file://$(runtime.outdir)/foo\", \"class\": \"File\"} }' > cwl.output.json\n"} -class: CommandLineTool -cwlVersion: v1.2 -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: [] -outputs: -- {id: foo, type: File} -requirements: -- {class: ShellCommandRequirement} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit.cwl deleted file mode 100644 index c885afe3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit.cwl +++ /dev/null @@ -1,9 +0,0 @@ -baseCommand: [sleep, '15'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: -- {class: ToolTimeLimit, timelimit: 3} -- {class: WorkReuse, enableReuse: false} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit2-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit2-wf.cwl deleted file mode 100644 index 39daba22..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit2-wf.cwl +++ /dev/null @@ -1,46 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: i - type: ['null', string] -outputs: -- id: o - outputSource: step2/o - type: ['null', string] -requirements: -- {class: ToolTimeLimit, timelimit: 5} -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: i, source: i} - out: [o] - run: - baseCommand: [sleep, '3'] - class: CommandLineTool - inputs: - - id: i - type: ['null', string] - outputs: - - id: o - outputBinding: {outputEval: $("time passed")} - type: ['null', string] - requirements: - - {class: InlineJavascriptRequirement} -- id: step2 - in: - - {id: i, source: step1/o} - out: [o] - run: - baseCommand: [sleep, '3'] - class: CommandLineTool - inputs: - - id: i - type: ['null', string] - outputs: - - id: o - outputBinding: {outputEval: $("time passed")} - type: ['null', string] - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit2.cwl deleted file mode 100644 index f00db890..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit2.cwl +++ /dev/null @@ -1,8 +0,0 @@ -baseCommand: [sleep, '15'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: -- {class: ToolTimeLimit, timelimit: -1} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit3-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit3-wf.cwl deleted file mode 100644 index 5282a797..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit3-wf.cwl +++ /dev/null @@ -1,31 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: i - type: ['null', int] -outputs: -- id: o - outputSource: step1/o - type: ['null', string] -requirements: -- {class: ToolTimeLimit, timelimit: 0} -- {class: WorkReuse, enableReuse: false} -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: step1 - in: - - {id: i, source: i} - out: [o] - run: - baseCommand: [sleep, '10'] - class: CommandLineTool - inputs: - - id: i - type: ['null', int] - outputs: - - id: o - outputBinding: {outputEval: $("time passed")} - type: ['null', string] - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit3.cwl deleted file mode 100644 index aa57039f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit3.cwl +++ /dev/null @@ -1,9 +0,0 @@ -baseCommand: [sleep, '15'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: -- {class: ToolTimeLimit, timelimit: 0} -- {class: WorkReuse, enableReuse: false} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit4.cwl deleted file mode 100644 index 943242b0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit4.cwl +++ /dev/null @@ -1,9 +0,0 @@ -baseCommand: [sleep, '15'] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: -- {class: InlineJavascriptRequirement} -- {class: ToolTimeLimit, timelimit: $(1+2)} -- {class: WorkReuse, enableReuse: false} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit5.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit5.cwl deleted file mode 100644 index 85fb3a7d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_timelimit5.cwl +++ /dev/null @@ -1,12 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.2 -expression: "${\n function sleep(milliseconds) {\n var start = new Date().getTime();\n\ - \ for (var i = 0; i < 1e7; i++) {\n if ((new Date().getTime() - start) >\ - \ milliseconds){\n break;\n }\n }\n };\n sleep(5000);\n return\ - \ {\"status\": \"Done\"}\n}" -inputs: [] -outputs: -- {id: status, type: string} -requirements: -- {class: ToolTimeLimit, timelimit: 3} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_tmap-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_tmap-tool.cwl deleted file mode 100644 index 67d85c13..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_tmap-tool.cwl +++ /dev/null @@ -1,111 +0,0 @@ -arguments: [tmap, mapall] -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -hints: -- {class: DockerRequirement, dockerPull: python:2-slim} -inputs: -- {id: reads, type: File} -- id: stages - inputBinding: {position: 1} - type: - items: - fields: - - inputBinding: {position: 0, prefix: stage, separate: false} - name: stageId - type: ['null', int] - - inputBinding: {position: 1, prefix: -n} - name: stageOption1 - type: ['null', boolean] - - inputBinding: {position: 2} - name: algos - type: - items: - - fields: - - inputBinding: {position: 0} - name: algo - type: - name: JustMap1 - symbols: [map1] - type: enum - - inputBinding: {position: 2, prefix: --max-seq-length} - name: maxSeqLen - type: ['null', int] - - inputBinding: {position: 2, prefix: --min-seq-length} - name: minSeqLen - type: ['null', int] - - inputBinding: {position: 2, prefix: --seed-length} - name: seedLength - type: ['null', int] - name: user_type_17 - type: record - - fields: - - inputBinding: {position: 0} - name: algo - type: - name: JustMap2 - symbols: [map2] - type: enum - - inputBinding: {position: 2, prefix: --max-seq-length} - name: maxSeqLen - type: ['null', int] - - inputBinding: {position: 2, prefix: --min-seq-length} - name: minSeqLen - type: ['null', int] - - inputBinding: {position: 2, prefix: --max-seed-hits} - name: maxSeedHits - type: ['null', int] - name: user_type_33 - type: record - - fields: - - inputBinding: {position: 0} - name: algo - type: - name: JustMap3 - symbols: [map3] - type: enum - - inputBinding: {position: 2, prefix: --max-seq-length} - name: maxSeqLen - type: ['null', int] - - inputBinding: {position: 2, prefix: --min-seq-length} - name: minSeqLen - type: ['null', int] - - inputBinding: {position: 2, prefix: --fwd-search} - name: fwdSearch - type: ['null', boolean] - name: user_type_49 - type: record - - fields: - - inputBinding: {position: 0} - name: algo - type: - name: JustMap4 - symbols: [map4] - type: enum - - inputBinding: {position: 2, prefix: --max-seq-length} - name: maxSeqLen - type: ['null', int] - - inputBinding: {position: 2, prefix: --min-seq-length} - name: minSeqLen - type: ['null', int] - - inputBinding: {position: 2, prefix: --seed-step} - name: seedStep - type: ['null', int] - name: user_type_65 - type: record - type: array - name: user_type_4 - type: record - type: array -- default: {class: File, location: args.py} - id: '#args.py' - inputBinding: {position: -1} - type: File -outputs: -- id: sam - outputBinding: {glob: output.sam} - type: ['null', File] -- id: args - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_tool-v12.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_tool-v12.cwl deleted file mode 100644 index 6cea1a66..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_tool-v12.cwl +++ /dev/null @@ -1,12 +0,0 @@ -arguments: [echo, $(inputs.inp1)] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: inp1 - secondaryFiles: - - {pattern: '.2', required: true} - type: File -outputs: [] -requirements: -- {class: ResourceRequirement, coresMin: 0.5} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_touch.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_touch.cwl deleted file mode 100644 index 490197a4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_touch.cwl +++ /dev/null @@ -1,15 +0,0 @@ -baseCommand: [touch] -class: CommandLineTool -cwlVersion: v1.2 -hints: - DockerRequirement: {dockerPull: debian:stretch-slim} -inputs: -- id: name - inputBinding: {position: 0} - type: string -outputs: -- id: empty_file - outputBinding: {glob: $(inputs.name)} - type: File -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_updatedir_inplace.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_updatedir_inplace.cwl deleted file mode 100644 index ffa6ee28..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_updatedir_inplace.cwl +++ /dev/null @@ -1,15 +0,0 @@ -arguments: [touch, inp/blurb] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: r, type: Directory} -outputs: -- id: out - outputBinding: {glob: inp} - type: Directory -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.r), entryname: inp, writable: true} -- {class: InplaceUpdateRequirement, inplaceUpdate: true} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_updateval_inplace.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_updateval_inplace.cwl deleted file mode 100644 index 62362c4c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_updateval_inplace.cwl +++ /dev/null @@ -1,20 +0,0 @@ -arguments: [python, $(inputs.script), $(inputs.r.basename)] -class: CommandLineTool -cwlVersion: v1.2 -hints: - DockerRequirement: {dockerPull: python:2.7.15-alpine3.7} -inputs: -- {id: r, type: File} -- default: {class: File, location: updateval.py} - id: script - type: File -outputs: -- id: out - outputBinding: {glob: $(inputs.r.basename)} - type: File -requirements: -- class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.r), writable: true} -- {class: InplaceUpdateRequirement, inplaceUpdate: true} -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_valid_schemadef_types_with_import-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_valid_schemadef_types_with_import-wf.cwl deleted file mode 100644 index 44ea1ce9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_valid_schemadef_types_with_import-wf.cwl +++ /dev/null @@ -1,64 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- id: readgroups_bam - type: - fields: - - {name: bam, type: File} - - name: readgroup_meta_list - type: - items: - fields: - - {name: CN, type: string} - - {name: DT, type: string} - - {name: ID, type: string} - - {name: LB, type: string} - - {name: PI, type: string} - - {name: PL, type: string} - - {name: SM, type: string} - name: readgroup_meta - type: record - type: array - name: readgroups_bam_file - type: record -outputs: -- {id: out, outputSource: step1/out, type: string} -requirements: [] -steps: -- id: step1 - in: - - {id: message, source: readgroups_bam} - out: [out] - run: - baseCommand: echo - class: CommandLineTool - cwlVersion: v1.2 - inputs: - - id: message - inputBinding: {valueFrom: '$(self.readgroup_meta_list[0][''DT''])'} - type: - fields: - - {name: bam, type: File} - - name: readgroup_meta_list - type: - items: - fields: - - {name: CN, type: string} - - {name: DT, type: string} - - {name: ID, type: string} - - {name: LB, type: string} - - {name: PI, type: string} - - {name: PL, type: string} - - {name: SM, type: string} - name: readgroup_meta_23 - type: record - type: array - name: readgroups_bam_file_18 - type: record - outputs: - - id: out - outputBinding: {glob: output.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string - requirements: - - {class: InlineJavascriptRequirement} - stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_valueFrom-constant.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_valueFrom-constant.cwl deleted file mode 100644 index 375f2281..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_valueFrom-constant.cwl +++ /dev/null @@ -1,19 +0,0 @@ -baseCommand: python -class: CommandLineTool -cwlVersion: v1.2 -hints: -- {class: DockerRequirement, dockerPull: python:2-slim} -inputs: -- id: array_input - inputBinding: {valueFrom: replacementValue} - type: - - {items: File, type: array} -- default: {class: File, location: args.py} - id: args.py - inputBinding: {position: -1} - type: File -outputs: -- id: args - type: {items: string, type: array} -requirements: -- {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_vf-concat.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_vf-concat.cwl deleted file mode 100644 index 87874a9c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_vf-concat.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: echo -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: file1 - inputBinding: {valueFrom: $("a ")$("string")} - type: ['null', File] -outputs: -- id: out - outputBinding: {glob: output.txt, loadContents: true, outputEval: '$(self[0].contents)'} - type: string -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc-tool-shortcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc-tool-shortcut.cwl deleted file mode 100644 index c00ef5c8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc-tool-shortcut.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: [wc] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: file1, type: stdin} -outputs: -- id: output - outputBinding: {glob: output} - type: File -requirements: -- {class: DockerRequirement, dockerPull: debian:stretch-slim} -- {class: InlineJavascriptRequirement} -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc-tool.cwl deleted file mode 100644 index 2eeef5e9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc-tool.cwl +++ /dev/null @@ -1,13 +0,0 @@ -baseCommand: [wc, -l] -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- {id: file1, type: File} -outputs: -- id: output - outputBinding: {glob: output} - type: File -requirements: -- {class: InlineJavascriptRequirement} -stdin: $(inputs.file1.path) -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc2-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc2-tool.cwl deleted file mode 100644 index 98692e35..