#389

Committed 30 Oct 2025 05:13PM UTC coverage: 58.693% (-0.8%) from 59.538%

Build # #389

Build Type

Pull #218

github

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web-flow

Commit Message

Merge 98b159202 into befd7e4b9

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

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/src/main/java/org/w3id/cwl/cwl1_2/WorkflowImpl.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#Workflow</I><BR> <BLOCKQUOTE>
 A workflow describes a set of **steps** and the **dependencies** between
 those steps.  When a step produces output that will be consumed by a
 second step, the first step is a dependency of the second step.
 
 When there is a dependency, the workflow engine must execute the preceding
 step and wait for it to successfully produce output before executing the
 dependent step.  If two steps are defined in the workflow graph that
 are not directly or indirectly dependent, these steps are **independent**,
 and may execute in any order or execute concurrently.  A workflow is
 complete when all steps have been executed.
 
 Dependencies between parameters are expressed using the `source`
 field on [workflow step input parameters](#WorkflowStepInput) and
 `outputSource` field on [workflow output
 parameters](#WorkflowOutputParameter).
 
 The `source` field on each workflow step input parameter expresses
 the data links that contribute to the value of the step input
 parameter (the "sink").  A workflow step can only begin execution
 when every data link connected to a step has been fulfilled.
 
 The `outputSource` field on each workflow step input parameter
 expresses the data links that contribute to the value of the
 workflow output parameter (the "sink").  Workflow execution cannot
 complete successfully until every data link connected to an output
 parameter has been fulfilled.
 
 ## Workflow success and failure
 
 A completed step must result in one of `success`, `temporaryFailure` or
 `permanentFailure` states.  An implementation may choose to retry a step
 execution which resulted in `temporaryFailure`.  An implementation may
 choose to either continue running other steps of a workflow, or terminate
 immediately upon `permanentFailure`.
 
 * If any step of a workflow execution results in `permanentFailure`, then
 the workflow status is `permanentFailure`.
 
 * If one or more steps result in `temporaryFailure` and all other steps
 complete `success` or are not executed, then the workflow status is
 `temporaryFailure`.
 
 * If all workflow steps are executed and complete with `success`, then the
 workflow status is `success`.
 
 # Extensions
 
 [ScatterFeatureRequirement](#ScatterFeatureRequirement) and
 [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are
 available as standard [extensions](#Extensions_and_Metadata) to core
 workflow semantics.
  </BLOCKQUOTE>
 */
public class WorkflowImpl extends SaveableImpl implements Workflow {
  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 Workflow_class class_;

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

   */

  public Workflow_class 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'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 java.util.List<Object> steps;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#Workflow/steps</I><BR>
   * <BLOCKQUOTE>
   * The individual steps that make up the workflow.  Each step is executed when all of its
   * input data links are fulfilled.  An implementation may choose to execute
   * the steps in a different order than listed and/or execute steps
   * concurrently, provided that dependencies between steps are met.
   *    * </BLOCKQUOTE>
   */

  public java.util.List<Object> getSteps() {
    return this.steps;
  }

  /**
   * Used by {@link org.w3id.cwl.cwl1_2.utils.RootLoader} to construct instances of WorkflowImpl.
   *
   * @param __doc_            Document fragment to load this record object from (presumably a
                              {@link java.util.Map}).
   * @param __baseUri_        Base URI to generate child document IDs against.
   * @param __loadingOptions  Context for loading URIs and populating objects.
   * @param __docRoot_        ID at this position in the document (if available) (maybe?)
   * @throws ValidationException If the document fragment is not a {@link java.util.Map}
   *                             or validation of fields fails.
   */
  public WorkflowImpl(
      final Object __doc_,
      final String __baseUri_,
      LoadingOptions __loadingOptions,
      final String __docRoot_) {
    super(__doc_, __baseUri_, __loadingOptions, __docRoot_);
    // Prefix plumbing variables with '__' to reduce likelihood of collision with
    // generated names.
    String __baseUri = __baseUri_;
    String __docRoot = __docRoot_;
    if (!(__doc_ instanceof java.util.Map)) {
      throw new ValidationException("WorkflowImpl called on non-map");
    }
    final java.util.Map<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);
    }
    Workflow_class class_;
    try {
      class_ =
          LoaderInstances
              .uri_Workflow_class_False_True_None_None
              .loadField(__doc.get("class"), __baseUri, __loadingOptions);
    } catch (ValidationException e) {
      class_ = null; // won't be used but prevents compiler from complaining.
      final String __message = "the `class` field is not valid because:";
      __errors.add(new ValidationException(__message, e));
    }
    java.util.Optional<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_WorkflowInputParameter
              .loadField(__doc.get("inputs"), __baseUri, __loadingOptions);
    } catch (ValidationException e) {
      inputs = null; // won't be used but prevents compiler from complaining.
      final String __message = "the `inputs` field is not valid because:";
      __errors.add(new ValidationException(__message, e));
    }
    java.util.List<Object> outputs;
    try {
      outputs =
          LoaderInstances
              .idmap_outputs_array_of_WorkflowOutputParameter
              .loadField(__doc.get("outputs"), __baseUri, __loadingOptions);
    } catch (ValidationException e) {
      outputs = null; // won't be used but prevents compiler from complaining.
      final String __message = "the `outputs` field is not valid because:";
      __errors.add(new ValidationException(__message, e));
    }
    java.util.Optional<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_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance
                .loadField(__doc.get("hints"), __baseUri, __loadingOptions);
      } catch (ValidationException e) {
        hints = null; // won't be used but prevents compiler from complaining.
        final String __message = "the `hints` field is not valid because:";
        __errors.add(new ValidationException(__message, e));
      }

    } else {
      hints = null;
    }
    java.util.Optional<CWLVersion> 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;
    }
    java.util.List<Object> steps;
    try {
      steps =
          LoaderInstances
              .idmap_steps_array_of_WorkflowStep
              .loadField(__doc.get("steps"), __baseUri, __loadingOptions);
    } catch (ValidationException e) {
      steps = null; // won't be used but prevents compiler from complaining.
      final String __message = "the `steps` field is not valid because:";
      __errors.add(new ValidationException(__message, e));
    }
    if (!__errors.isEmpty()) {
      throw new ValidationException("Trying 'RecordField'", __errors);
    }
    this.id = (java.util.Optional<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_ = (Workflow_class) class_;
    this.steps = (java.util.List<Object>) steps;
    for (String field:__doc.keySet()) {
      if (!attrs.contains(field)) {
        if (field.contains(":")) {
          String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null);
          extensionFields_.put(expanded_field, __doc.get(field));
        }
      }
    }
  }
  private java.util.List<String> attrs = java.util.Arrays.asList("id", "label", "doc", "inputs", "outputs", "requirements", "hints", "cwlVersion", "intent", "class", "steps");
}

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#Workflow</I><BR> <BLOCKQUOTE>
25	A workflow describes a set of steps and the dependencies between
26	those steps. When a step produces output that will be consumed by a
27	second step, the first step is a dependency of the second step.
28
29	When there is a dependency, the workflow engine must execute the preceding
30	step and wait for it to successfully produce output before executing the
31	dependent step. If two steps are defined in the workflow graph that
32	are not directly or indirectly dependent, these steps are independent,
33	and may execute in any order or execute concurrently. A workflow is
34	complete when all steps have been executed.
35
36	Dependencies between parameters are expressed using the `source`
37	field on [workflow step input parameters](#WorkflowStepInput) and
38	`outputSource` field on [workflow output
39	parameters](#WorkflowOutputParameter).
40
41	The `source` field on each workflow step input parameter expresses
42	the data links that contribute to the value of the step input
43	parameter (the "sink"). A workflow step can only begin execution
44	when every data link connected to a step has been fulfilled.
45
46	The `outputSource` field on each workflow step input parameter
47	expresses the data links that contribute to the value of the
48	workflow output parameter (the "sink"). Workflow execution cannot
49	complete successfully until every data link connected to an output
50	parameter has been fulfilled.
51
52	## Workflow success and failure
53
54	A completed step must result in one of `success`, `temporaryFailure` or
55	`permanentFailure` states. An implementation may choose to retry a step
56	execution which resulted in `temporaryFailure`. An implementation may
57	choose to either continue running other steps of a workflow, or terminate
58	immediately upon `permanentFailure`.
59
60	* If any step of a workflow execution results in `permanentFailure`, then
61	the workflow status is `permanentFailure`.
62
63	* If one or more steps result in `temporaryFailure` and all other steps
64	complete `success` or are not executed, then the workflow status is
65	`temporaryFailure`.
66
67	* If all workflow steps are executed and complete with `success`, then the
68	workflow status is `success`.
69
70	# Extensions
71
72	[ScatterFeatureRequirement](#ScatterFeatureRequirement) and
73	[SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are
74	available as standard [extensions](#Extensions_and_Metadata) to core
75	workflow semantics.
76	</BLOCKQUOTE>
77	*/
78	public class WorkflowImpl extends SaveableImpl implements Workflow {
