#339

Committed 29 Jan 2025 01:23PM UTC coverage: 59.538% (-0.6%) from 60.167%

Build # #339

Build Type

Pull #193

github

Committed by

web-flow

Commit Message

Merge 94c260498 into 0978523bc

Pull Request Pull Request #193: Add accessor for the extension field.

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/src/main/java/org/w3id/cwl/cwl1_1/SoftwarePackageImpl.java

// Copyright Common Workflow Language project contributors
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//      http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.

package org.w3id.cwl.cwl1_1;

import org.w3id.cwl.cwl1_1.utils.LoaderInstances;
import org.w3id.cwl.cwl1_1.utils.LoadingOptions;
import org.w3id.cwl.cwl1_1.utils.LoadingOptionsBuilder;
import org.w3id.cwl.cwl1_1.utils.SaveableImpl;
import org.w3id.cwl.cwl1_1.utils.ValidationException;

/**
* Auto-generated class implementation for <I>https://w3id.org/cwl/cwl#SoftwarePackage</I><BR>
 */
public class SoftwarePackageImpl extends SaveableImpl implements SoftwarePackage {
  private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();
  private java.util.Map<String, Object> extensionFields_ =
      new java.util.HashMap<String, Object>();
  public java.util.Map<String, Object> getExtensionFields() {
    return this.extensionFields_;
  }

  private String package_;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#SoftwarePackage/package</I><BR>
   * <BLOCKQUOTE>
   * 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.
   *    * </BLOCKQUOTE>
   */

  public String getPackage() {
    return this.package_;
  }

  private java.util.Optional<java.util.List<String>> version;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#SoftwarePackage/version</I><BR>
   * <BLOCKQUOTE>
   * The (optional) versions of the software that are known to be
   * compatible.
   *    * </BLOCKQUOTE>
   */

  public java.util.Optional<java.util.List<String>> getVersion() {
    return this.version;
  }

  private java.util.Optional<java.util.List<String>> specs;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#SoftwarePackage/specs</I><BR>
   * <BLOCKQUOTE>
   * 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.
   *    * </BLOCKQUOTE>
   */

  public java.util.Optional<java.util.List<String>> getSpecs() {
    return this.specs;
  }

  /**
   * Used by {@link org.w3id.cwl.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<String, Object> __doc = (java.util.Map<String, Object>) __doc_;
    final java.util.List<ValidationException> __errors =
        new java.util.ArrayList<ValidationException>();
    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<java.util.List<String>> 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<java.util.List<String>> 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<java.util.List<String>>) version;
    this.specs = (java.util.Optional<java.util.List<String>>) specs;
  }
}