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc2-tool.cwl +++ /dev/null @@ -1,14 +0,0 @@ -baseCommand: wc -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: file1 - inputBinding: {} - type: File -outputs: -- id: output - outputBinding: {glob: output.txt, loadContents: true, outputEval: '$(parseInt(self[0].contents))'} - type: int -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc3-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc3-tool.cwl deleted file mode 100644 index c73b7c21..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc3-tool.cwl +++ /dev/null @@ -1,15 +0,0 @@ -baseCommand: wc -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: file1 - inputBinding: {} - type: {items: File, type: array} -outputs: -- id: output - outputBinding: {glob: output.txt, loadContents: true, outputEval: "${\n var s =\ - \ self[0].contents.split(/\\r?\\n/);\n return parseInt(s[s.length-2]);\n}\n"} - type: int -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc4-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc4-tool.cwl deleted file mode 100644 index e31b4b4f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wc4-tool.cwl +++ /dev/null @@ -1,15 +0,0 @@ -baseCommand: wc -class: CommandLineTool -cwlVersion: v1.2 -inputs: -- id: file1 - inputBinding: {} - type: File -outputs: -- id: output - outputBinding: {glob: output.txt, loadContents: true, outputEval: "${\n var s =\ - \ self[0].contents.split(/\\r?\\n/);\n return parseInt(s[s.length-2]);\n}\n"} - type: int -requirements: -- {class: InlineJavascriptRequirement} -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf-loadContents.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf-loadContents.cwl deleted file mode 100644 index ec73bb47..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf-loadContents.cwl +++ /dev/null @@ -1,24 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: my_file, loadContents: true, type: File} -outputs: -- {id: my_int, outputSource: one/my_int, type: int} -requirements: -- {class: StepInputExpressionRequirement} -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: one - in: - - {id: my_number, source: my_file, valueFrom: $(parseInt(self.contents))} - out: [my_int] - run: - class: ExpressionTool - expression: "${ return { \"my_int\": inputs.my_number }; }\n" - inputs: - - {id: my_number, type: int} - outputs: - - {id: my_int, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf-loadContents2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf-loadContents2.cwl deleted file mode 100644 index ec73bb47..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf-loadContents2.cwl +++ /dev/null @@ -1,24 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: my_file, loadContents: true, type: File} -outputs: -- {id: my_int, outputSource: one/my_int, type: int} -requirements: -- {class: StepInputExpressionRequirement} -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: one - in: - - {id: my_number, source: my_file, valueFrom: $(parseInt(self.contents))} - out: [my_int] - run: - class: ExpressionTool - expression: "${ return { \"my_int\": inputs.my_number }; }\n" - inputs: - - {id: my_number, type: int} - outputs: - - {id: my_int, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf-loadContents3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf-loadContents3.cwl deleted file mode 100644 index 6f136d42..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf-loadContents3.cwl +++ /dev/null @@ -1,24 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: my_file, type: File} -outputs: -- {id: my_int, outputSource: one/my_int, type: int} -requirements: -- {class: StepInputExpressionRequirement} -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: one - in: - - {id: my_number, source: my_file} - out: [my_int] - run: - class: ExpressionTool - expression: "${ return { \"my_int\": parseInt(inputs.my_number.contents) }; }\n" - inputs: - - {id: my_number, loadContents: true, type: File} - outputs: - - {id: my_int, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf-loadContents4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf-loadContents4.cwl deleted file mode 100644 index 3d76d820..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf-loadContents4.cwl +++ /dev/null @@ -1,24 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- {id: my_file, type: File} -outputs: -- {id: my_int, outputSource: one/my_int, type: int} -requirements: -- {class: StepInputExpressionRequirement} -- {class: InlineJavascriptRequirement} -- {class: SubworkflowFeatureRequirement} -steps: -- id: one - in: - - {id: my_number, loadContents: true, source: my_file, valueFrom: $(parseInt(self.contents))} - out: [my_int] - run: - class: ExpressionTool - expression: "${ return { \"my_int\": inputs.my_number }; }\n" - inputs: - - {id: my_number, type: int} - outputs: - - {id: my_int, type: int} - requirements: - - {class: InlineJavascriptRequirement} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf_ren.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf_ren.cwl deleted file mode 100644 index 5de38b24..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_wf_ren.cwl +++ /dev/null @@ -1,48 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: -- default: {class: File, location: whale.txt} - id: f1 - type: File -- {default: badger.txt, id: newname, type: string} -outputs: [] -requirements: -- {class: StepInputExpressionRequirement} -- {class: InlineJavascriptRequirement} -steps: -- id: rename - in: - - {id: f1, source: f1} - - {id: newname, source: newname} - out: [out] - run: - baseCommand: 'true' - class: CommandLineTool - cwlVersion: v1.2 - inputs: - - {id: srcfile, type: File} - - {id: newname, type: string} - outputs: - - id: outfile - outputBinding: {glob: $(inputs.newname)} - type: File - requirements: - - class: InitialWorkDirRequirement - listing: - - {entry: $(inputs.srcfile), entryname: $(inputs.newname)} -- id: echo - in: - - {id: p, source: rename/out} - - {id: checkname, source: newname} - out: [] - run: - arguments: [sh, -c, "name=`basename $(inputs.p.path)`\nls -l $(inputs.p.path)\nif - test $name = $(inputs.checkname) ; then\n echo success\nelse\n echo expected - basename to be $(inputs.checkname) but was $name\n exit 1\nfi\n"] - class: CommandLineTool - cwlVersion: v1.2 - inputs: - - {id: p, type: File} - - {id: checkname, type: string} - outputs: [] - requirements: [] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_writable-dir-docker.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_writable-dir-docker.cwl deleted file mode 100644 index 93fff470..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_writable-dir-docker.cwl +++ /dev/null @@ -1,15 +0,0 @@ -arguments: [touch, emptyWritableDir/blurg] -class: CommandLineTool -cwlVersion: v1.2 -hints: -- {class: DockerRequirement, dockerPull: alpine} -inputs: [] -outputs: -- id: out - outputBinding: {glob: emptyWritableDir} - type: Directory -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "$({class: 'Directory', listing: []})", entryname: emptyWritableDir, writable: true} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_writable-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_writable-dir.cwl deleted file mode 100644 index 829ed0ab..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_packed_writable-dir.cwl +++ /dev/null @@ -1,13 +0,0 @@ -arguments: [touch, emptyWritableDir/blurg] -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: -- id: out - outputBinding: {glob: emptyWritableDir} - type: Directory -requirements: -- {class: InlineJavascriptRequirement} -- class: InitialWorkDirRequirement - listing: - - {entry: "$({class: 'Directory', listing: []})", entryname: emptyWritableDir, writable: true} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_params.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_params.cwl deleted file mode 100644 index 2b1d6fc9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_params.cwl +++ /dev/null @@ -1,16 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - bar: - type: Any - default: { - "baz": "zab1", - "b az": 2, - "b'az": true, - 'b"az': null, - "buz": ['a', 'b', 'c'] - } - -outputs: {"$import": params_inc.yml} - -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_params2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_params2.cwl deleted file mode 100644 index 49a6ad1d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_params2.cwl +++ /dev/null @@ -1,19 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: InlineJavascriptRequirement # needed by params_inc.yml - -inputs: - bar: - type: Any - default: { - "baz": "zab1", - "b az": 2, - "b'az": true, - 'b"az': null, - "buz": ['a', 'b', 'c'] - } - -outputs: {"$import": params_inc.yml} - -baseCommand: "true" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_params_input_length_non_array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_params_input_length_non_array.cwl deleted file mode 100644 index bbe50849..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_params_input_length_non_array.cwl +++ /dev/null @@ -1,40 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - length: - type: int - default: 1 - bar: - type: - type: record - name: bar_record - fields: - length: - type: int - baz: - type: - type: record - name: baz_record - fields: - length: - type: - type: record - name: length_record - fields: - bap: - type: int - -outputs: - output1: - type: int - outputBinding: - outputEval: $(inputs.length) - output2: - type: int - outputBinding: - outputEval: $(inputs.bar.length) - output3: - type: int - outputBinding: - outputEval: $(inputs.baz.length.bap) -baseCommand: "true" \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_parseInt-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_parseInt-tool.cwl deleted file mode 100755 index 844cc5d0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_parseInt-tool.cwl +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: ExpressionTool -requirements: - - class: InlineJavascriptRequirement -cwlVersion: v1.2 - -inputs: - file1: - type: File - loadContents: true - -outputs: - output: int - -expression: "$({'output': parseInt(inputs.file1.contents)})" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_pass-unconnected.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_pass-unconnected.cwl deleted file mode 100644 index ce07c71c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_pass-unconnected.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - inp1: - type: string - default: hello inp1 - inp2: - type: string - default: hello inp2 -outputs: - out: - type: string - outputSource: step1/out -steps: - step1: - in: - in: inp1 - in2: inp2 - out: [out] - run: echo-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-in-format.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-in-format.cwl deleted file mode 100644 index 006bf28c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-in-format.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - regular_input: - type: File - format: http://example.com/format1 - record_input: - type: - type: record - fields: - f1: - type: File - format: http://example.com/format1 - f2: - type: - type: array - items: File - format: http://example.com/format2 -outputs: [] -arguments: ['true'] \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-in-secondaryFiles-missing-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-in-secondaryFiles-missing-wf.cwl deleted file mode 100644 index 5d334bcb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-in-secondaryFiles-missing-wf.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - record_input: - type: - type: record - fields: - f1: - type: File - f2: - type: - type: array - items: File -outputs: [] -steps: - step1: - in: - record_input: record_input - out: [] - run: record-in-secondaryFiles.cwl \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-in-secondaryFiles-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-in-secondaryFiles-wf.cwl deleted file mode 100644 index f04d34b3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-in-secondaryFiles-wf.cwl +++ /dev/null @@ -1,22 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - record_input: - type: - type: record - fields: - f1: - type: File - secondaryFiles: .s2 - f2: - type: - type: array - items: File - secondaryFiles: .s3 -outputs: [] -steps: - step1: - in: - record_input: record_input - out: [] - run: record-in-secondaryFiles.cwl \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-in-secondaryFiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-in-secondaryFiles.cwl deleted file mode 100644 index b9efc64a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-in-secondaryFiles.cwl +++ /dev/null @@ -1,20 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - record_input: - type: - type: record - fields: - f1: - type: File - secondaryFiles: .s2 - f2: - type: - type: array - items: File - secondaryFiles: .s3 -outputs: [] -baseCommand: test -arguments: [-f, $(inputs.record_input.f1.path).s2, - '-a', '-f', '$(inputs.record_input.f2[0].path).s3', - '-a', '-f', '$(inputs.record_input.f2[1].path).s3'] \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-order.