79	private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();	1✔
80	private java.util.Map<String, Object> extensionFields_ =	1✔
81	new java.util.HashMap<String, Object>();
82	public LoadingOptions getLoadingOptions() {
NEW 83	return this.loadingOptions_;	×
84	}
85	public java.util.Map<String, Object> getExtensionFields() {
86	return this.extensionFields_;	×
87	}
88
89	private java.util.Optional<String> id;
90
91	/**
92	* Getter for property <I>https://w3id.org/cwl/cwl#Process/id</I><BR>
93	* <BLOCKQUOTE>
94	* The unique identifier for this object.
95	*
96	* Only useful for `$graph` at `Process` level. Should not be exposed
97	* to users in graphical or terminal user interfaces.
98	* * </BLOCKQUOTE>
99	*/
100
101	public java.util.Optional<String> getId() {
102	return this.id;	1✔
103	}
104
105	private Workflow_class class_;
106
107	/**
108	* Getter for property <I>https://w3id.org/cwl/cwl#Workflow/class</I><BR>
109
110	*/
111
112	public Workflow_class getClass_() {
113	return this.class_;	×
114	}
115
116	private java.util.Optional<String> label;
117
118	/**
119	* Getter for property <I>https://w3id.org/cwl/cwl#Labeled/label</I><BR>
120	* <BLOCKQUOTE>
121	* A short, human-readable label of this object. * </BLOCKQUOTE>
122	*/
123
124	public java.util.Optional<String> getLabel() {
125	return this.label;	×
126	}
127
128	private Object doc;
129
130	/**
131	* Getter for property <I>https://w3id.org/cwl/salad#Documented/doc</I><BR>
132	* <BLOCKQUOTE>
133	* A documentation string for this object, or an array of strings which should be concatenated. * </BLOCKQUOTE>
134	*/
135
136	public Object getDoc() {
137	return this.doc;	×
138	}
139
140	private java.util.List<Object> inputs;
141
142	/**
143	* Getter for property <I>https://w3id.org/cwl/cwl#inputs</I><BR>
144	* <BLOCKQUOTE>
145	* Defines the input parameters of the process. The process is ready to
146	* run when all required input parameters are associated with concrete
147	* values. Input parameters include a schema for each parameter which is
148	* used to validate the input object. It may also be used to build a user
149	* interface for constructing the input object.
150	*
151	* When accepting an input object, all input parameters must have a value.
152	* If an input parameter is missing from the input object, it must be
153	* assigned a value of `null` (or the value of `default` for that
154	* parameter, if provided) for the purposes of validation and evaluation
155	* of expressions.
156	* * </BLOCKQUOTE>
157	*/
158
159	public java.util.List<Object> getInputs() {
160	return this.inputs;	1✔
161	}
162
163	private java.util.List<Object> outputs;
164
165	/**
166	* Getter for property <I>https://w3id.org/cwl/cwl#outputs</I><BR>
167	* <BLOCKQUOTE>
168	* Defines the parameters representing the output of the process. May be
169	* used to generate and/or validate the output object.
170	* * </BLOCKQUOTE>
171	*/
172
173	public java.util.List<Object> getOutputs() {
174	return this.outputs;	×
175	}
176
177	private java.util.Optional<java.util.List<Object>> requirements;
178
179	/**
180	* Getter for property <I>https://w3id.org/cwl/cwl#requirements</I><BR>
181	* <BLOCKQUOTE>
182	* Declares requirements that apply to either the runtime environment or the
183	* workflow engine that must be met in order to execute this process. If
184	* an implementation cannot satisfy all requirements, or a requirement is
185	* listed which is not recognized by the implementation, it is a fatal
186	* error and the implementation must not attempt to run the process,
187	* unless overridden at user option.
188	* * </BLOCKQUOTE>
189	*/
190
191	public java.util.Optional<java.util.List<Object>> getRequirements() {
192	return this.requirements;	×
193	}
194
195	private java.util.Optional<java.util.List<Object>> hints;
196
197	/**
198	* Getter for property <I>https://w3id.org/cwl/cwl#hints</I><BR>
199	* <BLOCKQUOTE>
