#394

Committed 31 Oct 2025 04:10PM UTC coverage: 57.972% (-1.6%) from 59.538%

Build # #394

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push

github

Committed by

mr-c

Commit Message

rename package to a namespace that we control

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48.15

/src/main/java/org/commonwl/cwlsdk/cwl1_1/WorkflowStepImpl.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_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 <I>https://w3id.org/cwl/cwl#WorkflowStep</I><BR> <BLOCKQUOTE>
 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).
  </BLOCKQUOTE>
 */
public class WorkflowStepImpl extends SaveableImpl implements WorkflowStep {
  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#Identified/id</I><BR>
   * <BLOCKQUOTE>
   * The unique identifier for this object.   * </BLOCKQUOTE>
   */

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

  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> in;

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

  public java.util.List<Object> getIn() {
    return this.in;
  }

  private java.util.List<Object> out;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#out</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> getOut() {
    return this.out;
  }

  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 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.
   *    * </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 workflow step.  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 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;
  }

  private Object scatter;

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

   */

  public Object getScatter() {
    return this.scatter;
  }

  private java.util.Optional<ScatterMethod> scatterMethod;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#scatterMethod</I><BR>
   * <BLOCKQUOTE>
   * Required if `scatter` is an array of more than one element.
   *    * </BLOCKQUOTE>
   */

  public java.util.Optional<ScatterMethod> 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<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);
    }
    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> 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<Object> 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<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
                .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_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> 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<String>) id;
    this.label = (java.util.Optional<String>) label;
    this.doc = (Object) doc;
    this.in = (java.util.List<Object>) in;
    this.out = (java.util.List<Object>) out;
    this.requirements = (java.util.Optional<java.util.List<Object>>) requirements;
    this.hints = (java.util.Optional<java.util.List<Object>>) hints;
    this.run = (Object) run;
    this.scatter = (Object) scatter;
    this.scatterMethod = (java.util.Optional<ScatterMethod>) 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<String> attrs = java.util.Arrays.asList("id", "label", "doc", "in", "out", "requirements", "hints", "run", "scatter", "scatterMethod");
}

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_1;
16
17	import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances;
18	import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions;
19	import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder;
20	import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl;
21	import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException;
22
23	/**
24	* Auto-generated class implementation for <I>https://w3id.org/cwl/cwl#WorkflowStep</I><BR> <BLOCKQUOTE>
25	A workflow step is an executable element of a workflow. It specifies the
26	underlying process implementation (such as `CommandLineTool` or another
27	`Workflow`) in the `run` field and connects the input and output parameters
28	of the underlying process to workflow parameters.
29
30	# Scatter/gather
31
32	To use scatter/gather,
33	[ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified
34	in the workflow or workflow step requirements.
35
36	A "scatter" operation specifies that the associated workflow step or
37	subworkflow should execute separately over a list of input elements. Each
38	job making up a scatter operation is independent and may be executed
39	concurrently.
40
41	The `scatter` field specifies one or more input parameters which will be
42	scattered. An input parameter may be listed more than once. The declared
43	type of each input parameter is implicitly becomes an array of items of the
44	input parameter type. If a parameter is listed more than once, it becomes
45	a nested array. As a result, upstream parameters which are connected to
46	scattered parameters must be arrays.
47
48	All output parameter types are also implicitly wrapped in arrays. Each job
49	in the scatter results in an entry in the output array.
50
51	If any scattered parameter runtime value is an empty array, all outputs are
52	set to empty arrays and no work is done for the step, according to
53	applicable scattering rules.
54
55	If `scatter` declares more than one input parameter, `scatterMethod`
56	describes how to decompose the input into a discrete set of jobs.
57
58	* dotproduct specifies that each of the input arrays are aligned and one
59	element taken from each array to construct each job. It is an error
60	if all input arrays are not the same length.
61
62	* nested_crossproduct specifies the Cartesian product of the inputs,
63	producing a job for every combination of the scattered inputs. The
64	output must be nested arrays for each level of scattering, in the
65	order that the input arrays are listed in the `scatter` field.
66
67	* flat_crossproduct specifies the Cartesian product of the inputs,
68	producing a job for every combination of the scattered inputs. The
69	output arrays must be flattened to a single level, but otherwise listed in the
70	order that the input arrays are listed in the `scatter` field.
71
72	# Subworkflows
73
74	To specify a nested workflow as part of a workflow step,
75	[SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be
76	specified in the workflow or workflow step requirements.
77
78	It is a fatal error if a workflow directly or indirectly invokes itself as
79	a subworkflow (recursive workflows are not allowed).
80	</BLOCKQUOTE>
81	*/
82	public class WorkflowStepImpl extends SaveableImpl implements WorkflowStep {
83	private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();	1✔
84	private java.util.Map<String, Object> extensionFields_ =	1✔
85	new java.util.HashMap<String, Object>();
86	public LoadingOptions getLoadingOptions() {
NEW 87	return this.loadingOptions_;	×
88	}
89	public java.util.Map<String, Object> getExtensionFields() {
NEW 90	return this.extensionFields_;	×
91	}
92
93	private java.util.Optional<String> id;
94
95	/**
96	* Getter for property <I>https://w3id.org/cwl/cwl#Identified/id</I><BR>
97	* <BLOCKQUOTE>
98	* The unique identifier for this object. * </BLOCKQUOTE>
99	*/
100
101	public java.util.Optional<String> getId() {
NEW 102	return this.id;	×
103	}
104
105	private java.util.Optional<String> label;
106
107	/**
108	* Getter for property <I>https://w3id.org/cwl/cwl#Labeled/label</I><BR>
