#423

Committed 17 Dec 2025 10:33AM UTC coverage: 56.982% (-1.0%) from 57.972%

Build # #423

Build Type

push

github

Committed by

web-flow

Commit Message

refresh 2025-12 (including extensions) (#218)

* "id" is a required field in for Parameters and WorkflowSteps
* regen; drop CommandLineBindableImpl; add optional CWL extensions

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185 of 577 new or added lines in 21 files covered. (32.06%)

10 existing lines in 10 files now uncovered.

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0.0

/src/main/java/org/commonwl/cwlsdk/cwl1_2/ProcessGeneratorImpl.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.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 <I>http://commonwl.org/cwltool#ProcessGenerator</I><BR>
 */
public class ProcessGeneratorImpl extends SaveableImpl implements ProcessGenerator {
  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 java.util.Optional<String> id;

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

  public java.util.Optional<String> getId() {
    return this.id;
  }

  private String class_;

  /**
   * Getter for property <I>http://commonwl.org/cwltool#ProcessGenerator/class</I><BR>

   */

  public String getClass_() {
    return this.class_;
  }

  private java.util.Optional<String> label;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#Labeled/label</I><BR>
   * <BLOCKQUOTE>
   * A short, human-readable label of this object.   * </BLOCKQUOTE>
   */

  public java.util.Optional<String> getLabel() {
    return this.label;
  }

  private Object doc;

  /**
   * Getter for property <I>https://w3id.org/cwl/salad#Documented/doc</I><BR>
   * <BLOCKQUOTE>
   * A documentation string for this object, or an array of strings which should be concatenated.   * </BLOCKQUOTE>
   */

  public Object getDoc() {
    return this.doc;
  }

  private java.util.List<Object> inputs;

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

  public java.util.List<Object> getInputs() {
    return this.inputs;
  }

  private java.util.List<Object> outputs;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#outputs</I><BR>
   * <BLOCKQUOTE>
   * Defines the parameters representing the output of the process.  May be
   * used to generate and/or validate the output object.
   *    * </BLOCKQUOTE>
   */

  public java.util.List<Object> getOutputs() {
    return this.outputs;
  }

  private java.util.Optional<java.util.List<Object>> requirements;

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

  public java.util.Optional<java.util.List<Object>> getRequirements() {
    return this.requirements;
  }

  private java.util.Optional<java.util.List<Object>> hints;

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

  public java.util.Optional<java.util.List<Object>> getHints() {
    return this.hints;
  }

  private java.util.Optional<CWLVersion> cwlVersion;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#cwlVersion</I><BR>
   * <BLOCKQUOTE>
   * CWL document version. Always required at the document root. Not
   * required for a Process embedded inside another Process.
   *    * </BLOCKQUOTE>
   */

  public java.util.Optional<CWLVersion> getCwlVersion() {
    return this.cwlVersion;
  }

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

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#Process/intent</I><BR>
   * <BLOCKQUOTE>
   * 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&#x27;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).
   *    * </BLOCKQUOTE>
   */

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

  private Object run;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#run</I><BR>
   * <BLOCKQUOTE>
   * Specifies the process to run.
   *    * </BLOCKQUOTE>
   */

  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<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;
    }
    java.util.Optional<String> 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<String> 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<Object> 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<Object> 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<java.util.List<Object>> 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<java.util.List<Object>> 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> 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<java.util.List<String>> 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<String>) id;
    this.label = (java.util.Optional<String>) label;
    this.doc = (Object) doc;
    this.inputs = (java.util.List<Object>) inputs;
    this.outputs = (java.util.List<Object>) outputs;
    this.requirements = (java.util.Optional<java.util.List<Object>>) requirements;
    this.hints = (java.util.Optional<java.util.List<Object>>) hints;
    this.cwlVersion = (java.util.Optional<CWLVersion>) cwlVersion;
    this.intent = (java.util.Optional<java.util.List<String>>) 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<String> attrs = java.util.Arrays.asList("id", "label", "doc", "inputs", "outputs", "requirements", "hints", "cwlVersion", "intent", "class", "run");
}

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.commonwl.cwlsdk.cwl1_2;
16
17	import org.commonwl.cwlsdk.cwl1_2.utils.LoaderInstances;
18	import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptions;
19	import org.commonwl.cwlsdk.cwl1_2.utils.LoadingOptionsBuilder;
20	import org.commonwl.cwlsdk.cwl1_2.utils.SaveableImpl;
21	import org.commonwl.cwlsdk.cwl1_2.utils.ValidationException;
22
23	/**
24	* Auto-generated class implementation for <I>http://commonwl.org/cwltool#ProcessGenerator</I><BR>
25	*/
26	public class ProcessGeneratorImpl extends SaveableImpl implements ProcessGenerator {
NEW 27	private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();	×
NEW 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() {
NEW 34	return this.extensionFields_;	×
35	}
36
37	private java.util.Optional<String> id;
38
39	/**
40	* Getter for property <I>https://w3id.org/cwl/cwl#Process/id</I><BR>
41	* <BLOCKQUOTE>
42	* The unique identifier for this object.
43	*
44	* Only useful for `$graph` at `Process` level. Should not be exposed
45	* to users in graphical or terminal user interfaces.
46	* * </BLOCKQUOTE>
47	*/
48
49	public java.util.Optional<String> getId() {
NEW 50	return this.id;	×
51	}
52
53	private String class_;
54
55	/**
56	* Getter for property <I>http://commonwl.org/cwltool#ProcessGenerator/class</I><BR>
57
58	*/
59
60	public String getClass_() {
NEW 61	return this.class_;	×
62	}
63
64	private java.util.Optional<String> label;
65
66	/**
67	* Getter for property <I>https://w3id.org/cwl/cwl#Labeled/label</I><BR>
68	* <BLOCKQUOTE>
69	* A short, human-readable label of this object. * </BLOCKQUOTE>
70	*/
71
72	public java.util.Optional<String> getLabel() {
NEW 73	return this.label;	×
74	}
75
76	private Object doc;
77
78	/**
79	* Getter for property <I>https://w3id.org/cwl/salad#Documented/doc</I><BR>
80	* <BLOCKQUOTE>
81	* A documentation string for this object, or an array of strings which should be concatenated. * </BLOCKQUOTE>
82	*/
83
84	public Object getDoc() {
NEW 85	return this.doc;	×
86	}
87
88	private java.util.List<Object> inputs;
89
90	/**
91	* Getter for property <I>https://w3id.org/cwl/cwl#inputs</I><BR>
92	* <BLOCKQUOTE>
93	* Defines the input parameters of the process. The process is ready to
94	* run when all required input parameters are associated with concrete
95	* values. Input parameters include a schema for each parameter which is
96	* used to validate the input object. It may also be used to build a user
97	* interface for constructing the input object.
98	*
99	* When accepting an input object, all input parameters must have a value.
100	* If an input parameter is missing from the input object, it must be
101	* assigned a value of `null` (or the value of `default` for that
102	* parameter, if provided) for the purposes of validation and evaluation
103	* of expressions.
104	* * </BLOCKQUOTE>
105	*/
106
107	public java.util.List<Object> getInputs() {
NEW 108	return this.inputs;	×
109	}
110
111	private java.util.List<Object> outputs;
112
113	/**
114	* Getter for property <I>https://w3id.org/cwl/cwl#outputs</I><BR>
115	* <BLOCKQUOTE>
116	* Defines the parameters representing the output of the process. May be
117	* used to generate and/or validate the output object.
118	* * </BLOCKQUOTE>
119	*/
120
121	public java.util.List<Object> getOutputs() {
NEW 122	return this.outputs;	×
123	}
124
125	private java.util.Optional<java.util.List<Object>> requirements;
126
127	/**
128	* Getter for property <I>https://w3id.org/cwl/cwl#requirements</I><BR>
129	* <BLOCKQUOTE>
130	* Declares requirements that apply to either the runtime environment or the
131	* workflow engine that must be met in order to execute this process. If
132	* an implementation cannot satisfy all requirements, or a requirement is
133	* listed which is not recognized by the implementation, it is a fatal
134	* error and the implementation must not attempt to run the process,
135	* unless overridden at user option.
136	* * </BLOCKQUOTE>
137	*/
138
139	public java.util.Optional<java.util.List<Object>> getRequirements() {
NEW 140	return this.requirements;	×
141	}
142
143	private java.util.Optional<java.util.List<Object>> hints;
144
145	/**
146	* Getter for property <I>https://w3id.org/cwl/cwl#hints</I><BR>
147	* <BLOCKQUOTE>
148	* Declares hints applying to either the runtime environment or the
149	* workflow engine that may be helpful in executing this process. It is
150	* not an error if an implementation cannot satisfy all hints, however
151	* the implementation may report a warning.
152	* * </BLOCKQUOTE>
153	*/
154
155	public java.util.Optional<java.util.List<Object>> getHints() {
NEW 156	return this.hints;	×
157	}
158
159	private java.util.Optional<CWLVersion> cwlVersion;
160
161	/**
162	* Getter for property <I>https://w3id.org/cwl/cwl#cwlVersion</I><BR>
163	* <BLOCKQUOTE>
164	* CWL document version. Always required at the document root. Not
165	* required for a Process embedded inside another Process.
166	* * </BLOCKQUOTE>
167	*/
168
169	public java.util.Optional<CWLVersion> getCwlVersion() {
NEW 170	return this.cwlVersion;	×
171	}
172
173	private java.util.Optional<java.util.List<String>> intent;
174
175	/**
176	* Getter for property <I>https://w3id.org/cwl/cwl#Process/intent</I><BR>
177	* <BLOCKQUOTE>
178	* An identifier for the type of computational operation, of this Process.
179	* Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for
180	* [`CommandLineTool`](CommandLineTool.html#CommandLineTool),
181	* [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool).
182	*
183	* If provided, then this must be an IRI of a concept node that
184	* represents the type of operation, preferably defined within an ontology.
185	*
186	* For example, in the domain of bioinformatics, one can use an IRI from
187	* the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004),
188	* like [Alignment](http://edamontology.org/operation_2928),
189	* or [Clustering](http://edamontology.org/operation_3432); or a more
190	* specific Operation concept like
191	* [Split read mapping](http://edamontology.org/operation_3199).
192	* * </BLOCKQUOTE>
193	*/
194
195	public java.util.Optional<java.util.List<String>> getIntent() {
NEW 196	return this.intent;	×
197	}
198
199	private Object run;
200
201	/**
202	* Getter for property <I>https://w3id.org/cwl/cwl#run</I><BR>
203	* <BLOCKQUOTE>
204	* Specifies the process to run.
205	* * </BLOCKQUOTE>
206	*/
207
208	public Object getRun() {
NEW 209	return this.run;	×
210	}
211
212	/**
213	* Used by {@link org.commonwl.cwlsdk.cwl1_2.utils.RootLoader} to construct instances of ProcessGeneratorImpl.
214	*
215	* @param __doc_ Document fragment to load this record object from (presumably a
216	{@link java.util.Map}).
217	* @param __baseUri_ Base URI to generate child document IDs against.
218	* @param __loadingOptions Context for loading URIs and populating objects.
219	* @param __docRoot_ ID at this position in the document (if available) (maybe?)
220	* @throws ValidationException If the document fragment is not a {@link java.util.Map}
221	* or validation of fields fails.
222	*/
223	public ProcessGeneratorImpl(
224	final Object __doc_,
225	final String __baseUri_,
226	LoadingOptions __loadingOptions,
227	final String __docRoot_) {
NEW 228	super(__doc_, __baseUri_, __loadingOptions, __docRoot_);	×
229	// Prefix plumbing variables with '__' to reduce likelihood of collision with
230	// generated names.
NEW 231	String __baseUri = __baseUri_;	×
NEW 232	String __docRoot = __docRoot_;	×
NEW 233	if (!(__doc_ instanceof java.util.Map)) {	×
NEW 234	throw new ValidationException("ProcessGeneratorImpl called on non-map");	×
235	}
NEW 236	final java.util.Map<String, Object> __doc = (java.util.Map<String, Object>) __doc_;	×
NEW 237	final java.util.List<ValidationException> __errors =	×
238	new java.util.ArrayList<ValidationException>();
NEW 239	if (__loadingOptions != null) {	×
NEW 240	this.loadingOptions_ = __loadingOptions;	×
241	}
242	java.util.Optional<String> id;
243
NEW 244	if (__doc.containsKey("id")) {	×
245	try {
NEW 246	id =	×
247	LoaderInstances
248	.uri_optional_StringInstance_True_False_None_None
NEW 249	.loadField(__doc.get("id"), __baseUri, __loadingOptions);	×
NEW 250	} catch (ValidationException e) {	×
NEW 251	id = null; // won't be used but prevents compiler from complaining.	×
NEW 252	final String __message = "the `id` field is not valid because:";	×
NEW 253	__errors.add(new ValidationException(__message, e));	×
NEW 254	}	×
255
256	} else {
NEW 257	id = null;	×
258	}
259
NEW 260	Boolean __original_is_null = id == null;	×
NEW 261	if (id == null) {	×
NEW 262	if (__docRoot != null) {	×
NEW 263	id = java.util.Optional.of(__docRoot);	×
264	} else {
NEW 265	id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString());	×
266	}
267	}
NEW 268	if (__original_is_null) {	×
NEW 269	__baseUri = __baseUri_;	×
270	} else {
NEW 271	__baseUri = (String) id.orElse(null);	×
272	}
273	String class_;
274	try {
NEW 275	class_ =	×
276	LoaderInstances
277	.uri_StringInstance_False_True_None_None
NEW 278	.loadField(__doc.get("class"), __baseUri, __loadingOptions);	×
NEW 279	} catch (ValidationException e) {	×
NEW 280	class_ = null; // won't be used but prevents compiler from complaining.	×
NEW 281	final String __message = "the `class` field is not valid because:";	×
NEW 282	__errors.add(new ValidationException(__message, e));	×
NEW 283	}	×
284	java.util.Optional<String> label;
285
NEW 286	if (__doc.containsKey("label")) {	×
287	try {
NEW 288	label =	×
289	LoaderInstances
290	.optional_StringInstance
NEW 291	.loadField(__doc.get("label"), __baseUri, __loadingOptions);	×
NEW 292	} catch (ValidationException e) {	×
NEW 293	label = null; // won't be used but prevents compiler from complaining.	×
NEW 294	final String __message = "the `label` field is not valid because:";	×
NEW 295	__errors.add(new ValidationException(__message, e));	×
NEW 296	}	×
297
298	} else {
NEW 299	label = null;	×
300	}
301	Object doc;
302
NEW 303	if (__doc.containsKey("doc")) {	×
304	try {
NEW 305	doc =	×
306	LoaderInstances
307	.union_of_NullInstance_or_StringInstance_or_array_of_StringInstance
NEW 308	.loadField(__doc.get("doc"), __baseUri, __loadingOptions);	×
NEW 309	} catch (ValidationException e) {	×
NEW 310	doc = null; // won't be used but prevents compiler from complaining.	×
NEW 311	final String __message = "the `doc` field is not valid because:";	×
NEW 312	__errors.add(new ValidationException(__message, e));	×
NEW 313	}	×
314
315	} else {
NEW 316	doc = null;	×
317	}
318	java.util.List<Object> inputs;
319	try {
NEW 320	inputs =	×
321	LoaderInstances
322	.idmap_inputs_array_of_union_of_CommandInputParameter_or_WorkflowInputParameter_or_OperationInputParameter
NEW 323	.loadField(__doc.get("inputs"), __baseUri, __loadingOptions);	×
NEW 324	} catch (ValidationException e) {	×
NEW 325	inputs = null; // won't be used but prevents compiler from complaining.	×
NEW 326	final String __message = "the `inputs` field is not valid because:";	×
NEW 327	__errors.add(new ValidationException(__message, e));	×
NEW 328	}	×
329	java.util.List<Object> outputs;
330	try {
NEW 331	outputs =	×
332	LoaderInstances
333	.idmap_outputs_array_of_union_of_CommandOutputParameter_or_ExpressionToolOutputParameter_or_WorkflowOutputParameter_or_OperationOutputParameter
NEW 334	.loadField(__doc.get("outputs"), __baseUri, __loadingOptions);	×
NEW 335	} catch (ValidationException e) {	×
NEW 336	outputs = null; // won't be used but prevents compiler from complaining.	×
NEW 337	final String __message = "the `outputs` field is not valid because:";	×
NEW 338	__errors.add(new ValidationException(__message, e));	×
NEW 339	}	×
340	java.util.Optional<java.util.List<Object>> requirements;
341
NEW 342	if (__doc.containsKey("requirements")) {	×
343	try {
NEW 344	requirements =	×
345	LoaderInstances
346	.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 347	.loadField(__doc.get("requirements"), __baseUri, __loadingOptions);	×
NEW 348	} catch (ValidationException e) {	×
