#388

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

Build # #388

Build Type

Pull #218

github

Committed by

web-flow

Commit Message

Merge ab8576a5b into befd7e4b9

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

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

28 existing lines in 27 files now uncovered.

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65.12

/src/main/java/org/w3id/cwl/cwl1_2/SecondaryFileSchemaImpl.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#SecondaryFileSchema</I><BR> <BLOCKQUOTE>
 Secondary files are specified using the following micro-DSL for secondary files:
 
 * If the value is a string, it is transformed to an object with two fields
   `pattern` and `required`
 * By default, the value of `required` is `null`
   (this indicates default behavior, which may be based on the context)
 * If the value ends with a question mark `?` the question mark is
   stripped off and the value of the field `required` is set to `False`
 * The remaining value is assigned to the field `pattern`
 
 For implementation details and examples, please see
 [this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files)
 in the Schema Salad specification.
  </BLOCKQUOTE>
 */
public class SecondaryFileSchemaImpl extends SaveableImpl implements SecondaryFileSchema {
  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 Object pattern;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#SecondaryFileSchema/pattern</I><BR>
   * <BLOCKQUOTE>
   * Provides a pattern or expression specifying files or directories that
   * should be included alongside the primary file.
   * 
   * If the value is an expression, the value of `self` in the
   * expression must be the primary input or output File object to
   * which this binding applies.  The `basename`, `nameroot` and
   * `nameext` fields must be present in `self`.  For
   * `CommandLineTool` inputs the `location` field must also be
   * present.  For `CommandLineTool` outputs the `path` field must
   * also be present.  If secondary files were included on an input
   * File object as part of the Process invocation, they must also
   * be present in `secondaryFiles` on `self`.
   * 
   * The expression must return either: a filename string relative
   * to the path to the primary File, a File or Directory object
   * (`class: File` or `class: Directory`) with either `location`
   * (for inputs) or `path` (for outputs) and `basename` fields
   * set, or an array consisting of strings or File or Directory
   * objects as previously described.
   * 
   * It is legal to use `location` from a File or Directory object
   * passed in as input, including `location` from secondary files
   * on `self`.  If an expression returns a File object with the
   * same `location` but a different `basename` as a secondary file
   * that was passed in, the expression result takes precedence.
   * Setting the basename with an expression this way affects the
   * `path` where the secondary file will be staged to in the
   * CommandLineTool.
   * 
   * The expression may return "null" in which case there is no
   * secondary file from that expression.
   * 
   * To work on non-filename-preserving storage systems, portable
   * tool descriptions should treat `location` as an
   * [opaque identifier](#opaque-strings) and avoid constructing new
   * values from `location`, but should construct relative references
   * using `basename` or `nameroot` instead, or propagate `location`
   * from defined inputs.
   * 
   * If a value in `secondaryFiles` is a string that is not an expression,
   * it specifies that the following pattern should be applied to the path
   * of the primary file to yield a filename relative to the primary File:
   * 
   *   1. If string ends with `?` character, remove the last `?` and mark
   *     the resulting secondary file as optional.
   *   2. If string begins with one or more caret `^` characters, for each
   *     caret, remove the last file extension from the path (the last
   *     period `.` and all following characters).  If there are no file
   *     extensions, the path is unchanged.
   *   3. Append the remainder of the string to the end of the file path.
   *    * </BLOCKQUOTE>
   */

  public Object getPattern() {
    return this.pattern;
  }

  private Object required;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#SecondaryFileSchema/required</I><BR>
   * <BLOCKQUOTE>
   * An implementation must not fail workflow execution if `required` is
   * set to `false` and the expected secondary file does not exist.
   * Default value for `required` field is `true` for secondary files on
   * input and `false` for secondary files on output.
   *    * </BLOCKQUOTE>
   */

  public Object getRequired() {
    return this.required;
  }

  /**
   * Used by {@link org.w3id.cwl.cwl1_2.utils.RootLoader} to construct instances of SecondaryFileSchemaImpl.
   *
   * @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 SecondaryFileSchemaImpl(
      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("SecondaryFileSchemaImpl 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;
    }
    Object pattern;
    try {
      pattern =
          LoaderInstances
              .union_of_StringInstance_or_ExpressionLoader
              .loadField(__doc.get("pattern"), __baseUri, __loadingOptions);
    } catch (ValidationException e) {
      pattern = null; // won't be used but prevents compiler from complaining.
      final String __message = "the `pattern` field is not valid because:";
      __errors.add(new ValidationException(__message, e));
    }
    Object required;