109	* <BLOCKQUOTE>
110	* A short, human-readable label of this object. * </BLOCKQUOTE>
111	*/
112
113	public java.util.Optional<String> getLabel() {
NEW 114	return this.label;	×
115	}
116
117	private Object doc;
118
119	/**
120	* Getter for property <I>https://w3id.org/cwl/salad#Documented/doc</I><BR>
121	* <BLOCKQUOTE>
122	* A documentation string for this object, or an array of strings which should be concatenated. * </BLOCKQUOTE>
123	*/
124
125	public Object getDoc() {
NEW 126	return this.doc;	×
127	}
128
129	private java.util.List<Object> in;
130
131	/**
132	* Getter for property <I>https://w3id.org/cwl/cwl#in</I><BR>
133	* <BLOCKQUOTE>
134	* Defines the input parameters of the workflow step. The process is ready to
135	* run when all required input parameters are associated with concrete
136	* values. Input parameters include a schema for each parameter which is
137	* used to validate the input object. It may also be used build a user
138	* interface for constructing the input object.
139	* * </BLOCKQUOTE>
140	*/
141
142	public java.util.List<Object> getIn() {
143	return this.in;	1✔
144	}
145
146	private java.util.List<Object> out;
147
148	/**
149	* Getter for property <I>https://w3id.org/cwl/cwl#out</I><BR>
150	* <BLOCKQUOTE>
151	* Defines the parameters representing the output of the process. May be
152	* used to generate and/or validate the output object.
153	* * </BLOCKQUOTE>
154	*/
155
156	public java.util.List<Object> getOut() {
NEW 157	return this.out;	×
158	}
159
160	private java.util.Optional<java.util.List<Object>> requirements;
161
162	/**
163	* Getter for property <I>https://w3id.org/cwl/cwl#requirements</I><BR>
164	* <BLOCKQUOTE>
165	* Declares requirements that apply to either the runtime environment or the
166	* workflow engine that must be met in order to execute this workflow step. If
167	* an implementation cannot satisfy all requirements, or a requirement is
168	* listed which is not recognized by the implementation, it is a fatal
169	* error and the implementation must not attempt to run the process,
170	* unless overridden at user option.
171	* * </BLOCKQUOTE>
172	*/
173
174	public java.util.Optional<java.util.List<Object>> getRequirements() {
NEW 175	return this.requirements;	×
176	}
177
178	private java.util.Optional<java.util.List<Object>> hints;
179
180	/**
181	* Getter for property <I>https://w3id.org/cwl/cwl#hints</I><BR>
182	* <BLOCKQUOTE>
183	* Declares hints applying to either the runtime environment or the
184	* workflow engine that may be helpful in executing this workflow step. It is
185	* not an error if an implementation cannot satisfy all hints, however
186	* the implementation may report a warning.
187	* * </BLOCKQUOTE>
188	*/
189
190	public java.util.Optional<java.util.List<Object>> getHints() {
NEW 191	return this.hints;	×
192	}
193
194	private Object run;
195
196	/**
197	* Getter for property <I>https://w3id.org/cwl/cwl#run</I><BR>
198	* <BLOCKQUOTE>
199	* Specifies the process to run.
200	* * </BLOCKQUOTE>
201	*/
202
203	public Object getRun() {
NEW 204	return this.run;	×
205	}
206
207	private Object scatter;
208
209	/**
210	* Getter for property <I>https://w3id.org/cwl/cwl#scatter</I><BR>
211
212	*/
213
214	public Object getScatter() {
NEW 215	return this.scatter;	×
216	}
217
218	private java.util.Optional<ScatterMethod> scatterMethod;
219
220	/**
221	* Getter for property <I>https://w3id.org/cwl/cwl#scatterMethod</I><BR>
222	* <BLOCKQUOTE>
223	* Required if `scatter` is an array of more than one element.
224	* * </BLOCKQUOTE>
225	*/
226
227	public java.util.Optional<ScatterMethod> getScatterMethod() {
NEW 228	return this.scatterMethod;	×
229	}
230
231	/**
232	* Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of WorkflowStepImpl.
233	*
234	* @param __doc_ Document fragment to load this record object from (presumably a
235	{@link java.util.Map}).
236	* @param __baseUri_ Base URI to generate child document IDs against.
237	* @param __loadingOptions Context for loading URIs and populating objects.