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-order.cwl deleted file mode 100644 index 19762da4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-order.cwl +++ /dev/null @@ -1,55 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 - -baseCommand: python -inputs: - - id: args.py - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - - id: a - type: - type: record - fields: - - name: b - type: int - inputBinding: - position: 1 - prefix: -b - - name: c - type: int - inputBinding: - position: 3 - prefix: -c - inputBinding: - position: 5 - prefix: -a - - id: d - type: - type: record - fields: - - name: e - type: int - inputBinding: - position: 2 - prefix: -e - - name: f - type: int - inputBinding: - position: 4 - prefix: -f - inputBinding: - position: 6 - prefix: -d -outputs: - - id: args - type: - type: array - items: string - -hints: - - class: DockerRequirement - dockerPull: docker.io/python:3-slim diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-out-format.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-out-format.cwl deleted file mode 100644 index 560eb230..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-out-format.cwl +++ /dev/null @@ -1,25 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: - record_input: - type: - type: record - fields: - f1: File - f2: File[] -outputs: - f1out: - type: File - format: http://example.com/format1 - outputBinding: - outputEval: $(inputs.record_input.f1) - record_output: - type: - type: record - fields: - f2out: - type: File - format: http://example.com/format2 - outputBinding: - outputEval: $(inputs.record_input.f2[0]) -arguments: ['true'] \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-out-secondaryFiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-out-secondaryFiles.cwl deleted file mode 100644 index bc4ca6e6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-out-secondaryFiles.cwl +++ /dev/null @@ -1,23 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: - record_output: - type: - type: record - fields: - f1: - type: File - secondaryFiles: .s2 - outputBinding: - glob: A - f2: - type: - type: array - items: File - secondaryFiles: .s3 - outputBinding: - glob: [B, C] - -baseCommand: touch -arguments: [A, A.s2, B, B.s3, C, C.s3] \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-output-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-output-wf.cwl deleted file mode 100644 index bb207780..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-output-wf.cwl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -inputs: - irec: - type: - name: irec - type: record - fields: - - name: ifoo - type: File - - name: ibar - type: File - -outputs: - orec: - type: - name: orec - type: record - fields: - - name: ofoo - type: File - - name: obar - type: File - outputSource: step1/orec - -steps: - step1: - run: record-output.cwl - in: - irec: irec - out: [orec] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-output.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-output.cwl deleted file mode 100644 index dbbc8390..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-output.cwl +++ /dev/null @@ -1,38 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: ShellCommandRequirement -inputs: - irec: - type: - name: irec - type: record - fields: - - name: ifoo - type: File - inputBinding: - position: 2 - - name: ibar - type: File - inputBinding: - position: 6 -outputs: - orec: - type: - name: orec - type: record - fields: - - name: ofoo - type: File - outputBinding: - glob: foo - - name: obar - type: File - outputBinding: - glob: bar -arguments: - - {valueFrom: "cat", position: 1} - - {valueFrom: "> foo", position: 3, shellQuote: false} - - {valueFrom: "&&", position: 4, shellQuote: false} - - {valueFrom: "cat", position: 5} - - {valueFrom: "> bar", position: 7, shellQuote: false} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-sd-secondaryFiles.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-sd-secondaryFiles.cwl deleted file mode 100644 index c1b61c64..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record-sd-secondaryFiles.cwl +++ /dev/null @@ -1,26 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - SchemaDefRequirement: - types: - - name: RecordTestType - type: record - doc: Type test record - fields: - f1: - type: File - secondaryFiles: .s2 - f2: - type: - type: array - items: File - secondaryFiles: .s3 -inputs: - record_input: - type: RecordTestType - -outputs: [] -baseCommand: test -arguments: [-f, $(inputs.record_input.f1.path).s2, - '-a', '-f', '$(inputs.record_input.f2[0].path).s3', - '-a', '-f', '$(inputs.record_input.f2[1].path).s3'] \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record_outputeval.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record_outputeval.cwl deleted file mode 100644 index 6540c1e1..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record_outputeval.cwl +++ /dev/null @@ -1,36 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -requirements: - InlineJavascriptRequirement: {} - -inputs: - gtf_version: - type: string - default: M21 - organism: - type: string - default: mouse - organism_prefix: - type: string - default: m - -baseCommand: - - bash - - -c -arguments: - - touch GRC$(inputs.organism_prefix)38.primary_assembly.genome.fa ; touch gencode.v$(inputs.gtf_version).primary_assembly.annotation.gtf -outputs: - - id: references - type: - name: References - fields: - - name: genome_fa - type: File - - name: annotation_gtf - type: File - type: record - outputBinding: - outputEval: '$({ "genome_fa": { "class": "File", "path": runtime.outdir+"/"+"GRC" - + inputs.organism_prefix + "38.primary_assembly.genome.fa" }, "annotation_gtf": - { "class": "File", "path": runtime.outdir+"/"+"gencode.v" + inputs.gtf_version - + ".primary_assembly.annotation.gtf" } })' diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record_outputeval_nojs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record_outputeval_nojs.cwl deleted file mode 100644 index b29c6622..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_record_outputeval_nojs.cwl +++ /dev/null @@ -1,26 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -inputs: - ref: - type: - type: record - fields: - genome_fa: string - annotation_gtf: string - default: { genome_fa: GRCm38.primary_assembly.genome.fa, - annotation_gtf: gencode.vM21.primary_assembly.annotation.gtf } - -baseCommand: echo -arguments: - - $(inputs.ref.genome_fa) $(inputs.ref.annotation_gtf) -outputs: - references: - type: - type: record - fields: - genome_fa: string - annotation_gtf: string - outputBinding: - outputEval: $(inputs.ref) - summary: - type: stdout diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_recursive-input-directory.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_recursive-input-directory.cwl deleted file mode 100644 index 07b11227..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_recursive-input-directory.cwl +++ /dev/null @@ -1,33 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.input_dir) - entryname: work_dir - writable: true - ShellCommandRequirement: {} -stdout: output.txt -arguments: - - shellQuote: false - valueFrom: | - touch work_dir/e; - if [ ! -w work_dir ]; then echo work_dir not writable; fi; - if [ -L work_dir ]; then echo work_dir is a symlink; fi; - if [ ! -w work_dir/a ]; then echo work_dir/a not writable; fi; - if [ -L work_dir/a ]; then echo work_dir/a is a symlink; fi; - if [ ! -w work_dir/c ]; then echo work_dir/c not writable; fi; - if [ -L work_dir/c ]; then echo work_dir/c is a symlink; fi; - if [ ! -w work_dir/c/d ]; then echo work_dir/c/d not writable; fi; - if [ -L work_dir/c/d ]; then echo work_dir/c/d is a symlink; fi; - if [ ! -w work_dir/e ]; then echo work_dir/e not writable; fi; - if [ -L work_dir/e ]; then echo work_dir/e is a symlink ; fi; -inputs: - input_dir: Directory -outputs: - output_dir: - type: Directory - outputBinding: - glob: work_dir - test_result: - type: stdout diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_rename-inputs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_rename-inputs.cwl deleted file mode 100644 index bffc0311..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_rename-inputs.cwl +++ /dev/null @@ -1,63 +0,0 @@ -#!/usr/bin/env cwl-runner -id: InputSecondaryFileConformanceTest -baseCommand: -- ls -class: CommandLineTool -cwlVersion: v1.2 -doc: | - Simple test to confirm the implementation of expressions returning a File within a CommandInputParameter.secondaryFile field. - - Use GREP to filter the result from ls to ensure we only get the secondary files in there. - - Related links: - - Issue: https://github.com/common-workflow-language/cwltool/issues/1232 - - PR: https://github.com/common-workflow-language/cwltool/pull/1233 - - Discourse: https://cwl.discourse.group/t/ask-cwl-to-rename-a-secondary-file/72 - -inputs: -- id: inputWithSecondary - type: File - doc: | - This input will with a secondary file `.accessory`. You could create these files (and its accessory) with: - ```bash - touch secondary_file_test.txt - touch secondary_file_test.txt.accessory - ``` - secondaryFiles: - - .accessory - - | - ${ - function resolveSecondary(base, secPattern) { - if (secPattern[0] == '^') { - var spl = base.split('.'); - var endIndex = spl.length > 1 ? spl.length - 1 : 1; - return resolveSecondary(spl.slice(undefined, endIndex).join("."), secPattern.slice(1)); - } - return base + secPattern; - } - return [{ - "class": "File", - "location": self.secondaryFiles[0].location, - "basename": resolveSecondary(self.basename, '^.accessory') - }]; - } - -arguments: -- valueFrom: "|" - shellQuote: false - position: 0 -- valueFrom: "grep" - position: 1 -- valueFrom: "secondary" - position: 2 - -outputs: -- id: output_file - type: stdout -stdout: result -requirements: - InlineJavascriptRequirement: {} - ShellCommandRequirement: {} - InitialWorkDirRequirement: - listing: - - $(inputs.inputWithSecondary) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_rename-outputs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_rename-outputs.cwl deleted file mode 100644 index 92b287d2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_rename-outputs.cwl +++ /dev/null @@ -1,49 +0,0 @@ -#!/usr/bin/env cwl-runner -id: OutputSecondaryFileConformanceTest -baseCommand: -- ls -class: CommandLineTool -cwlVersion: v1.2 -doc: | - Simple test to confirm the implementation of expressions returning a File within a CommandOutputParameter.secondaryFile field. - - Related links: - - Issue: https://github.com/common-workflow-language/cwltool/issues/1232 - - PR: https://github.com/common-workflow-language/cwltool/pull/1233 - - Discourse: https://cwl.discourse.group/t/ask-cwl-to-rename-a-secondary-file/72 - -inputs: [] -outputs: -- id: output_file - label: out - outputBinding: - glob: "*.txt" - secondaryFiles: | - ${ - function resolveSecondary(base, secPattern) { - if (secPattern[0] == "^") { - var spl = base.split("."); - var endIndex = spl.length > 1 ? spl.length - 1 : 1; - return resolveSecondary(spl.slice(undefined, endIndex).join("."), secPattern.slice(1)); - } - return base + secPattern; - } - return [ - { - "class": "File", - "path": resolveSecondary(self.path, "^.accessory"), - "basename": resolveSecondary(self.basename, ".accessory") - } - ]; - } - type: File -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entry: "" - entryname: secondary_file_test.txt - writable: true - - entry: "" - entryname: secondary_file_test.accessory - writable: true diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_rename.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_rename.cwl deleted file mode 100644 index 7bc0025a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_rename.cwl +++ /dev/null @@ -1,16 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -baseCommand: "true" -requirements: - InitialWorkDirRequirement: - listing: - - entryname: $(inputs.newname) - entry: $(inputs.srcfile) -inputs: - srcfile: File - newname: string -outputs: - outfile: - type: File - outputBinding: - glob: $(inputs.newname) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_revsort-abstract.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_revsort-abstract.cwl deleted file mode 100644 index 9a54ddc6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_revsort-abstract.cwl +++ /dev/null @@ -1,52 +0,0 @@ -# -# This is a variant of revsort.cwl where the "sorted" -# step has not yet been implemented, but has a placeholder -# Operation. -# -class: Workflow -doc: "Reverse the lines in a document, then sort those lines." -cwlVersion: v1.2 - -inputs: - input: - type: File - doc: "The input file to be processed." - reverse_sort: - type: boolean - default: true - doc: "If true, reverse (decending) sort" - -outputs: - output: - type: File - outputSource: sort/sorted - doc: "The output with the lines reversed and sorted." - -steps: - rev: - in: - input: input - out: [output] - run: revtool.cwl - - sort: - in: - input: rev/output - reverse: reverse_sort - out: [sorted] - run: - class: Operation - id: "sort" - doc: "Sort the lines of the file" - inputs: - input: - type: File - doc: "The input file to be sorted." - reverse: - type: boolean - default: true - doc: "If true, reverse (decending) sort" - outputs: - sorted: - type: File - doc: "The sorted file" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_revsort-packed.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_revsort-packed.cwl deleted file mode 100644 index ccaed394..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_revsort-packed.cwl +++ /dev/null @@ -1,125 +0,0 @@ -{ - "cwlVersion": "v1.2", - "$graph": [ - { - "class": "Workflow", - "doc": "Reverse the lines in a document, then sort those lines.", - "hints": [ - { - "class": "DockerRequirement", - "dockerPull": "debian:stretch-slim" - } - ], - "inputs": [ - { - "type": "File", - "doc": "The input file to be processed.", - "id": "#main/input" - }, - { - "type": "boolean", - "default": true, - "doc": "If true, reverse (decending) sort", - "id": "#main/reverse_sort" - } - ], - "outputs": [ - { - "type": "File", - "outputSource": "#main/sorted/output", - "doc": "The output with the lines reversed and sorted.", - "id": "#main/output" - } - ], - "steps": [ - { - "in": [ - { - "source": "#main/input", - "id": "#main/rev/input" - } - ], - "out": [ - "#main/rev/output" - ], - "run": "#revtool.cwl", - "id": "#main/rev" - }, - { - "in": [ - { - "source": "#main/rev/output", - "id": "#main/sorted/input" - }, - { - "source": "#main/reverse_sort", - "id": "#main/sorted/reverse" - } - ], - "out": [ - "#main/sorted/output" - ], - "run": "#sorttool.cwl", - "id": "#main/sorted" - } - ], - "id": "#main" - }, - { - "class": "CommandLineTool", - "doc": "Reverse each line using the `rev` command", - "inputs": [ - { - "type": "File", - "inputBinding": {}, - "id": "#revtool.cwl/input" - } - ], - "outputs": [ - { - "type": "File", - "outputBinding": { - "glob": "output.txt" - }, - "id": "#revtool.cwl/output" - } - ], - "baseCommand": "rev", - "stdout": "output.txt", - "id": "#revtool.cwl" - }, - { - "class": "CommandLineTool", - "doc": "Sort lines using the `sort` command", - "inputs": [ - { - "id": "#sorttool.cwl/reverse", - "type": "boolean", - "inputBinding": { - "position": 1, - "prefix": "-r" - } - }, - { - "id": "#sorttool.cwl/input", - "type": "File", - "inputBinding": { - "position": 2 - } - } - ], - "outputs": [ - { - "id": "#sorttool.cwl/output", - "type": "File", - "outputBinding": { - "glob": "output.txt" - } - } - ], - "baseCommand": "sort", - "stdout": "output.txt", - "id": "#sorttool.cwl" - } - ] -} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_revsort.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_revsort.cwl deleted file mode 100644 index 244601de..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_revsort.cwl +++ /dev/null @@ -1,65 +0,0 @@ -# -# This is a two-step workflow which uses "revtool" and "sorttool" defined above. -# -class: Workflow -doc: "Reverse the lines in a document, then sort those lines." -cwlVersion: v1.2 - -# Requirements & hints specify prerequisites and extensions to the workflow. -# In this example, DockerRequirement specifies a default Docker container -# in which the command line tools will execute. -hints: - - class: DockerRequirement - dockerPull: debian:stretch-slim - - -# The inputs array defines the structure of the input object that describes -# the inputs to the workflow. -# -# The "reverse_sort" input parameter demonstrates the "default" field. If the -# field "reverse_sort" is not provided in the input object, the default value will -# be used. -inputs: - input: - type: File - doc: "The input file to be processed." - reverse_sort: - type: boolean - default: true - doc: "If true, reverse (decending) sort" - -# The "outputs" array defines the structure of the output object that describes -# the outputs of the workflow. -# -# Each output field must be connected to the output of one of the workflow -# steps using the "connect" field. Here, the parameter "#output" of the -# workflow comes from the "#sorted" output of the "sort" step. -outputs: - output: - type: File - outputSource: sorted/output - doc: "The output with the lines reversed and sorted." - -# The "steps" array lists the executable steps that make up the workflow. -# The tool to execute each step is listed in the "run" field. -# -# In the first step, the "inputs" field of the step connects the upstream -# parameter "#input" of the workflow to the input parameter of the tool -# "revtool.cwl#input" -# -# In the second step, the "inputs" field of the step connects the output -# parameter "#reversed" from the first step to the input parameter of the -# tool "sorttool.cwl#input". -steps: - rev: - in: - input: input - out: [output] - run: revtool.cwl - - sorted: - in: - input: rev/output - reverse: reverse_sort - out: [output] - run: sorttool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_revtool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_revtool.cwl deleted file mode 100644 index c4c0d035..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_revtool.cwl +++ /dev/null @@ -1,37 +0,0 @@ -# -# Simplest example command line program wrapper for the Unix tool "rev". -# -class: CommandLineTool -cwlVersion: v1.2 -doc: "Reverse each line using the `rev` command" - -# The "inputs" array defines the structure of the input object that describes -# the inputs to the underlying program. Here, there is one input field -# defined that will be called "input" and will contain a "File" object. -# -# The input binding indicates that the input value should be turned into a -# command line argument. In this example inputBinding is an empty object, -# which indicates that the file name should be added to the command line at -# a default location. -inputs: - input: - type: File - inputBinding: {} - -# The "outputs" array defines the structure of the output object that -# describes the outputs of the underlying program. Here, there is one -# output field defined that will be called "output", must be a "File" type, -# and after the program executes, the output value will be the file -# output.txt in the designated output directory. -outputs: - output: - type: File - outputBinding: - glob: output.txt - -# The actual program to execute. -baseCommand: rev - -# Specify that the standard output stream must be redirected to a file called -# output.txt in the designated output directory. -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_runtime-outdir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_runtime-outdir.cwl deleted file mode 100644 index 41bb7b0b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_runtime-outdir.cwl +++ /dev/null @@ -1,14 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -baseCommand: [bash, -c] -arguments: - - | - mkdir -p foo - touch baz.txt - touch foo/bar.txt -inputs: [] -outputs: - stuff: - type: Directory - outputBinding: - glob: $(runtime.outdir) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_runtime-paths-distinct.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_runtime-paths-distinct.cwl deleted file mode 100644 index 4d190f30..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_runtime-paths-distinct.cwl +++ /dev/null @@ -1,13 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - ShellCommandRequirement: {} -inputs: {} -outputs: - foo: File -arguments: - - shellQuote: false - valueFrom: | - echo "cow" > "$(runtime.outdir)/foo" && - echo "moo" > "$(runtime.tmpdir)/foo" && - echo '{"foo": {"path": "$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valueFrom-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valueFrom-tool.cwl deleted file mode 100644 index 8d0fef14..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valueFrom-tool.cwl +++ /dev/null @@ -1,15 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -inputs: - scattered_message: - type: string - inputBinding: - position: 2 - message: - type: string - inputBinding: - position: 1 -outputs: - out_message: - type: stdout -baseCommand: echo diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-inputs-wf1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-inputs-wf1.cwl deleted file mode 100644 index e0bb8732..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-inputs-wf1.cwl +++ /dev/null @@ -1,59 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: Workflow -inputs: - inp: - type: - type: array - items: - type: record - name: instr - fields: - - name: instr - type: string -outputs: - out: - type: - type: array - items: string - outputSource: step1/echo_out - -requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - -steps: - step1: - in: - echo_unused: inp - echo_in: - valueFrom: $(inputs.echo_unused.instr) - first: - source: inp - valueFrom: "$(self[0].instr)" - out: [echo_out] - scatter: echo_unused - run: - class: CommandLineTool - inputs: - first: - type: string - inputBinding: - position: 1 - echo_in: - type: string - inputBinding: - position: 2 - echo_unused: Any - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: - - "-n" - - "foo" - stdout: "step1_out" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf1.cwl deleted file mode 100644 index 49873e4c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf1.cwl +++ /dev/null @@ -1,58 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: Workflow -inputs: - inp: - type: - type: array - items: - type: record - name: instr - fields: - - name: instr - type: string -outputs: - out: - type: - type: array - items: string - outputSource: step1/echo_out - -requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - -steps: - step1: - in: - echo_in: - source: inp - valueFrom: $(self.instr) - first: - source: inp - valueFrom: "$(self[0].instr)" - out: [echo_out] - scatter: echo_in - run: - class: CommandLineTool - inputs: - first: - type: string - inputBinding: - position: 1 - echo_in: - type: string - inputBinding: - position: 2 - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: - - "-n" - - "foo" - stdout: "step1_out" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf2.cwl deleted file mode 100644 index 1f441a3b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf2.cwl +++ /dev/null @@ -1,73 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: Workflow - -inputs: - inp1: - type: - type: array - items: - type: record - name: instr - fields: - - name: instr - type: string - inp2: - type: - type: array - items: string -outputs: - out: - outputSource: step1/echo_out - type: - type: array - items: - type: array - items: string - -requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - -steps: - step1: - in: - echo_in1: - source: inp1 - valueFrom: $(self.instr) - echo_in2: inp2 - first: - source: inp1 - valueFrom: "$(self[0].instr)" - out: [echo_out] - - scatter: [echo_in1, echo_in2] - scatterMethod: nested_crossproduct - run: - class: CommandLineTool - id: step1command - inputs: - first: - type: string - inputBinding: - position: 1 - echo_in1: - type: string - inputBinding: - position: 2 - echo_in2: - type: string - inputBinding: - position: 3 - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: - - "-n" - - "foo" - stdout: step1_out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf3.cwl deleted file mode 100644 index b97092d9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf3.cwl +++ /dev/null @@ -1,69 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 -$graph: - -- id: echo - class: CommandLineTool - inputs: - first: - type: string - inputBinding: - position: 1 - echo_in1: - type: string - inputBinding: - position: 2 - echo_in2: - type: string - inputBinding: - position: 3 - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: ["-n", "foo"] - stdout: step1_out - -- id: main - class: Workflow - inputs: - inp1: - type: - type: array - items: - type: record - name: instr - fields: - - name: instr - type: string - inp2: - type: { type: array, items: string } - requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - steps: - step1: - scatter: [echo_in1, echo_in2] - scatterMethod: flat_crossproduct - in: - echo_in1: - source: inp1 - valueFrom: $(self.instr) - echo_in2: inp2 - first: - source: inp1 - valueFrom: "$(self[0].instr)" - out: [echo_out] - run: "#echo" - - outputs: - out: - outputSource: step1/echo_out - type: - type: array - items: string diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf4.cwl deleted file mode 100644 index 3b8c70f6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf4.cwl +++ /dev/null @@ -1,67 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -$graph: -- id: echo - class: CommandLineTool - inputs: - first: - type: string - inputBinding: - position: 1 - echo_in1: - type: string - inputBinding: - position: 2 - echo_in2: - type: string - inputBinding: - position: 3 - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: ["-n", "foo"] - stdout: step1_out - -- id: main - class: Workflow - inputs: - inp1: - type: - type: array - items: - type: record - name: instr - fields: - - name: instr - type: string - inp2: - type: { type: array, items: string } - requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - steps: - step1: - scatter: [echo_in1, echo_in2] - scatterMethod: dotproduct - in: - echo_in1: - source: inp1 - valueFrom: $(self.instr) - echo_in2: inp2 - first: - source: inp1 - valueFrom: "$(self[0].instr)" - out: [echo_out] - run: "#echo" - - outputs: - out: - outputSource: step1/echo_out - type: - type: array - items: string diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf5.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf5.cwl deleted file mode 100644 index 57b61b17..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf5.cwl +++ /dev/null @@ -1,58 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: Workflow -inputs: - inp: - type: - type: array - items: - type: record - name: instr - fields: - - name: instr - type: string -outputs: - out: - type: - type: array - items: string - outputSource: step1/echo_out - -requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - -steps: - step1: - in: - echo_in: - source: inp - valueFrom: $(self.instr) - first: - source: inp - valueFrom: $(inputs.echo_in.instr) - out: [echo_out] - scatter: echo_in - run: - class: CommandLineTool - inputs: - first: - type: string - inputBinding: - position: 1 - echo_in: - type: string - inputBinding: - position: 2 - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: - - "-n" - - "foo" - stdout: "step1_out" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf6.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf6.cwl deleted file mode 100644 index bb7cb050..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-valuefrom-wf6.cwl +++ /dev/null @@ -1,21 +0,0 @@ -cwlVersion: v1.2 -class: Workflow -requirements: - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement -inputs: - scattered_messages: string[] -outputs: - out_message: - type: File[] - outputSource: step1/out_message -steps: - step1: - run: scatter-valueFrom-tool.cwl - scatter: [scattered_message] - scatterMethod: dotproduct - in: - scattered_message: scattered_messages - message: - valueFrom: "Hello" - out: [out_message] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-wf1.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-wf1.cwl deleted file mode 100644 index 4ba50728..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-wf1.cwl +++ /dev/null @@ -1,37 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: Workflow -inputs: - inp: string[] -outputs: - out: - type: string[] - outputSource: step1/echo_out - -requirements: - - class: ScatterFeatureRequirement - -steps: - step1: - in: - echo_in: inp - out: [echo_out] - scatter: echo_in - run: - class: CommandLineTool - inputs: - echo_in: - type: string - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: - - "-n" - - "foo" - stdout: "step1_out" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-wf2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-wf2.cwl deleted file mode 100644 index a6f85515..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-wf2.cwl +++ /dev/null @@ -1,51 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: Workflow - -inputs: - inp1: string[] - inp2: string[] - -outputs: - out: - outputSource: step1/echo_out - type: - type: array - items: - type: array - items: string - -requirements: - - class: ScatterFeatureRequirement - -steps: - step1: - in: - echo_in1: inp1 - echo_in2: inp2 - out: [echo_out] - - scatter: [echo_in1, echo_in2] - scatterMethod: nested_crossproduct - run: - class: CommandLineTool - id: step1command - inputs: - echo_in1: - type: string - inputBinding: {} - echo_in2: - type: string - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: - - "-n" - - "foo" - stdout: step1_out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-wf3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-wf3.cwl deleted file mode 100644 index 2cdc1d3f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-wf3.cwl +++ /dev/null @@ -1,48 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 -$graph: - -- id: echo - class: CommandLineTool - inputs: - echo_in1: - type: string - inputBinding: {} - echo_in2: - type: string - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: ["-n", "foo"] - stdout: step1_out - -- id: main - class: Workflow - inputs: - inp1: string[] - inp2: string[] - requirements: - - class: ScatterFeatureRequirement - steps: - step1: - scatter: [echo_in1, echo_in2] - scatterMethod: flat_crossproduct - in: - echo_in1: inp1 - echo_in2: inp2 - out: [echo_out] - run: "#echo" - - outputs: - out: - outputSource: step1/echo_out - type: - type: array - items: string diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-wf4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-wf4.cwl deleted file mode 100644 index a3203cb7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_scatter-wf4.cwl +++ /dev/null @@ -1,46 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -$graph: -- id: echo - class: CommandLineTool - inputs: - echo_in1: - type: string - inputBinding: {} - echo_in2: - type: string - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - arguments: ["-n", "foo"] - stdout: step1_out - -- id: main - class: Workflow - inputs: - inp1: string[] - inp2: string[] - requirements: - - class: ScatterFeatureRequirement - steps: - step1: - scatter: [echo_in1, echo_in2] - scatterMethod: dotproduct - in: - echo_in1: inp1 - echo_in2: inp2 - out: [echo_out] - run: "#echo" - - outputs: - - id: out - outputSource: step1/echo_out - type: - type: array - items: string diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_schemadef-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_schemadef-tool.cwl deleted file mode 100644 index 90343981..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_schemadef-tool.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - - $import: schemadef-type.yml - -inputs: - - id: hello - type: "schemadef-type.yml#HelloType" - inputBinding: - valueFrom: $(self.a)/$(self.b) - -outputs: - - id: output - type: File - outputBinding: - glob: output.txt - -stdout: output.txt -baseCommand: echo diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_schemadef-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_schemadef-wf.cwl deleted file mode 100644 index 4ba75fb9..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_schemadef-wf.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 -class: Workflow - -requirements: - - $import: schemadef-type.yml - -inputs: - hello: "schemadef-type.yml#HelloType" - -outputs: - output: - type: File - outputSource: step1/output - -steps: - step1: - in: - hello: hello - out: [output] - run: schemadef-tool.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_schemadef_types_with_import-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_schemadef_types_with_import-wf.cwl deleted file mode 100644 index 6af93dde..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_schemadef_types_with_import-wf.cwl +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env cwl-runner -# See https://github.com/jeremiahsavage/cwl_schemadef/, thanks to Jeremiah H. Savage. -cwlVersion: v1.2 -class: Workflow - -requirements: - - class: SchemaDefRequirement - types: - - $import: schemadef_types_with_import_readgroup.yml - -inputs: - readgroups_bam: - type: "schemadef_types_with_import_readgroup.yml#readgroups_bam_file" - -steps: - step1: - run: schemadef_types_with_import-tool.cwl - in: - message: readgroups_bam - out: [out] - -outputs: - out: - type: string - outputSource: step1/out diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_search.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_search.cwl deleted file mode 100644 index 745b49bf..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_search.cwl +++ /dev/null @@ -1,110 +0,0 @@ -cwlVersion: v1.2 -$graph: -- id: index - class: CommandLineTool - baseCommand: python - arguments: - - valueFrom: input.txt - position: 1 - requirements: - - class: InitialWorkDirRequirement - listing: - - entryname: input.txt - entry: $(inputs.file) - - class: InlineJavascriptRequirement - hints: - - class: DockerRequirement - dockerPull: python:2-slim - - inputs: - file: File - secondfile: File - index.py: - type: File - default: - class: File - location: index.py - inputBinding: - position: 0 - outputs: - result: - type: File - outputBinding: - glob: input.txt - secondaryFiles: - - ".idx1" - - "^.idx2" - - '$(self.basename).idx3' - - '${ return self.basename+".idx4"; }' - - '$({"path": self.path+".idx5", "class": "File"})' - - '$(self.nameroot).idx6$(self.nameext)' - - '${ return [self.basename+".idx7", inputs.secondfile]; }' - - "_idx8" - -- id: search - class: CommandLineTool - baseCommand: python - requirements: - - class: InlineJavascriptRequirement - hints: - - class: DockerRequirement - dockerPull: python:2-slim - inputs: - file: - type: File - inputBinding: - position: 1 - secondaryFiles: - - ".idx1" - - "^.idx2" - - '$(self.basename).idx3' - - '${ return self.basename+".idx4"; }' - - '$(self.nameroot).idx6$(self.nameext)' - - '${ return [self.basename+".idx7"]; }' - - "_idx8" - search.py: - type: File - default: - class: File - location: search.py - inputBinding: - position: 0 - term: - type: string - inputBinding: - position: 2 - outputs: - result: - type: File - outputBinding: - glob: result.txt - stdout: result.txt - -- id: main - class: Workflow - inputs: - infile: File - secondfile: File - term: string - outputs: - outfile: - type: File - outputSource: search/result - indexedfile: - type: File - outputSource: index/result - - steps: - index: - run: "#index" - in: - file: infile - secondfile: secondfile - out: [result] - - search: - run: "#search" - in: - file: index/result - term: term - out: [result] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_shellchar.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_shellchar.cwl deleted file mode 100644 index d563804d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_shellchar.cwl +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: | - Ensure that arguments containing shell directives are not interpreted and - that `shellQuote: false` has no effect when ShellCommandRequirement is not in - effect. -inputs: [] -outputs: - stdout_file: stdout - stderr_file: stderr -baseCommand: echo -arguments: [{valueFrom: "foo 1>&2", shellQuote: false}] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_shellchar2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_shellchar2.cwl deleted file mode 100644 index df3f52d2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_shellchar2.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: | - Ensure that `shellQuote: true` is the default behavior when - ShellCommandRequirement is in effect. -requirements: - ShellCommandRequirement: {} -inputs: [] -outputs: - stdout_file: stdout - stderr_file: stderr -baseCommand: echo -arguments: ["foo 1>&2"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_size-expression-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_size-expression-tool.cwl deleted file mode 100644 index 9d1e768a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_size-expression-tool.cwl +++ /dev/null @@ -1,43 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 - -requirements: - - class: InlineJavascriptRequirement - -class: CommandLineTool - -inputs: - - id: input - type: - type: array - items: File - -outputs: - output_file: - type: File - outputBinding: {glob: output.txt} - -arguments: - - valueFrom: | - ${ - var cmd = ["echo"]; - if (inputs.input.length == 0) { - cmd.push('no_inputs'); - } - else { - for (var i = 0; i < inputs.input.length; i++) { - var filesize = inputs.input[i].size; - if (filesize == 0) { - cmd.push("empty_file"); - } else if (filesize <= 16) { - cmd.push("small_file"); - } else { - cmd.push("big_file") - } - } - } - return cmd; - } -baseCommand: [] -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_sorttool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_sorttool.cwl deleted file mode 100644 index e8c5dd48..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_sorttool.cwl +++ /dev/null @@ -1,35 +0,0 @@ -# Example command line program wrapper for the Unix tool "sort" -# demonstrating command line flags. -class: CommandLineTool -doc: "Sort lines using the `sort` command" -cwlVersion: v1.2 - -# This example is similar to the previous one, with an additional input -# parameter called "reverse". It is a boolean parameter, which is -# intepreted as a command line flag. The value of "prefix" is used for -# flag to put on the command line if "reverse" is true, if "reverse" is -# false, no flag is added. -# -# This example also introduced the "position" field. This indicates the -# sorting order of items on the command line. Lower numbers are placed -# before higher numbers. Here, the "-r" (same as "--reverse") flag (if -# present) will be added to the command line before the input file path. -inputs: - - id: reverse - type: boolean - inputBinding: - position: 1 - prefix: "-r" - - id: input - type: File - inputBinding: - position: 2 - -outputs: - - id: output - type: File - outputBinding: - glob: output.txt - -baseCommand: sort -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage-array-dirs.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage-array-dirs.cwl deleted file mode 100644 index 6b41d75b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage-array-dirs.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -id: stage_array_dirs -baseCommand: - - ls -inputs: - - id: input_list - type: Directory[] -outputs: - - id: output - type: File[] - outputBinding: - glob: - - testdir/a - - rec/B -label: stage-array-dirs.cwl -requirements: - - class: InitialWorkDirRequirement - listing: - - $(inputs.input_list) diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage-array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage-array.cwl deleted file mode 100644 index 36a669ab..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage-array.cwl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -id: stage_array -arguments: - - {shellQuote: false, valueFrom: "ls | grep -v lsout"} -inputs: - - id: input_file - type: File - - id: optional_file - type: File? - - id: input_list - type: 'File[]' - secondaryFiles: - - ^.tar -stdout: lsout -outputs: - - id: output - type: File? - outputBinding: - glob: lsout -label: stage-array.cwl -requirements: - - class: InitialWorkDirRequirement - listing: - - $(inputs.input_file) - - $(inputs.optional_file) - - entry: $(inputs.input_list) - - entry: $(null) - - entryname: a - entry: b - - class: ShellCommandRequirement diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage-unprovided-file.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage-unprovided-file.cwl deleted file mode 100644 index d8ad8d76..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage-unprovided-file.cwl +++ /dev/null @@ -1,24 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -hints: - - class: DockerRequirement - dockerPull: python:2-slim -inputs: - - id: infile - type: File? - inputBinding: - prefix: -cfg - valueFrom: $(self.basename) - - id: "args.py" - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - -baseCommand: python - -outputs: -- id: args - type: string[] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage_file_array.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage_file_array.cwl deleted file mode 100644 index 2136d898..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage_file_array.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -id: stage_file_array -label: Stage File Array -arguments: [ls] -inputs: - - id: input_list - type: 'File[]' - secondaryFiles: - - .sec -outputs: - - id: output - type: File[] - outputBinding: - glob: input_dir/* -requirements: - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: - - entryname: input_dir - entry: "${ return {class: 'Directory', listing: inputs.input_list} }" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage_file_array_basename.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage_file_array_basename.cwl deleted file mode 100644 index fb9caebb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage_file_array_basename.cwl +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -id: stage_file_array_basename -label: Stage File Array (with Directory Basename) -arguments: [ls] -inputs: - - id: input_list - type: 'File[]' - secondaryFiles: - - .sec -outputs: - - id: output - type: File[] - outputBinding: - glob: input_dir/* -requirements: - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: - - entry: "${ return {class: 'Directory', basename: 'input_dir', listing: inputs.input_list} }" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage_file_array_basename_and_entryname.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage_file_array_basename_and_entryname.cwl deleted file mode 100644 index 049c4142..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stage_file_array_basename_and_entryname.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 -id: stage_file_array_basename_and_entryname -label: Stage File Array (with Directory Basename AND entryname) -arguments: [ls] -inputs: - - id: input_list - type: 'File[]' - secondaryFiles: - - .sec -outputs: - - id: output - type: File[] - outputBinding: - glob: input_dir/* -requirements: - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: - - entryname: input_dir - entry: "${ return {class: 'Directory', basename: 'not_input_dir', listing: inputs.input_list} }" diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stagefile.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stagefile.cwl deleted file mode 100644 index 8a9fdbc4..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stagefile.cwl +++ /dev/null @@ -1,26 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -hints: - - class: DockerRequirement - dockerPull: python:2-slim -requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.infile) - entryname: bob.txt - writable: true -inputs: - infile: File -outputs: - outfile: - type: File - outputBinding: - glob: bob.txt -baseCommand: "python" -arguments: - - "-c" - - | - f = open("bob.txt", "r+") - f.seek(8) - f.write("Bob. ") - f.close() diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stderr-mediumcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stderr-mediumcut.cwl deleted file mode 100644 index 8c07c72a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stderr-mediumcut.cwl +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "Test of capturing stderr output in a docker container." -requirements: - ShellCommandRequirement: {} -inputs: [] -outputs: - output_file: - type: stderr -arguments: - - { valueFrom: "echo foo 1>&2", shellQuote: False } -stderr: std.err diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stderr-shortcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stderr-shortcut.cwl deleted file mode 100644 index 6fd7aac0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stderr-shortcut.cwl +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "Test of capturing stderr output." -requirements: - ShellCommandRequirement: {} -inputs: [] -outputs: - output_file: - type: stderr -arguments: - - { valueFrom: "echo foo 1>&2", shellQuote: False } diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stderr.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stderr.cwl deleted file mode 100644 index ab5848b3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stderr.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "Test of capturing stderr output." -requirements: - ShellCommandRequirement: {} -inputs: [] -outputs: - output_file: - type: File - outputBinding: {glob: error.txt} -arguments: - - { valueFrom: "echo foo 1>&2", shellQuote: False } -stderr: error.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stdout_chained_commands.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stdout_chained_commands.cwl deleted file mode 100644 index b0cf25db..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_stdout_chained_commands.cwl +++ /dev/null @@ -1,19 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -requirements: - - class: ShellCommandRequirement -inputs: [] -outputs: - out: - type: string - outputBinding: - glob: out.txt - loadContents: true - outputEval: $(self[0].contents) -stdout: out.txt -arguments: - - echo - - a - - {valueFrom: '&&', shellQuote: false} - - echo - - b diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom-wf.cwl deleted file mode 100644 index 5a7d28a3..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom-wf.cwl +++ /dev/null @@ -1,34 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -requirements: - - class: StepInputExpressionRequirement - -inputs: - in: - type: - name: in - type: record - fields: - - name: file1 - type: File - -outputs: - count_output: - type: int - outputSource: step2/output - -steps: - step1: - run: wc-tool.cwl - in: - file1: - source: in - valueFrom: $(self.file1) - out: [output] - - step2: - run: parseInt-tool.cwl - in: - file1: step1/output - out: [output] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom2-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom2-wf.cwl deleted file mode 100644 index 5b347f4d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom2-wf.cwl +++ /dev/null @@ -1,41 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -requirements: - - class: StepInputExpressionRequirement - - class: InlineJavascriptRequirement - - class: MultipleInputFeatureRequirement - -inputs: - a: int - b: int - -outputs: - val: - type: string - outputSource: step1/echo_out - -steps: - step1: - run: - id: echo - class: CommandLineTool - inputs: - c: - type: int - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - stdout: step1_out - - in: - c: - source: [a, b] - valueFrom: "$(self[0] + self[1])" - out: [echo_out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom3-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom3-wf.cwl deleted file mode 100644 index 780be638..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom3-wf.cwl +++ /dev/null @@ -1,41 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -requirements: - - class: StepInputExpressionRequirement - - class: InlineJavascriptRequirement - -inputs: - a: int - b: int - -outputs: - val: - type: string - outputSource: step1/echo_out - -steps: - step1: - run: - id: echo - class: CommandLineTool - inputs: - c: - type: int - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: "step1_out" - loadContents: true - outputEval: $(self[0].contents) - baseCommand: "echo" - stdout: step1_out - - in: - a: a - b: b - c: - valueFrom: "$(inputs.a + inputs.b)" - out: [echo_out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom4-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom4-wf.cwl deleted file mode 100644 index e4efa0e2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom4-wf.cwl +++ /dev/null @@ -1,36 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -requirements: - StepInputExpressionRequirement: {} - -inputs: [] - -outputs: - val: - type: string - outputSource: step1/echo_out - -steps: - step1: - run: - id: echo - class: CommandLineTool - inputs: - a: - type: string - inputBinding: {} - outputs: - echo_out: - type: string - outputBinding: - glob: step1_out - loadContents: true - outputEval: $(self[0].contents) - baseCommand: echo - stdout: step1_out - - in: - a: - valueFrom: moocow - out: [echo_out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom5-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom5-wf.cwl deleted file mode 100644 index 3ecc7d8a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_step-valuefrom5-wf.cwl +++ /dev/null @@ -1,74 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 -requirements: - StepInputExpressionRequirement: {} - -inputs: - file1: File - -outputs: - val1: - type: string - outputSource: step1/echo_out - val2: - type: string - outputSource: step2/echo_out - -steps: - step1: - run: - class: CommandLineTool - - inputs: - name: - type: string - inputBinding: {} - - outputs: - echo_out: - type: string - outputBinding: - glob: step1_out - loadContents: true - outputEval: $(self[0].contents) - echo_out_file: - type: File - outputBinding: - glob: step1_out - - baseCommand: echo - stdout: step1_out - - in: - name: - source: file1 - valueFrom: $(self.basename) - out: [echo_out, echo_out_file] - - - step2: - run: - class: CommandLineTool - - inputs: - name: - type: string - inputBinding: {} - - outputs: - echo_out: - type: string - outputBinding: - glob: step1_out - loadContents: true - outputEval: $(self[0].contents) - - baseCommand: echo - stdout: step1_out - - in: - name: - source: step1/echo_out_file - valueFrom: $(self.basename) - out: [echo_out] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_steplevel-resreq.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_steplevel-resreq.cwl deleted file mode 100644 index 88f1a22a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_steplevel-resreq.cwl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -requirements: - ResourceRequirement: - coresMin: 4 - coresMax: 4 - -inputs: [] - -steps: - step1: - requirements: - ResourceRequirement: - coresMin: 1 - coresMax: 1 - run: - class: CommandLineTool - inputs: [] - outputs: - output: - type: stdout - baseCommand: echo - stdout: cores.txt - arguments: [ $(runtime.cores) ] - in: [] - out: [output] - -outputs: - out: - type: File - outputSource: step1/output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_storage_float.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_storage_float.cwl deleted file mode 100644 index 473c2c82..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_storage_float.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - ResourceRequirement: - ramMin: 254.1 - ramMax: 254.9 - tmpdirMin: 255.1 - tmpdirMax: 255.9 - outdirMin: 256.1 - outdirMax: 256.9 - -inputs: [] - -outputs: - output: stdout - -baseCommand: echo - -stdout: values.txt - -arguments: [ $(runtime.ram), $(runtime.tmpdirSize), $(runtime.outdirSize) ] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_sum-wf-noET.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_sum-wf-noET.cwl deleted file mode 100644 index 13526808..