#388

Committed 30 Oct 2025 04:55PM UTC coverage: 58.693% (-0.8%) from 59.538%

Build # #388

Build Type

Pull #218

github

Committed by

web-flow

Commit Message

Merge ab8576a5b into befd7e4b9

Pull Request Pull Request #218: Populate the extensionFields; add public accessors for LoadingOptions

Run Details

230 of 569 new or added lines in 67 files covered. (40.42%)

28 existing lines in 27 files now uncovered.

7535 of 12838 relevant lines covered (58.69%)

0.59 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

0.0

/src/main/java/org/w3id/cwl/cwl1_2/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_2;

import org.w3id.cwl.cwl1_2.utils.LoaderInstances;
import org.w3id.cwl.cwl1_2.utils.LoadingOptions;
import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder;
import org.w3id.cwl.cwl1_2.utils.SaveableImpl;
import org.w3id.cwl.cwl1_2.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 LoadingOptions getLoadingOptions() {
    return this.loadingOptions_;
  }
  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 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.
   *    * </BLOCKQUOTE>
   */

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

  /**
   * Used by {@link org.w3id.cwl.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<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;
    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<String> attrs = java.util.Arrays.asList("package", "version", "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_2;
16
17	import org.w3id.cwl.cwl1_2.utils.LoaderInstances;
18	import org.w3id.cwl.cwl1_2.utils.LoadingOptions;
19	import org.w3id.cwl.cwl1_2.utils.LoadingOptionsBuilder;
20	import org.w3id.cwl.cwl1_2.utils.SaveableImpl;
21	import org.w3id.cwl.cwl1_2.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 LoadingOptions getLoadingOptions() {
NEW 31	return this.loadingOptions_;	×
32	}
33	public java.util.Map<String, Object> getExtensionFields() {
34	return this.extensionFields_;	×
35	}
36
37	private String package_;
38
39	/**
40	* Getter for property <I>https://w3id.org/cwl/cwl#SoftwarePackage/package</I><BR>
41	* <BLOCKQUOTE>
42	* The name of the software to be made available. If the name is
43	* common, inconsistent, or otherwise ambiguous it should be combined with
44	* one or more identifiers in the `specs` field.
45	* * </BLOCKQUOTE>
46	*/
47
48	public String getPackage() {
49	return this.package_;	×
50	}
51
52	private java.util.Optional<java.util.List<String>> version;
53
54	/**
55	* Getter for property <I>https://w3id.org/cwl/cwl#SoftwarePackage/version</I><BR>
56	* <BLOCKQUOTE>
57	* The (optional) versions of the software that are known to be
58	* compatible.
59	* * </BLOCKQUOTE>
60	*/
61
62	public java.util.Optional<java.util.List<String>> getVersion() {
63	return this.version;	×
64	}
65
66	private java.util.Optional<java.util.List<String>> specs;
67
68	/**
69	* Getter for property <I>https://w3id.org/cwl/cwl#SoftwarePackage/specs</I><BR>
70	* <BLOCKQUOTE>
71	* One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s
72	* identifying resources for installing or enabling the software named in
73	* the `package` field. Implementations may provide resolvers which map
74	* these software identifier IRIs to some configuration action; or they can
75	* use only the name from the `package` field on a best effort basis.
76	*
77	* For example, the IRI https://packages.debian.org/bowtie could
78	* be resolved with `apt-get install bowtie`. The IRI
79	* https://anaconda.org/bioconda/bowtie could be resolved with `conda
80	* install -c bioconda bowtie`.
81	*
82	* IRIs can also be system independent and used to map to a specific
83	* software installation or selection mechanism.
84	* Using [RRID](https://www.identifiers.org/rrid/) as an example:
85	* https://identifiers.org/rrid/RRID:SCR_005476
86	* could be fulfilled using the above-mentioned Debian or bioconda
87	* package, a local installation managed by [Environment Modules](https://modules.sourceforge.net/),
88	* or any other mechanism the platform chooses. IRIs can also be from
89	* identifier sources that are discipline specific yet still system
90	* independent. As an example, the equivalent [ELIXIR Tools and Data
91	* Service Registry](https://bio.tools) IRI to the previous RRID example is
92	* https://bio.tools/tool/bowtie2/version/2.2.8.
93	* If supported by a given registry, implementations are encouraged to
94	* query these system independent software identifier IRIs directly for
95	* links to packaging systems.
96	*
97	* A site specific IRI can be listed as well. For example, an academic
98	* computing cluster using Environment Modules could list the IRI