NEW 349	requirements = null; // won't be used but prevents compiler from complaining.	×
NEW 350	final String __message = "the `requirements` field is not valid because:";	×
NEW 351	__errors.add(new ValidationException(__message, e));	×
NEW 352	}	×
353
354	} else {
NEW 355	requirements = null;	×
356	}
357	java.util.Optional<java.util.List<Object>> hints;
358
NEW 359	if (__doc.containsKey("hints")) {	×
360	try {
NEW 361	hints =	×
362	LoaderInstances
363	.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 364	.loadField(__doc.get("hints"), __baseUri, __loadingOptions);	×
NEW 365	} catch (ValidationException e) {	×
NEW 366	hints = null; // won't be used but prevents compiler from complaining.	×
NEW 367	final String __message = "the `hints` field is not valid because:";	×
NEW 368	__errors.add(new ValidationException(__message, e));	×
NEW 369	}	×
370
371	} else {
NEW 372	hints = null;	×
373	}
374	java.util.Optional<CWLVersion> cwlVersion;
375
NEW 376	if (__doc.containsKey("cwlVersion")) {	×
377	try {
NEW 378	cwlVersion =	×
379	LoaderInstances
380	.uri_optional_CWLVersion_False_True_None_None
NEW 381	.loadField(__doc.get("cwlVersion"), __baseUri, __loadingOptions);	×
NEW 382	} catch (ValidationException e) {	×
NEW 383	cwlVersion = null; // won't be used but prevents compiler from complaining.	×
NEW 384	final String __message = "the `cwlVersion` field is not valid because:";	×
NEW 385	__errors.add(new ValidationException(__message, e));	×
NEW 386	}	×
387
388	} else {
NEW 389	cwlVersion = null;	×
390	}
391	java.util.Optional<java.util.List<String>> intent;
392
NEW 393	if (__doc.containsKey("intent")) {	×
394	try {
NEW 395	intent =	×
396	LoaderInstances
397	.uri_optional_array_of_StringInstance_True_False_None_None
NEW 398	.loadField(__doc.get("intent"), __baseUri, __loadingOptions);	×
NEW 399	} catch (ValidationException e) {	×
NEW 400	intent = null; // won't be used but prevents compiler from complaining.	×
NEW 401	final String __message = "the `intent` field is not valid because:";	×
NEW 402	__errors.add(new ValidationException(__message, e));	×
NEW 403	}	×
404
405	} else {
NEW 406	intent = null;	×
407	}
408	Object run;
409	try {
NEW 410	run =	×
411	LoaderInstances
412	.uri_union_of_StringInstance_or_CommandLineTool_or_ExpressionTool_or_Workflow_or_Operation_or_ProcessGenerator_False_False_None_None
NEW 413	.loadField(__doc.get("run"), __baseUri, __loadingOptions);	×
NEW 414	} catch (ValidationException e) {	×
NEW 415	run = null; // won't be used but prevents compiler from complaining.	×
NEW 416	final String __message = "the `run` field is not valid because:";	×
NEW 417	__errors.add(new ValidationException(__message, e));	×
NEW 418	}	×
NEW 419	if (!__errors.isEmpty()) {	×
NEW 420	throw new ValidationException("Trying 'RecordField'", __errors);	×
421	}
NEW 422	this.id = (java.util.Optional<String>) id;	×
NEW 423	this.label = (java.util.Optional<String>) label;	×
NEW 424	this.doc = (Object) doc;	×
NEW 425	this.inputs = (java.util.List<Object>) inputs;	×
NEW 426	this.outputs = (java.util.List<Object>) outputs;	×
NEW 427	this.requirements = (java.util.Optional<java.util.List<Object>>) requirements;	×
NEW 428	this.hints = (java.util.Optional<java.util.List<Object>>) hints;	×
NEW 429	this.cwlVersion = (java.util.Optional<CWLVersion>) cwlVersion;	×
NEW 430	this.intent = (java.util.Optional<java.util.List<String>>) intent;	×
NEW 431	this.class_ = (String) class_;	×
NEW 432	this.run = (Object) run;	×
NEW 433	for (String field:__doc.keySet()) {	×
NEW 434	if (!attrs.contains(field)) {	×
NEW 435	if (field.contains(":")) {	×
NEW 436	String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null);	×
NEW 437	extensionFields_.put(expanded_field, __doc.get(field));	×
438	}
439	}
NEW 440	}	×
NEW 441	}	×
NEW 442	private java.util.List<String> attrs = java.util.Arrays.asList("id", "label", "doc", "inputs", "outputs", "requirements", "hints", "cwlVersion", "intent", "class", "run");	×
443	}

common-workflow-language / cwljava / #423

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