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_sum-wf-noET.cwl +++ /dev/null @@ -1,50 +0,0 @@ -cwlVersion: v1.2 -class: Workflow - -requirements: - - class: StepInputExpressionRequirement - - class: MultipleInputFeatureRequirement - - class: InlineJavascriptRequirement - -inputs: - int_1: - type: - - int - - string - int_2: - type: - - int - - string - -outputs: - result: - type: File - outputSource: sum/result - -steps: - sum: - in: - data: - source: [int_1, int_2] - valueFrom: | - ${ - var sum = 0; - for (var i = 0; i < self.length; i++){ - sum += self[i]; - }; - return sum; - } - out: - - result - run: - class: CommandLineTool - inputs: - data: - type: int - inputBinding: {} - baseCommand: echo - stdout: result.txt - outputs: - result: - type: stdout - diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_sum-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_sum-wf.cwl deleted file mode 100644 index d2a37cf8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_sum-wf.cwl +++ /dev/null @@ -1,49 +0,0 @@ -cwlVersion: v1.2 -class: Workflow - -requirements: - - class: StepInputExpressionRequirement - - class: MultipleInputFeatureRequirement - - class: InlineJavascriptRequirement - -inputs: - int_1: - type: - - int - - string - int_2: - type: - - int - - string - -outputs: - result: - type: int - outputSource: sum/result - -steps: - sum: - in: - data: - source: [int_1, int_2] - valueFrom: | - ${ - var sum = 0; - for (var i = 0; i < self.length; i++){ - sum += self[i]; - }; - return sum; - } - out: - - result - run: - class: ExpressionTool - inputs: - data: - type: int - outputs: - result: int - expression: | - ${ - return {"result": inputs.data}; - } diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_symlink-illegal.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_symlink-illegal.cwl deleted file mode 100644 index 579539b0..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_symlink-illegal.cwl +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "Create a file under /tmp, symlink it to working directory and glob symlink. The executor should NOT resolve this symlink" -hints: - DockerRequirement: - dockerPull: alpine -inputs: [] -outputs: - output_file: - type: File - outputBinding: {glob: symlink.txt} - -requirements: - - class: ShellCommandRequirement - -arguments: - - echo - - "Who's gonna drive you home" - - {valueFrom: "> /tmp/original.txt", shellQuote: false} - - {valueFrom: " && ", shellQuote: false} - - ln - - -s - - /tmp/original.txt - - symlink.txt \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_symlink-legal.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_symlink-legal.cwl deleted file mode 100644 index f6735c51..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_symlink-legal.cwl +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -doc: "Create a file under adir/, symlink it to working directory (./) and glob symlink. The executor should resolve this symlink" -hints: - DockerRequirement: - dockerPull: alpine -inputs: [] -outputs: - output_file: - type: File - outputBinding: {glob: symlink.txt} - -requirements: - - class: ShellCommandRequirement - -arguments: - - mkdir - - adir - - {valueFrom: " && ", shellQuote: false} - - echo - - "Who's gonna drive you home" - - {valueFrom: "> adir/original.txt", shellQuote: false} - - {valueFrom: " && ", shellQuote: false} - - ln - - -s - - adir/original.txt - - symlink.txt \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_synth-file.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_synth-file.cwl deleted file mode 100644 index 10b59c26..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_synth-file.cwl +++ /dev/null @@ -1,14 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool - -inputs: - names: - type: File - inputBinding: - position: 1 - -baseCommand: [ cat ] - -outputs: - sequence: - type: stdout diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_template-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_template-tool.cwl deleted file mode 100755 index 1c20dfb2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_template-tool.cwl +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: CommandLineTool -requirements: - - class: InlineJavascriptRequirement - expressionLib: - - { $include: underscore.js } - - "var t = function(s) { return _.template(s, {variable: 'data'})({'inputs': inputs}); };" - - class: InitialWorkDirRequirement - listing: - - entryname: foo.txt - entry: $(t("The file is <%= data.inputs.file1.path.split('/').slice(-1)[0] %>\n")) -hints: - DockerRequirement: - dockerPull: "debian:stretch-slim" -inputs: - - id: file1 - type: File -outputs: - - id: foo - type: File - outputBinding: - glob: foo.txt -baseCommand: [cat, foo.txt] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_test-cwl-out.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_test-cwl-out.cwl deleted file mode 100644 index 3de92294..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_test-cwl-out.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: ShellCommandRequirement -hints: - DockerRequirement: - dockerPull: "debian:stretch-slim" - -inputs: [] - -outputs: - - id: foo - type: File - -arguments: - - valueFrom: > - echo foo > foo && echo '{"foo": {"path": "$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json - shellQuote: false diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_test-cwl-out2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_test-cwl-out2.cwl deleted file mode 100644 index 547b6f18..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_test-cwl-out2.cwl +++ /dev/null @@ -1,18 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: ShellCommandRequirement -hints: - DockerRequirement: - dockerPull: "debian:stretch-slim" - -inputs: [] - -outputs: - - id: foo - type: File - -arguments: - - valueFrom: > - echo foo > foo && echo '{"foo": {"location": "file://$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json - shellQuote: false diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit.cwl deleted file mode 100644 index 359f26a7..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit.cwl +++ /dev/null @@ -1,10 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: - ToolTimeLimit: - timelimit: 3 - WorkReuse: - enableReuse: false -baseCommand: [sleep, "15"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit2-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit2-wf.cwl deleted file mode 100644 index 9abafe5c..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit2-wf.cwl +++ /dev/null @@ -1,49 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -requirements: - ToolTimeLimit: - timelimit: 5 - InlineJavascriptRequirement: {} - -inputs: - i: - type: string? - -outputs: - o: - type: string? - outputSource: step2/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: CommandLineTool - baseCommand: ["sleep", "3"] - inputs: - i: - type: string? - outputs: - o: - type: string? - outputBinding: - outputEval: $("time passed") - step2: - in: - i: step1/o - out: [o] - run: - class: CommandLineTool - baseCommand: ["sleep", "3"] - inputs: - i: - type: string? - outputs: - o: - type: string? - outputBinding: - outputEval: $("time passed") diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit2.cwl deleted file mode 100644 index ea5107c6..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit2.cwl +++ /dev/null @@ -1,8 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: - ToolTimeLimit: - timelimit: -1 -baseCommand: [sleep, "15"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit3-wf.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit3-wf.cwl deleted file mode 100644 index 7550ad43..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit3-wf.cwl +++ /dev/null @@ -1,36 +0,0 @@ -#!/usr/bin/env cwl-runner -class: Workflow -cwlVersion: v1.2 - -requirements: - ToolTimeLimit: - timelimit: 0 - WorkReuse: - enableReuse: false - InlineJavascriptRequirement: {} - -inputs: - i: - type: int? - -outputs: - o: - type: string? - outputSource: step1/o - -steps: - step1: - in: - i: i - out: [o] - run: - class: CommandLineTool - baseCommand: ["sleep", "10"] - inputs: - i: - type: int? - outputs: - o: - type: string? - outputBinding: - outputEval: $("time passed") diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit3.cwl deleted file mode 100644 index 70da7771..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit3.cwl +++ /dev/null @@ -1,10 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: - ToolTimeLimit: - timelimit: 0 - WorkReuse: - enableReuse: false -baseCommand: [sleep, "15"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit4.cwl deleted file mode 100644 index 9975a47f..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit4.cwl +++ /dev/null @@ -1,11 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 -inputs: [] -outputs: [] -requirements: - InlineJavascriptRequirement: {} - ToolTimeLimit: - timelimit: $(1+2) - WorkReuse: - enableReuse: false -baseCommand: [sleep, "15"] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit5.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit5.cwl deleted file mode 100644 index ec4eb0a2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_timelimit5.cwl +++ /dev/null @@ -1,22 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.2 -inputs: [] -outputs: - status: string -requirements: - ToolTimeLimit: - timelimit: 3 - InlineJavascriptRequirement: {} -expression: | - ${ - function sleep(milliseconds) { - var start = new Date().getTime(); - for (var i = 0; i < 1e7; i++) { - if ((new Date().getTime() - start) > milliseconds){ - break; - } - } - }; - sleep(5000); - return {"status": "Done"} - } \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_tmap-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_tmap-tool.cwl deleted file mode 100755 index 58f75391..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_tmap-tool.cwl +++ /dev/null @@ -1,257 +0,0 @@ -#!/usr/bin/env cwl-runner -{ - "cwlVersion": "v1.2", - - "class": "CommandLineTool", - "hints": [ - { - "class": "DockerRequirement", - "dockerPull": "python:2-slim" - } - ], - "inputs": [ - { - "id": "reads", - "type": "File" - }, - { - "id": "stages", - "inputBinding": { - "position": 1 - }, - "type": { - "type": "array", - "items": "#Stage" - } - }, - { - id: "#args.py", - type: File, - default: { - class: File, - location: args.py - }, - inputBinding: { - position: -1 - } - } - ], - "outputs": [ - { - "id": "sam", - "outputBinding": { - "glob": "output.sam" - }, - "type": ["null", "File"] - }, - {"id": "args", "type": "string[]"} - ], - "requirements": [ - {"class": "SchemaDefRequirement", - "types": [ - { - "fields": [ - { - "inputBinding": { - "position": 0 - }, - "name": "algo", - "type": { - "type": "enum", - "name": "JustMap1", - "symbols": ["map1"] - } - }, - { - "name": "maxSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--max-seq-length", - "position": 2 - } - }, - { - "name": "minSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--min-seq-length", - "position": 2 - } - }, - { - "inputBinding": { - "position": 2, - "prefix": "--seed-length" - }, - "name": "seedLength", - "type": ["null", "int"] - } - ], - "name": "Map1", - "type": "record" - }, - { - "fields": [ - { - "inputBinding": { - "position": 0 - }, - "name": "algo", - "type": { - "type": "enum", - "name": "JustMap2", - "symbols": ["map2"] - } - }, - { - "name": "maxSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--max-seq-length", - "position": 2 - } - }, - { - "name": "minSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--min-seq-length", - "position": 2 - } - }, - { - "inputBinding": { - "position": 2, - "prefix": "--max-seed-hits" - }, - "name": "maxSeedHits", - "type": ["null", "int"] - } - ], - "name": "Map2", - "type": "record" - }, - { - "fields": [ - { - "inputBinding": { - "position": 0 - }, - "name": "algo", - "type": { - "type": "enum", - "name": "JustMap3", - "symbols": ["map3"] - } - }, - { - "name": "maxSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--max-seq-length", - "position": 2 - } - }, - { - "name": "minSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--min-seq-length", - "position": 2 - } - }, - { - "inputBinding": { - "position": 2, - "prefix": "--fwd-search" - }, - "name": "fwdSearch", - "type": ["null", "boolean"] - } - ], - "name": "Map3", - "type": "record" - }, - { - "fields": [ - { - "inputBinding": { - "position": 0 - }, - "name": "algo", - "type": { - "type": "enum", - "name": "JustMap4", - "symbols": ["map4"] - } - }, - { - "name": "maxSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--max-seq-length", - "position": 2 - } - }, - { - "name": "minSeqLen", - "type": ["null", "int"], - "inputBinding": { - "prefix": "--min-seq-length", - "position": 2 - } - }, - { - "inputBinding": { - "position": 2, - "prefix": "--seed-step" - }, - "name": "seedStep", - "type": ["null", "int"] - } - ], - "name": "Map4", - "type": "record" - }, - { - "type": "record", - "name": "Stage", - "fields": [ - { - "inputBinding": { - "position": 0, - "prefix": "stage", - "separate": false - }, - "name": "stageId", - "type": ["null", "int"] - }, - { - "inputBinding": { - "position": 1, - "prefix": "-n" - }, - "name": "stageOption1", - "type": ["null", "boolean"] - }, - { - "inputBinding": { - "position": 2 - }, - "name": "algos", - "type": { - "type": "array", - "items": [ - "#Map1", - "#Map2", - "#Map3", - "#Map4" - ] - } - } - ] - } - ]}], - "baseCommand": "python", - "arguments": ["tmap", "mapall"] -} diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_tool-v12.