    if (__doc.containsKey("required")) {
      try {
        required =
            LoaderInstances
                .union_of_NullInstance_or_BooleanInstance_or_ExpressionLoader
                .loadField(__doc.get("required"), __baseUri, __loadingOptions);
      } catch (ValidationException e) {
        required = null; // won't be used but prevents compiler from complaining.
        final String __message = "the `required` field is not valid because:";
        __errors.add(new ValidationException(__message, e));
      }

    } else {
      required = null;
    }
    if (!__errors.isEmpty()) {
      throw new ValidationException("Trying 'RecordField'", __errors);
    }
    this.pattern = (Object) pattern;
    this.required = (Object) required;
    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("pattern", "required");
}

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#SecondaryFileSchema</I><BR> <BLOCKQUOTE>
25	Secondary files are specified using the following micro-DSL for secondary files:
26
27	* If the value is a string, it is transformed to an object with two fields
28	`pattern` and `required`
29	* By default, the value of `required` is `null`
30	(this indicates default behavior, which may be based on the context)
31	* If the value ends with a question mark `?` the question mark is
32	stripped off and the value of the field `required` is set to `False`
33	* The remaining value is assigned to the field `pattern`
34
35	For implementation details and examples, please see
36	[this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files)
37	in the Schema Salad specification.
38	</BLOCKQUOTE>
39	*/
40	public class SecondaryFileSchemaImpl extends SaveableImpl implements SecondaryFileSchema {
41	private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();	1✔
42	private java.util.Map<String, Object> extensionFields_ =	1✔
43	new java.util.HashMap<String, Object>();
44	public LoadingOptions getLoadingOptions() {
NEW 45	return this.loadingOptions_;	×
46	}
47	public java.util.Map<String, Object> getExtensionFields() {
48	return this.extensionFields_;	×
49	}
50
51	private Object pattern;
52
53	/**
54	* Getter for property <I>https://w3id.org/cwl/cwl#SecondaryFileSchema/pattern</I><BR>
55	* <BLOCKQUOTE>
56	* Provides a pattern or expression specifying files or directories that
57	* should be included alongside the primary file.
58	*
59	* If the value is an expression, the value of `self` in the
60	* expression must be the primary input or output File object to
61	* which this binding applies. The `basename`, `nameroot` and
62	* `nameext` fields must be present in `self`. For
63	* `CommandLineTool` inputs the `location` field must also be
64	* present. For `CommandLineTool` outputs the `path` field must
65	* also be present. If secondary files were included on an input
66	* File object as part of the Process invocation, they must also
67	* be present in `secondaryFiles` on `self`.
68	*
69	* The expression must return either: a filename string relative
70	* to the path to the primary File, a File or Directory object
71	* (`class: File` or `class: Directory`) with either `location`
72	* (for inputs) or `path` (for outputs) and `basename` fields
73	* set, or an array consisting of strings or File or Directory
74	* objects as previously described.
75	*
76	* It is legal to use `location` from a File or Directory object
77	* passed in as input, including `location` from secondary files
78	* on `self`. If an expression returns a File object with the
79	* same `location` but a different `basename` as a secondary file
80	* that was passed in, the expression result takes precedence.
81	* Setting the basename with an expression this way affects the
82	* `path` where the secondary file will be staged to in the
83	* CommandLineTool.
84	*
85	* The expression may return "null" in which case there is no
86	* secondary file from that expression.
87	*
88	* To work on non-filename-preserving storage systems, portable
89	* tool descriptions should treat `location` as an
90	* [opaque identifier](#opaque-strings) and avoid constructing new
91	* values from `location`, but should construct relative references
92	* using `basename` or `nameroot` instead, or propagate `location`
93	* from defined inputs.
94	*
95	* If a value in `secondaryFiles` is a string that is not an expression,
96	* it specifies that the following pattern should be applied to the path
97	* of the primary file to yield a filename relative to the primary File:
98	*
99	* 1. If string ends with `?` character, remove the last `?` and mark
100	* the resulting secondary file as optional.
101	* 2. If string begins with one or more caret `^` characters, for each
102	* caret, remove the last file extension from the path (the last
103	* period `.` and all following characters). If there are no file
104	* extensions, the path is unchanged.
105	* 3. Append the remainder of the string to the end of the file path.
106	* * </BLOCKQUOTE>
107	*/
108
109	public Object getPattern() {
110	return this.pattern;	1✔
111	}
112
113	private Object required;
114
115	/**
116	* Getter for property <I>https://w3id.org/cwl/cwl#SecondaryFileSchema/required</I><BR>
117	* <BLOCKQUOTE>
118	* An implementation must not fail workflow execution if `required` is
119	* set to `false` and the expected secondary file does not exist.
120	* Default value for `required` field is `true` for secondary files on
121	* input and `false` for secondary files on output.
122	* * </BLOCKQUOTE>
123	*/
124
125	public Object getRequired() {
126	return this.required;	1✔
127	}
128
129	/**
130	* Used by {@link org.w3id.cwl.cwl1_2.utils.RootLoader} to construct instances of SecondaryFileSchemaImpl.
131	*
132	* @param __doc_ Document fragment to load this record object from (presumably a
133	{@link java.util.Map}).
134	* @param __baseUri_ Base URI to generate child document IDs against.
135	* @param __loadingOptions Context for loading URIs and populating objects.
136	* @param __docRoot_ ID at this position in the document (if available) (maybe?)
137	* @throws ValidationException If the document fragment is not a {@link java.util.Map}
138	* or validation of fields fails.
139	*/
140	public SecondaryFileSchemaImpl(
141	final Object __doc_,
142	final String __baseUri_,
143	LoadingOptions __loadingOptions,
144	final String __docRoot_) {
145	super(__doc_, __baseUri_, __loadingOptions, __docRoot_);	1✔
146	// Prefix plumbing variables with '__' to reduce likelihood of collision with
147	// generated names.
148	String __baseUri = __baseUri_;	1✔
149	String __docRoot = __docRoot_;	1✔
150	if (!(__doc_ instanceof java.util.Map)) {	1✔
151	throw new ValidationException("SecondaryFileSchemaImpl called on non-map");	×
152	}
153	final java.util.Map<String, Object> __doc = (java.util.Map<String, Object>) __doc_;	1✔
154	final java.util.List<ValidationException> __errors =	1✔
155	new java.util.ArrayList<ValidationException>();
156	if (__loadingOptions != null) {	1✔
157	this.loadingOptions_ = __loadingOptions;	1✔
158	}
159	Object pattern;
160	try {
161	pattern =	1✔
162	LoaderInstances
163	.union_of_StringInstance_or_ExpressionLoader
164	.loadField(__doc.get("pattern"), __baseUri, __loadingOptions);	1✔
165	} catch (ValidationException e) {	×
166	pattern = null; // won't be used but prevents compiler from complaining.	×
167	final String __message = "the `pattern` field is not valid because:";	×
168	__errors.add(new ValidationException(__message, e));	×
169	}	1✔
170	Object required;
171
172	if (__doc.containsKey("required")) {	1✔
173	try {
174	required =	1✔
175	LoaderInstances
176	.union_of_NullInstance_or_BooleanInstance_or_ExpressionLoader
177	.loadField(__doc.get("required"), __baseUri, __loadingOptions);	1✔
178	} catch (ValidationException e) {	×
179	required = null; // won't be used but prevents compiler from complaining.	×
180	final String __message = "the `required` field is not valid because:";	×
181	__errors.add(new ValidationException(__message, e));	×
182	}	1✔
183
184	} else {
185	required = null;	1✔
186	}
187	if (!__errors.isEmpty()) {	1✔
188	throw new ValidationException("Trying 'RecordField'", __errors);	×
189	}
190	this.pattern = (Object) pattern;	1✔
191	this.required = (Object) required;	1✔
192	for (String field:__doc.keySet()) {	1✔
193	if (!attrs.contains(field)) {	1✔
NEW 194	if (field.contains(":")) {	×
NEW 195	String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null);	×
NEW 196	extensionFields_.put(expanded_field, __doc.get(field));	×
197	}
198	}
199	}	1✔
200	}	1✔
201	private java.util.List<String> attrs = java.util.Arrays.asList("pattern", "required");	1✔
202	}

common-workflow-language / cwljava / #388

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