238	* @param __docRoot_ ID at this position in the document (if available) (maybe?)
239	* @throws ValidationException If the document fragment is not a {@link java.util.Map}
240	* or validation of fields fails.
241	*/
242	public WorkflowStepImpl(
243	final Object __doc_,
244	final String __baseUri_,
245	LoadingOptions __loadingOptions,
246	final String __docRoot_) {
247	super(__doc_, __baseUri_, __loadingOptions, __docRoot_);	1✔
248	// Prefix plumbing variables with '__' to reduce likelihood of collision with
249	// generated names.
250	String __baseUri = __baseUri_;	1✔
251	String __docRoot = __docRoot_;	1✔
252	if (!(__doc_ instanceof java.util.Map)) {	1✔
NEW 253	throw new ValidationException("WorkflowStepImpl called on non-map");	×
254	}
255	final java.util.Map<String, Object> __doc = (java.util.Map<String, Object>) __doc_;	1✔
256	final java.util.List<ValidationException> __errors =	1✔
257	new java.util.ArrayList<ValidationException>();
258	if (__loadingOptions != null) {	1✔
259	this.loadingOptions_ = __loadingOptions;	1✔
260	}
261	java.util.Optional<String> id;
262
263	if (__doc.containsKey("id")) {	1✔
264	try {
265	id =	1✔
266	LoaderInstances
267	.uri_optional_StringInstance_True_False_None_None
268	.loadField(__doc.get("id"), __baseUri, __loadingOptions);	1✔
NEW 269	} catch (ValidationException e) {	×
NEW 270	id = null; // won't be used but prevents compiler from complaining.	×
NEW 271	final String __message = "the `id` field is not valid because:";	×
NEW 272	__errors.add(new ValidationException(__message, e));	×
273	}	1✔
274
275	} else {
NEW 276	id = null;	×
277	}
278
279	Boolean __original_is_null = id == null;	1✔
280	if (id == null) {	1✔
NEW 281	if (__docRoot != null) {	×
NEW 282	id = java.util.Optional.of(__docRoot);	×
283	} else {
NEW 284	id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString());	×
285	}
286	}
287	if (__original_is_null) {	1✔
NEW 288	__baseUri = __baseUri_;	×
289	} else {
290	__baseUri = (String) id.orElse(null);	1✔
291	}
292	java.util.Optional<String> label;
293
294	if (__doc.containsKey("label")) {	1✔
295	try {
NEW 296	label =	×
297	LoaderInstances
298	.optional_StringInstance
NEW 299	.loadField(__doc.get("label"), __baseUri, __loadingOptions);	×
NEW 300	} catch (ValidationException e) {	×
NEW 301	label = null; // won't be used but prevents compiler from complaining.	×
NEW 302	final String __message = "the `label` field is not valid because:";	×
NEW 303	__errors.add(new ValidationException(__message, e));	×
NEW 304	}	×
305
306	} else {
307	label = null;	1✔
308	}
309	Object doc;
310
311	if (__doc.containsKey("doc")) {	1✔
312	try {
NEW 313	doc =	×
314	LoaderInstances
315	.union_of_NullInstance_or_StringInstance_or_array_of_StringInstance
NEW 316	.loadField(__doc.get("doc"), __baseUri, __loadingOptions);	×
NEW 317	} catch (ValidationException e) {	×
NEW 318	doc = null; // won't be used but prevents compiler from complaining.	×
NEW 319	final String __message = "the `doc` field is not valid because:";	×
NEW 320	__errors.add(new ValidationException(__message, e));	×
NEW 321	}	×
322
323	} else {
324	doc = null;	1✔
325	}
326	java.util.List<Object> in;
327	try {
328	in =	1✔
329	LoaderInstances
330	.idmap_in_array_of_WorkflowStepInput
331	.loadField(__doc.get("in"), __baseUri, __loadingOptions);	1✔
NEW 332	} catch (ValidationException e) {	×
NEW 333	in = null; // won't be used but prevents compiler from complaining.	×
NEW 334	final String __message = "the `in` field is not valid because:";	×
NEW 335	__errors.add(new ValidationException(__message, e));	×
336	}	1✔
337	java.util.List<Object> out;
338	try {
339	out =	1✔
340	LoaderInstances
341	.uri_array_of_union_of_StringInstance_or_WorkflowStepOutput_True_False_None_None
342	.loadField(__doc.get("out"), __baseUri, __loadingOptions);	1✔
NEW 343	} catch (ValidationException e) {	×
NEW 344	out = null; // won't be used but prevents compiler from complaining.	×
NEW 345	final String __message = "the `out` field is not valid because:";	×
NEW 346	__errors.add(new ValidationException(__message, e));	×
347	}	1✔
348	java.util.Optional<java.util.List<Object>> requirements;
349