200	* Declares hints applying to either the runtime environment or the
201	* workflow engine that may be helpful in executing this process. It is
202	* not an error if an implementation cannot satisfy all hints, however
203	* the implementation may report a warning.
204	* * </BLOCKQUOTE>
205	*/
206
207	public java.util.Optional<java.util.List<Object>> getHints() {
208	return this.hints;	×
209	}
210
211	private java.util.Optional<CWLVersion> cwlVersion;
212
213	/**
214	* Getter for property <I>https://w3id.org/cwl/cwl#cwlVersion</I><BR>
215	* <BLOCKQUOTE>
216	* CWL document version. Always required at the document root. Not
217	* required for a Process embedded inside another Process.
218	* * </BLOCKQUOTE>
219	*/
220
221	public java.util.Optional<CWLVersion> getCwlVersion() {
222	return this.cwlVersion;	1✔
223	}
224
225	private java.util.Optional<java.util.List<String>> intent;
226
227	/**
228	* Getter for property <I>https://w3id.org/cwl/cwl#Process/intent</I><BR>
229	* <BLOCKQUOTE>
230	* An identifier for the type of computational operation, of this Process.
231	* Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for
232	* [`CommandLineTool`](CommandLineTool.html#CommandLineTool),
233	* [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool).
234	*
235	* If provided, then this must be an IRI of a concept node that
236	* represents the type of operation, preferably defined within an ontology.
237	*
238	* For example, in the domain of bioinformatics, one can use an IRI from
239	* the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004),
240	* like [Alignment](http://edamontology.org/operation_2928),
241	* or [Clustering](http://edamontology.org/operation_3432); or a more
242	* specific Operation concept like
243	* [Split read mapping](http://edamontology.org/operation_3199).
244	* * </BLOCKQUOTE>
245	*/
246
247	public java.util.Optional<java.util.List<String>> getIntent() {
248	return this.intent;	×
249	}
250
251	private java.util.List<Object> steps;
252
253	/**
254	* Getter for property <I>https://w3id.org/cwl/cwl#Workflow/steps</I><BR>
255	* <BLOCKQUOTE>
256	* The individual steps that make up the workflow. Each step is executed when all of its
257	* input data links are fulfilled. An implementation may choose to execute
258	* the steps in a different order than listed and/or execute steps
259	* concurrently, provided that dependencies between steps are met.
260	* * </BLOCKQUOTE>
261	*/
262
263	public java.util.List<Object> getSteps() {
264	return this.steps;	1✔
265	}
266
267	/**
268	* Used by {@link org.w3id.cwl.cwl1_2.utils.RootLoader} to construct instances of WorkflowImpl.
269	*
270	* @param __doc_ Document fragment to load this record object from (presumably a
271	{@link java.util.Map}).
272	* @param __baseUri_ Base URI to generate child document IDs against.
273	* @param __loadingOptions Context for loading URIs and populating objects.
274	* @param __docRoot_ ID at this position in the document (if available) (maybe?)
275	* @throws ValidationException If the document fragment is not a {@link java.util.Map}
276	* or validation of fields fails.
277	*/
278	public WorkflowImpl(
279	final Object __doc_,
280	final String __baseUri_,
281	LoadingOptions __loadingOptions,
282	final String __docRoot_) {
283	super(__doc_, __baseUri_, __loadingOptions, __docRoot_);	1✔
284	// Prefix plumbing variables with '__' to reduce likelihood of collision with
285	// generated names.
286	String __baseUri = __baseUri_;	1✔
287	String __docRoot = __docRoot_;	1✔
288	if (!(__doc_ instanceof java.util.Map)) {	1✔
289	throw new ValidationException("WorkflowImpl called on non-map");	×
290	}
291	final java.util.Map<String, Object> __doc = (java.util.Map<String, Object>) __doc_;	1✔
292	final java.util.List<ValidationException> __errors =	1✔
293	new java.util.ArrayList<ValidationException>();
294	if (__loadingOptions != null) {	1✔
295	this.loadingOptions_ = __loadingOptions;	1✔
296	}
297	java.util.Optional<String> id;