1	// Copyright Common Workflow Language project contributors
2	//
3	// Licensed under the Apache License, Version 2.0 (the "License");
4	// you may not use this file except in compliance with the License.
5	// You may obtain a copy of the License at
6	//
7	// http://www.apache.org/licenses/LICENSE-2.0
8	//
9	// Unless required by applicable law or agreed to in writing, software
10	// distributed under the License is distributed on an "AS IS" BASIS,
11	// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12	// See the License for the specific language governing permissions and
13	// limitations under the License.
14
15	package org.w3id.cwl.cwl1_1;
16
17	import org.w3id.cwl.cwl1_1.utils.LoaderInstances;
18	import org.w3id.cwl.cwl1_1.utils.LoadingOptions;
19	import org.w3id.cwl.cwl1_1.utils.LoadingOptionsBuilder;
20	import org.w3id.cwl.cwl1_1.utils.SaveableImpl;
21	import org.w3id.cwl.cwl1_1.utils.ValidationException;
22
23	/**
24	* Auto-generated class implementation for <I>https://w3id.org/cwl/cwl#SoftwarePackage</I><BR>
25	*/
26	public class SoftwarePackageImpl extends SaveableImpl implements SoftwarePackage {
27	private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();	×
28	private java.util.Map<String, Object> extensionFields_ =	×
29	new java.util.HashMap<String, Object>();
30	public java.util.Map<String, Object> getExtensionFields() {
NEW 31	return this.extensionFields_;	×
32	}
33
34	private String package_;
35
36	/**
37	* Getter for property <I>https://w3id.org/cwl/cwl#SoftwarePackage/package</I><BR>
38	* <BLOCKQUOTE>
39	* The name of the software to be made available. If the name is
40	* common, inconsistent, or otherwise ambiguous it should be combined with
41	* one or more identifiers in the `specs` field.
42	* * </BLOCKQUOTE>
43	*/
44
45	public String getPackage() {
46	return this.package_;	×
47	}
48
49	private java.util.Optional<java.util.List<String>> version;
50
51	/**
52	* Getter for property <I>https://w3id.org/cwl/cwl#SoftwarePackage/version</I><BR>
53	* <BLOCKQUOTE>
54	* The (optional) versions of the software that are known to be
55	* compatible.
56	* * </BLOCKQUOTE>
57	*/
58
59	public java.util.Optional<java.util.List<String>> getVersion() {
60	return this.version;	×
61	}
62
63	private java.util.Optional<java.util.List<String>> specs;
64
65	/**
66	* Getter for property <I>https://w3id.org/cwl/cwl#SoftwarePackage/specs</I><BR>
67	* <BLOCKQUOTE>
68	* One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s
69	* identifying resources for installing or enabling the software named in
70	* the `package` field. Implementations may provide resolvers which map
71	* these software identifer IRIs to some configuration action; or they can
72	* use only the name from the `package` field on a best effort basis.
73	*
74	* For example, the IRI https://packages.debian.org/bowtie could
75	* be resolved with `apt-get install bowtie`. The IRI
76	* https://anaconda.org/bioconda/bowtie could be resolved with `conda
77	* install -c bioconda bowtie`.
78	*
79	* IRIs can also be system independent and used to map to a specific
80	* software installation or selection mechanism.
81	* Using [RRID](https://www.identifiers.org/rrid/) as an example:
82	* https://identifiers.org/rrid/RRID:SCR_005476
83	* could be fulfilled using the above mentioned Debian or bioconda
84	* package, a local installation managed by [Environement Modules](http://modules.sourceforge.net/),
85	* or any other mechanism the platform chooses. IRIs can also be from
86	* identifer sources that are discipline specific yet still system
87	* independent. As an example, the equivalent [ELIXIR Tools and Data
88	* Service Registry](https://bio.tools) IRI to the previous RRID example is
89	* https://bio.tools/tool/bowtie2/version/2.2.8.
90	* If supported by a given registry, implementations are encouraged to
91	* query these system independent sofware identifier IRIs directly for
92	* links to packaging systems.
93	*
94	* A site specific IRI can be listed as well. For example, an academic
95	* computing cluster using Environement Modules could list the IRI
96	* `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that
97	* `module load bowtie-tbb/1.1.2` should be executed to make available
98	* `bowtie` version 1.1.2 compiled with the TBB library prior to running
99	* the accompanying Workflow or CommandLineTool. Note that the example IRI
100	* is specific to a particular institution and computing environment as
101	* the Environment Modules system does not have a common namespace or
102	* standardized naming convention.
103	*
104	* This last example is the least portable and should only be used if
105	* mechanisms based off of the `package` field or more generic IRIs are
106	* unavailable or unsuitable. While harmless to other sites, site specific
107	* software IRIs should be left out of shared CWL descriptions to avoid
108	* clutter.
109	* * </BLOCKQUOTE>
110	*/
111
112	public java.util.Optional<java.util.List<String>> getSpecs() {
113	return this.specs;	×
114	}
115
116	/**
117	* Used by {@link org.w3id.cwl.cwl1_1.utils.RootLoader} to construct instances of SoftwarePackageImpl.
118	*
119	* @param __doc_ Document fragment to load this record object from (presumably a
120	{@link java.util.Map}).
121	* @param __baseUri_ Base URI to generate child document IDs against.
122	* @param __loadingOptions Context for loading URIs and populating objects.
123	* @param __docRoot_ ID at this position in the document (if available) (maybe?)
124	* @throws ValidationException If the document fragment is not a {@link java.util.Map}
125	* or validation of fields fails.
126	*/
127	public SoftwarePackageImpl(
128	final Object __doc_,
129	final String __baseUri_,
130	LoadingOptions __loadingOptions,
131	final String __docRoot_) {
132	super(__doc_, __baseUri_, __loadingOptions, __docRoot_);	×
133	// Prefix plumbing variables with '__' to reduce likelihood of collision with
134	// generated names.
135	String __baseUri = __baseUri_;	×
136	String __docRoot = __docRoot_;	×
137	if (!(__doc_ instanceof java.util.Map)) {	×
138	throw new ValidationException("SoftwarePackageImpl called on non-map");	×
139	}
140	final java.util.Map<String, Object> __doc = (java.util.Map<String, Object>) __doc_;	×
141	final java.util.List<ValidationException> __errors =	×
142	new java.util.ArrayList<ValidationException>();
143	if (__loadingOptions != null) {	×
144	this.loadingOptions_ = __loadingOptions;	×
145	}
146	String package_;
147	try {
148	package_ =	×
149	LoaderInstances
150	.StringInstance
151	.loadField(__doc.get("package"), __baseUri, __loadingOptions);	×
152	} catch (ValidationException e) {	×
153	package_ = null; // won't be used but prevents compiler from complaining.	×
154	final String __message = "the `package` field is not valid because:";	×
155	__errors.add(new ValidationException(__message, e));	×
156	}	×
157	java.util.Optional<java.util.List<String>> version;
158
159	if (__doc.containsKey("version")) {	×
160	try {
161	version =	×
162	LoaderInstances
163	.optional_array_of_StringInstance
164	.loadField(__doc.get("version"), __baseUri, __loadingOptions);	×
165	} catch (ValidationException e) {	×
166	version = null; // won't be used but prevents compiler from complaining.	×
167	final String __message = "the `version` field is not valid because:";	×
168	__errors.add(new ValidationException(__message, e));	×
169	}	×
170
171	} else {
172	version = null;	×
173	}
174	java.util.Optional<java.util.List<String>> specs;
175
176	if (__doc.containsKey("specs")) {	×
177	try {
178	specs =	×
179	LoaderInstances
180	.uri_optional_array_of_StringInstance_False_False_None_True
181	.loadField(__doc.get("specs"), __baseUri, __loadingOptions);	×
182	} catch (ValidationException e) {	×
183	specs = null; // won't be used but prevents compiler from complaining.	×
184	final String __message = "the `specs` field is not valid because:";	×
185	__errors.add(new ValidationException(__message, e));	×
186	}	×
187
188	} else {
189	specs = null;	×
190	}
191	if (!__errors.isEmpty()) {	×
192	throw new ValidationException("Trying 'RecordField'", __errors);	×
193	}
194	this.package_ = (String) package_;	×
195	this.version = (java.util.Optional<java.util.List<String>>) version;	×
196	this.specs = (java.util.Optional<java.util.List<String>>) specs;	×
197	}	×
198	}

common-workflow-language / cwljava / #339

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