350	if (__doc.containsKey("requirements")) {	1✔
351	try {
352	requirements =	1✔
353	LoaderInstances
354	.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
355	.loadField(__doc.get("requirements"), __baseUri, __loadingOptions);	1✔
NEW 356	} catch (ValidationException e) {	×
NEW 357	requirements = null; // won't be used but prevents compiler from complaining.	×
NEW 358	final String __message = "the `requirements` field is not valid because:";	×
NEW 359	__errors.add(new ValidationException(__message, e));	×
360	}	1✔
361
362	} else {
363	requirements = null;	1✔
364	}
365	java.util.Optional<java.util.List<Object>> hints;
366
367	if (__doc.containsKey("hints")) {	1✔
368	try {
NEW 369	hints =	×
370	LoaderInstances
371	.idmap_hints_optional_array_of_AnyInstance
NEW 372	.loadField(__doc.get("hints"), __baseUri, __loadingOptions);	×
NEW 373	} catch (ValidationException e) {	×
NEW 374	hints = null; // won't be used but prevents compiler from complaining.	×
NEW 375	final String __message = "the `hints` field is not valid because:";	×
NEW 376	__errors.add(new ValidationException(__message, e));	×
NEW 377	}	×
378
379	} else {
380	hints = null;	1✔
381	}
382	Object run;
383	try {
384	run =	1✔
385	LoaderInstances
386	.uri_union_of_StringInstance_or_CommandLineTool_or_ExpressionTool_or_Workflow_False_False_None_None
387	.loadField(__doc.get("run"), __baseUri, __loadingOptions);	1✔
NEW 388	} catch (ValidationException e) {	×
NEW 389	run = null; // won't be used but prevents compiler from complaining.	×
NEW 390	final String __message = "the `run` field is not valid because:";	×
NEW 391	__errors.add(new ValidationException(__message, e));	×
392	}	1✔
393	Object scatter;
394
395	if (__doc.containsKey("scatter")) {	1✔
396	try {
397	scatter =	1✔
398	LoaderInstances
399	.uri_union_of_NullInstance_or_StringInstance_or_array_of_StringInstance_False_False_0_None
400	.loadField(__doc.get("scatter"), __baseUri, __loadingOptions);	1✔
NEW 401	} catch (ValidationException e) {	×
NEW 402	scatter = null; // won't be used but prevents compiler from complaining.	×
NEW 403	final String __message = "the `scatter` field is not valid because:";	×
NEW 404	__errors.add(new ValidationException(__message, e));	×
405	}	1✔
406
407	} else {
408	scatter = null;	1✔
409	}
410	java.util.Optional<ScatterMethod> scatterMethod;
411
412	if (__doc.containsKey("scatterMethod")) {	1✔
413	try {
414	scatterMethod =	1✔
415	LoaderInstances
416	.uri_optional_ScatterMethod_False_True_None_None
417	.loadField(__doc.get("scatterMethod"), __baseUri, __loadingOptions);	1✔
NEW 418	} catch (ValidationException e) {	×
NEW 419	scatterMethod = null; // won't be used but prevents compiler from complaining.	×
NEW 420	final String __message = "the `scatterMethod` field is not valid because:";	×
NEW 421	__errors.add(new ValidationException(__message, e));	×
422	}	1✔
423
424	} else {
425	scatterMethod = null;	1✔
426	}
427	if (!__errors.isEmpty()) {	1✔
NEW 428	throw new ValidationException("Trying 'RecordField'", __errors);	×
429	}
430	this.id = (java.util.Optional<String>) id;	1✔
431	this.label = (java.util.Optional<String>) label;	1✔
432	this.doc = (Object) doc;	1✔
433	this.in = (java.util.List<Object>) in;	1✔
434	this.out = (java.util.List<Object>) out;	1✔
435	this.requirements = (java.util.Optional<java.util.List<Object>>) requirements;	1✔
436	this.hints = (java.util.Optional<java.util.List<Object>>) hints;	1✔
437	this.run = (Object) run;	1✔
438	this.scatter = (Object) scatter;	1✔
439	this.scatterMethod = (java.util.Optional<ScatterMethod>) scatterMethod;	1✔
440	for (String field:__doc.keySet()) {	1✔
441	if (!attrs.contains(field)) {	1✔
NEW 442	if (field.contains(":")) {	×
NEW 443	String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null);	×
NEW 444	extensionFields_.put(expanded_field, __doc.get(field));	×
445	}
446	}
447	}	1✔
448	}	1✔
449	private java.util.List<String> attrs = java.util.Arrays.asList("id", "label", "doc", "in", "out", "requirements", "hints", "run", "scatter", "scatterMethod");	1✔
450	}

common-workflow-language / cwljava / #394

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