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_tool-v12.cwl deleted file mode 100644 index 4de64361..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_tool-v12.cwl +++ /dev/null @@ -1,13 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -inputs: - inp1: - type: File - secondaryFiles: - - pattern: ".2" - required: true -requirements: - ResourceRequirement: - coresMin: .5 -outputs: [] -arguments: [echo, $(inputs.inp1)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_touch.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_touch.cwl deleted file mode 100644 index f4714933..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_touch.cwl +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: CommandLineTool - -hints: - DockerRequirement: - dockerPull: debian:stretch-slim - -inputs: - name: - type: string - inputBinding: - position: 0 - -outputs: - empty_file: - type: File - outputBinding: - glob: $(inputs.name) - -baseCommand: [touch] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_updatedir_inplace.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_updatedir_inplace.cwl deleted file mode 100755 index fe4f284d..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_updatedir_inplace.cwl +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.r) - entryname: inp - writable: true - InplaceUpdateRequirement: - inplaceUpdate: true -inputs: - r: Directory -outputs: - out: - type: Directory - outputBinding: - glob: inp -arguments: [touch, inp/blurb] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_updateval_inplace.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_updateval_inplace.cwl deleted file mode 100755 index d3b45048..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_updateval_inplace.cwl +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - InitialWorkDirRequirement: - listing: - - entry: $(inputs.r) - writable: true - InplaceUpdateRequirement: - inplaceUpdate: true -hints: - DockerRequirement: - dockerPull: "python:2.7.15-alpine3.7" -inputs: - r: File - script: - type: File - default: - class: File - location: updateval.py -outputs: - out: - type: File - outputBinding: - glob: $(inputs.r.basename) -arguments: [python, $(inputs.script), $(inputs.r.basename)] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_valueFrom-constant.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_valueFrom-constant.cwl deleted file mode 100644 index c8b975c2..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_valueFrom-constant.cwl +++ /dev/null @@ -1,28 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.2 - -hints: - - class: DockerRequirement - dockerPull: python:2-slim - -inputs: - - id: array_input - type: - - type: array - items: File - inputBinding: - valueFrom: replacementValue - - - id: args.py - type: File - default: - class: File - location: args.py - inputBinding: - position: -1 - -outputs: - - id: args - type: string[] - -baseCommand: python diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_vf-concat.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_vf-concat.cwl deleted file mode 100644 index 787fed6a..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_vf-concat.cwl +++ /dev/null @@ -1,19 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -requirements: - - class: InlineJavascriptRequirement - -baseCommand: echo -inputs: - file1: - type: File? - inputBinding: - valueFrom: $("a ")$("string") -outputs: - out: - type: string - outputBinding: - glob: output.txt - loadContents: true - outputEval: $(self[0].contents) -stdout: output.txt diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc-tool-shortcut.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc-tool-shortcut.cwl deleted file mode 100755 index 645fd430..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc-tool-shortcut.cwl +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - - class: DockerRequirement - dockerPull: debian:stretch-slim - -inputs: - file1: stdin - -outputs: - output: - type: File - outputBinding: { glob: output } - -baseCommand: [wc] - -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc-tool.cwl deleted file mode 100755 index ed9852d8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 - -inputs: - file1: File - -outputs: - output: - type: File - outputBinding: { glob: output } - -baseCommand: [wc, -l] - -stdin: $(inputs.file1.path) -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc2-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc2-tool.cwl deleted file mode 100755 index 279ed20b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc2-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: InlineJavascriptRequirement - -inputs: - - { id: file1, type: File, inputBinding: {} } -outputs: - - id: output - type: int - outputBinding: - glob: output.txt - loadContents: true - outputEval: "$(parseInt(self[0].contents))" -stdout: output.txt -baseCommand: wc diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc3-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc3-tool.cwl deleted file mode 100644 index d14cc809..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc3-tool.cwl +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - file1: - type: File[] - inputBinding: {} -outputs: - output: - type: int - outputBinding: - glob: output.txt - loadContents: true - outputEval: | - ${ - var s = self[0].contents.split(/\r?\n/); - return parseInt(s[s.length-2]); - } -stdout: output.txt -baseCommand: wc diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc4-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc4-tool.cwl deleted file mode 100644 index 18819592..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wc4-tool.cwl +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: InlineJavascriptRequirement - -inputs: - file1: - type: File - inputBinding: {} -outputs: - - id: output - type: int - outputBinding: - glob: output.txt - loadContents: true - outputEval: | - ${ - var s = self[0].contents.split(/\r?\n/); - return parseInt(s[s.length-2]); - } -stdout: output.txt -baseCommand: wc diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf-loadContents.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf-loadContents.cwl deleted file mode 100644 index 5224a4dd..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf-loadContents.cwl +++ /dev/null @@ -1,29 +0,0 @@ -cwlVersion: v1.2 -class: Workflow -requirements: - StepInputExpressionRequirement: {} - InlineJavascriptRequirement: {} -inputs: - my_file: - type: File - loadContents: true - -steps: - one: - run: - class: ExpressionTool - requirements: { InlineJavascriptRequirement: {} } - inputs: { my_number: int } - outputs: { my_int: int } - expression: | - ${ return { "my_int": inputs.my_number }; } - in: - my_number: - source: my_file - valueFrom: $(parseInt(self.contents)) - out: [ my_int ] - -outputs: - my_int: - type: int - outputSource: one/my_int diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf-loadContents2.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf-loadContents2.cwl deleted file mode 100644 index f0d224dc..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf-loadContents2.cwl +++ /dev/null @@ -1,29 +0,0 @@ -cwlVersion: v1.2 -class: Workflow -requirements: - StepInputExpressionRequirement: {} - InlineJavascriptRequirement: {} -inputs: - my_file: - type: File - loadContents: true - -steps: - one: - run: - class: ExpressionTool - requirements: { InlineJavascriptRequirement: {} } - inputs: { my_number: int } - outputs: { my_int: int } - expression: | - ${ return { "my_int": inputs.my_number }; } - in: - my_number: - source: my_file - valueFrom: $(parseInt(self.contents)) - out: [ my_int ] - -outputs: - my_int: - type: int - outputSource: one/my_int \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf-loadContents3.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf-loadContents3.cwl deleted file mode 100644 index a0e2bce5..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf-loadContents3.cwl +++ /dev/null @@ -1,28 +0,0 @@ -cwlVersion: v1.2 -class: Workflow -requirements: - StepInputExpressionRequirement: {} - InlineJavascriptRequirement: {} -inputs: - my_file: File - -steps: - one: - run: - class: ExpressionTool - requirements: { InlineJavascriptRequirement: {} } - inputs: - my_number: - type: File - loadContents: true - outputs: { my_int: int } - expression: | - ${ return { "my_int": parseInt(inputs.my_number.contents) }; } - in: - my_number: my_file - out: [ my_int ] - -outputs: - my_int: - type: int - outputSource: one/my_int \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf-loadContents4.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf-loadContents4.cwl deleted file mode 100644 index ecaf2f8e..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf-loadContents4.cwl +++ /dev/null @@ -1,28 +0,0 @@ -cwlVersion: v1.2 -class: Workflow -requirements: - StepInputExpressionRequirement: {} - InlineJavascriptRequirement: {} -inputs: - my_file: File - -steps: - one: - run: - class: ExpressionTool - requirements: { InlineJavascriptRequirement: {} } - inputs: { my_number: int } - outputs: { my_int: int } - expression: | - ${ return { "my_int": inputs.my_number }; } - in: - my_number: - source: my_file - loadContents: true - valueFrom: $(parseInt(self.contents)) - out: [ my_int ] - -outputs: - my_int: - type: int - outputSource: one/my_int \ No newline at end of file diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf_ren.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf_ren.cwl deleted file mode 100644 index d2affceb..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_wf_ren.cwl +++ /dev/null @@ -1,29 +0,0 @@ -class: Workflow -cwlVersion: v1.2 -inputs: - f1: - type: File - default: - class: File - location: whale.txt - newname: - type: string - default: "badger.txt" -outputs: [] -requirements: - StepInputExpressionRequirement: {} - InlineJavascriptRequirement: {} -steps: - rename: - in: - f1: f1 - newname: newname - run: rename.cwl - out: [out] - - echo: - in: - p: rename/out - checkname: newname - out: [] - run: check.cwl diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_writable-dir-docker.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_writable-dir-docker.cwl deleted file mode 100644 index 756be158..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_writable-dir-docker.cwl +++ /dev/null @@ -1,23 +0,0 @@ -cwlVersion: v1.2 - -class: CommandLineTool - -requirements: - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: - - entryname: emptyWritableDir - entry: "$({class: 'Directory', listing: []})" - writable: true - -hints: - - class: DockerRequirement - dockerPull: alpine - -inputs: [] -outputs: - out: - type: Directory - outputBinding: - glob: emptyWritableDir -arguments: [touch, emptyWritableDir/blurg] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_writable-dir.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_writable-dir.cwl deleted file mode 100644 index 78faf003..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/valid_writable-dir.cwl +++ /dev/null @@ -1,16 +0,0 @@ -cwlVersion: v1.2 -class: CommandLineTool -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: emptyWritableDir - writable: true - entry: "$({class: 'Directory', listing: []})" -inputs: [] -outputs: - out: - type: Directory - outputBinding: - glob: emptyWritableDir -arguments: [touch, emptyWritableDir/blurg] diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/wc-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/wc-tool.cwl deleted file mode 100755 index ed9852d8..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/wc-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.2 - -inputs: - file1: File - -outputs: - output: - type: File - outputBinding: { glob: output } - -baseCommand: [wc, -l] - -stdin: $(inputs.file1.path) -stdout: output diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/wc2-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/wc2-tool.cwl deleted file mode 100755 index 279ed20b..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/wc2-tool.cwl +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 -requirements: - - class: InlineJavascriptRequirement - -inputs: - - { id: file1, type: File, inputBinding: {} } -outputs: - - id: output - type: int - outputBinding: - glob: output.txt - loadContents: true - outputEval: "$(parseInt(self[0].contents))" -stdout: output.txt -baseCommand: wc diff --git a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/wc3-tool.cwl b/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/wc3-tool.cwl deleted file mode 100644 index d14cc809..00000000 --- a/src/test/resources/org/commonwl/cwlsdk/cwl1_2/utils/wc3-tool.cwl +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env cwl-runner -class: CommandLineTool -cwlVersion: v1.2 - -requirements: - - class: InlineJavascriptRequirement - -inputs: - file1: - type: File[] - inputBinding: {} -outputs: - output: - type: int - outputBinding: - glob: output.txt - loadContents: true - outputEval: | - ${ - var s = self[0].contents.split(/\r?\n/); - return parseInt(s[s.length-2]); - } -stdout: output.txt -baseCommand: wc