#339

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

Build # #339

Build Type

Pull #193

github

Committed by

web-flow

Commit Message

Merge 94c260498 into 0978523bc

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

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/src/main/java/org/w3id/cwl/cwl1_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 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;
  }
}

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

common-workflow-language / cwljava / #339

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