298
299	if (__doc.containsKey("id")) {	1✔
300	try {
301	id =	1✔
302	LoaderInstances
303	.uri_optional_StringInstance_True_False_None_None
304	.loadField(__doc.get("id"), __baseUri, __loadingOptions);	1✔
305	} catch (ValidationException e) {	×
306	id = null; // won't be used but prevents compiler from complaining.	×
307	final String __message = "the `id` field is not valid because:";	×
308	__errors.add(new ValidationException(__message, e));	×
309	}	1✔
310
311	} else {
312	id = null;	1✔
313	}
314
315	Boolean __original_is_null = id == null;	1✔
316	if (id == null) {	1✔
317	if (__docRoot != null) {	1✔
318	id = java.util.Optional.of(__docRoot);	1✔
319	} else {
320	id = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString());	1✔
321	}
322	}
323	if (__original_is_null) {	1✔
324	__baseUri = __baseUri_;	1✔
325	} else {
326	__baseUri = (String) id.orElse(null);	1✔
327	}
328	Workflow_class class_;
329	try {
330	class_ =	1✔
331	LoaderInstances
332	.uri_Workflow_class_False_True_None_None
333	.loadField(__doc.get("class"), __baseUri, __loadingOptions);	1✔
334	} catch (ValidationException e) {	1✔
335	class_ = null; // won't be used but prevents compiler from complaining.	1✔
336	final String __message = "the `class` field is not valid because:";	1✔
337	__errors.add(new ValidationException(__message, e));	1✔
338	}	1✔
339	java.util.Optional<String> label;
340
341	if (__doc.containsKey("label")) {	1✔
342	try {
343	label =	×
344	LoaderInstances
345	.optional_StringInstance
346	.loadField(__doc.get("label"), __baseUri, __loadingOptions);	×
347	} catch (ValidationException e) {	×
348	label = null; // won't be used but prevents compiler from complaining.	×
349	final String __message = "the `label` field is not valid because:";	×
350	__errors.add(new ValidationException(__message, e));	×
351	}	×
352
353	} else {
354	label = null;	1✔
355	}
356	Object doc;
357
358	if (__doc.containsKey("doc")) {	1✔
359	try {
360	doc =	1✔
361	LoaderInstances
362	.union_of_NullInstance_or_StringInstance_or_array_of_StringInstance
363	.loadField(__doc.get("doc"), __baseUri, __loadingOptions);	1✔
364	} catch (ValidationException e) {	×
365	doc = null; // won't be used but prevents compiler from complaining.	×
366	final String __message = "the `doc` field is not valid because:";	×
367	__errors.add(new ValidationException(__message, e));	×
368	}	1✔
369
370	} else {
371	doc = null;	1✔
372	}
373	java.util.List<Object> inputs;
374	try {
375	inputs =	1✔
376	LoaderInstances
377	.idmap_inputs_array_of_WorkflowInputParameter
378	.loadField(__doc.get("inputs"), __baseUri, __loadingOptions);	1✔
379	} catch (ValidationException e) {	×
380	inputs = null; // won't be used but prevents compiler from complaining.	×
381	final String __message = "the `inputs` field is not valid because:";	×
382	__errors.add(new ValidationException(__message, e));	×
383	}	1✔
384	java.util.List<Object> outputs;
385	try {
386	outputs =	1✔
387	LoaderInstances
388	.idmap_outputs_array_of_WorkflowOutputParameter
389	.loadField(__doc.get("outputs"), __baseUri, __loadingOptions);	1✔
390	} catch (ValidationException e) {	×
391	outputs = null; // won't be used but prevents compiler from complaining.	×
392	final String __message = "the `outputs` field is not valid because:";	×
393	__errors.add(new ValidationException(__message, e));	×
394	}	1✔
395	java.util.Optional<java.util.List<Object>> requirements;
396
397	if (__doc.containsKey("requirements")) {	1✔
398	try {
399	requirements =	1✔
400	LoaderInstances
401	.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
402	.loadField(__doc.get("requirements"), __baseUri, __loadingOptions);	1✔
403	} catch (ValidationException e) {	×
404	requirements = null; // won't be used but prevents compiler from complaining.	×
405	final String __message = "the `requirements` field is not valid because:";	×
406	__errors.add(new ValidationException(__message, e));	×
407	}	1✔
408
409	} else {
410	requirements = null;	1✔
411	}
412	java.util.Optional<java.util.List<Object>> hints;
413
414	if (__doc.containsKey("hints")) {	1✔
415	try {
416	hints =	1✔
417	LoaderInstances
418	.idmap_hints_optional_array_of_union_of_InlineJavascriptRequirement_or_SchemaDefRequirement_or_LoadListingRequirement_or_DockerRequirement_or_SoftwareRequirement_or_InitialWorkDirRequirement_or_EnvVarRequirement_or_ShellCommandRequirement_or_ResourceRequirement_or_WorkReuse_or_NetworkAccess_or_InplaceUpdateRequirement_or_ToolTimeLimit_or_SubworkflowFeatureRequirement_or_ScatterFeatureRequirement_or_MultipleInputFeatureRequirement_or_StepInputExpressionRequirement_or_AnyInstance
419	.loadField(__doc.get("hints"), __baseUri, __loadingOptions);	1✔
420	} catch (ValidationException e) {	×
421	hints = null; // won't be used but prevents compiler from complaining.	×
422	final String __message = "the `hints` field is not valid because:";	×
423	__errors.add(new ValidationException(__message, e));	×
424	}	1✔
425
426	} else {
427	hints = null;	1✔
428	}
429	java.util.Optional<CWLVersion> cwlVersion;
430
431	if (__doc.containsKey("cwlVersion")) {	1✔
432	try {
433	cwlVersion =	1✔
434	LoaderInstances
435	.uri_optional_CWLVersion_False_True_None_None
436	.loadField(__doc.get("cwlVersion"), __baseUri, __loadingOptions);	1✔
437	} catch (ValidationException e) {	×
438	cwlVersion = null; // won't be used but prevents compiler from complaining.	×
439	final String __message = "the `cwlVersion` field is not valid because:";	×
440	__errors.add(new ValidationException(__message, e));	×
441	}	1✔
442
443	} else {
444	cwlVersion = null;	1✔
445	}
446	java.util.Optional<java.util.List<String>> intent;
447
448	if (__doc.containsKey("intent")) {	1✔
449	try {
450	intent =	×
451	LoaderInstances
452	.uri_optional_array_of_StringInstance_True_False_None_None
453	.loadField(__doc.get("intent"), __baseUri, __loadingOptions);	×
454	} catch (ValidationException e) {	×
455	intent = null; // won't be used but prevents compiler from complaining.	×
456	final String __message = "the `intent` field is not valid because:";	×
457	__errors.add(new ValidationException(__message, e));	×
458	}	×
459
460	} else {
461	intent = null;	1✔
462	}
463	java.util.List<Object> steps;
464	try {
465	steps =	1✔
466	LoaderInstances
467	.idmap_steps_array_of_WorkflowStep
468	.loadField(__doc.get("steps"), __baseUri, __loadingOptions);	1✔
469	} catch (ValidationException e) {	1✔
470	steps = null; // won't be used but prevents compiler from complaining.	1✔
471	final String __message = "the `steps` field is not valid because:";	1✔
472	__errors.add(new ValidationException(__message, e));	1✔
473	}	1✔
474	if (!__errors.isEmpty()) {	1✔
475	throw new ValidationException("Trying 'RecordField'", __errors);	1✔
476	}
477	this.id = (java.util.Optional<String>) id;	1✔
478	this.label = (java.util.Optional<String>) label;	1✔
479	this.doc = (Object) doc;	1✔
480	this.inputs = (java.util.List<Object>) inputs;	1✔
481	this.outputs = (java.util.List<Object>) outputs;	1✔
482	this.requirements = (java.util.Optional<java.util.List<Object>>) requirements;	1✔
483	this.hints = (java.util.Optional<java.util.List<Object>>) hints;	1✔
484	this.cwlVersion = (java.util.Optional<CWLVersion>) cwlVersion;	1✔
485	this.intent = (java.util.Optional<java.util.List<String>>) intent;	1✔
486	this.class_ = (Workflow_class) class_;	1✔
487	this.steps = (java.util.List<Object>) steps;	1✔
488	for (String field:__doc.keySet()) {	1✔
489	if (!attrs.contains(field)) {	1✔
NEW 490	if (field.contains(":")) {	×
NEW 491	String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null);	×
NEW 492	extensionFields_.put(expanded_field, __doc.get(field));	×
493	}
494	}
495	}	1✔
496	}	1✔
497	private java.util.List<String> attrs = java.util.Arrays.asList("id", "label", "doc", "inputs", "outputs", "requirements", "hints", "cwlVersion", "intent", "class", "steps");	1✔
498	}

common-workflow-language / cwljava / #389

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