99	* `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that
100	* `module load bowtie-tbb/1.1.2` should be executed to make available
101	* `bowtie` version 1.1.2 compiled with the TBB library prior to running
102	* the accompanying Workflow or CommandLineTool. Note that the example IRI
103	* is specific to a particular institution and computing environment as
104	* the Environment Modules system does not have a common namespace or
105	* standardized naming convention.
106	*
107	* This last example is the least portable and should only be used if
108	* mechanisms based off of the `package` field or more generic IRIs are
109	* unavailable or unsuitable. While harmless to other sites, site specific
110	* software IRIs should be left out of shared CWL descriptions to avoid
111	* clutter.
112	* * </BLOCKQUOTE>
113	*/
114
115	public java.util.Optional<java.util.List<String>> getSpecs() {
116	return this.specs;	×
117	}
118
119	/**
120	* Used by {@link org.w3id.cwl.cwl1_2.utils.RootLoader} to construct instances of SoftwarePackageImpl.
121	*
122	* @param __doc_ Document fragment to load this record object from (presumably a
123	{@link java.util.Map}).
124	* @param __baseUri_ Base URI to generate child document IDs against.
125	* @param __loadingOptions Context for loading URIs and populating objects.
126	* @param __docRoot_ ID at this position in the document (if available) (maybe?)
127	* @throws ValidationException If the document fragment is not a {@link java.util.Map}
128	* or validation of fields fails.
129	*/
130	public SoftwarePackageImpl(
131	final Object __doc_,
132	final String __baseUri_,
133	LoadingOptions __loadingOptions,
134	final String __docRoot_) {
135	super(__doc_, __baseUri_, __loadingOptions, __docRoot_);	×
136	// Prefix plumbing variables with '__' to reduce likelihood of collision with
137	// generated names.
138	String __baseUri = __baseUri_;	×
139	String __docRoot = __docRoot_;	×
140	if (!(__doc_ instanceof java.util.Map)) {	×
141	throw new ValidationException("SoftwarePackageImpl called on non-map");	×
142	}
143	final java.util.Map<String, Object> __doc = (java.util.Map<String, Object>) __doc_;	×
144	final java.util.List<ValidationException> __errors =	×
145	new java.util.ArrayList<ValidationException>();
146	if (__loadingOptions != null) {	×
147	this.loadingOptions_ = __loadingOptions;	×
148	}
149	String package_;
150	try {
151	package_ =	×
152	LoaderInstances
153	.StringInstance
154	.loadField(__doc.get("package"), __baseUri, __loadingOptions);	×
155	} catch (ValidationException e) {	×
156	package_ = null; // won't be used but prevents compiler from complaining.	×
157	final String __message = "the `package` field is not valid because:";	×
158	__errors.add(new ValidationException(__message, e));	×
159	}	×
160	java.util.Optional<java.util.List<String>> version;
161
162	if (__doc.containsKey("version")) {	×
163	try {
164	version =	×
165	LoaderInstances
166	.optional_array_of_StringInstance
167	.loadField(__doc.get("version"), __baseUri, __loadingOptions);	×
168	} catch (ValidationException e) {	×
169	version = null; // won't be used but prevents compiler from complaining.	×
170	final String __message = "the `version` field is not valid because:";	×
171	__errors.add(new ValidationException(__message, e));	×
172	}	×
173
174	} else {
175	version = null;	×
176	}
177	java.util.Optional<java.util.List<String>> specs;
178
179	if (__doc.containsKey("specs")) {	×
180	try {
181	specs =	×
182	LoaderInstances
183	.uri_optional_array_of_StringInstance_False_False_None_True
184	.loadField(__doc.get("specs"), __baseUri, __loadingOptions);	×
185	} catch (ValidationException e) {	×
186	specs = null; // won't be used but prevents compiler from complaining.	×
187	final String __message = "the `specs` field is not valid because:";	×
188	__errors.add(new ValidationException(__message, e));	×
189	}	×
190
191	} else {
192	specs = null;	×
193	}
194	if (!__errors.isEmpty()) {	×
195	throw new ValidationException("Trying 'RecordField'", __errors);	×
196	}
197	this.package_ = (String) package_;	×
198	this.version = (java.util.Optional<java.util.List<String>>) version;	×
199	this.specs = (java.util.Optional<java.util.List<String>>) specs;	×
NEW 200	for (String field:__doc.keySet()) {	×
NEW 201	if (!attrs.contains(field)) {	×
NEW 202	if (field.contains(":")) {	×
NEW 203	String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null);	×
NEW 204	extensionFields_.put(expanded_field, __doc.get(field));	×
205	}
206	}
NEW 207	}	×
UNCOV 208	}	×
NEW 209	private java.util.List<String> attrs = java.util.Arrays.asList("package", "version", "specs");	×
210	}

common-workflow-language / cwljava / #388

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous