#394

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

Build # #394

Build Type

push

github

Committed by

mr-c

Commit Message

rename package to a namespace that we control

Coverage Stats

7575 of 12994 new or added lines in 261 files covered. (58.3%)

7752 of 13372 relevant lines covered (57.97%)

0.58 hits per line

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65.12

/src/main/java/org/commonwl/cwlsdk/cwl1_1/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.commonwl.cwlsdk.cwl1_1;

import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances;
import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions;
import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder;
import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl;
import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException;

/**
* Auto-generated class implementation for <I>https://w3id.org/cwl/cwl#SecondaryFileSchema</I><BR>
 */
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` outputs the `path` field must
   * also be present.  The expression must return a filename string relative
   * to the path to the primary File, a File or Directory object with either
   * `path` or `location` and `basename` fields set, or an array consisting
   * of strings or File or Directory objects.  It is legal to reference an
   * unchanged File or Directory object taken from input as a secondaryFile.
   * The expression may return "null" in which case there is no secondaryFile
   * from that expression.
   * 
   * To work on non-filename-preserving storage systems, portable tool
   * descriptions should avoid constructing new values from `location`, but
   * should construct relative references using `basename` or `nameroot`
   * instead.
   * 
   * 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.commonwl.cwlsdk.cwl1_1.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.commonwl.cwlsdk.cwl1_1;
16
17	import org.commonwl.cwlsdk.cwl1_1.utils.LoaderInstances;
18	import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptions;
19	import org.commonwl.cwlsdk.cwl1_1.utils.LoadingOptionsBuilder;
20	import org.commonwl.cwlsdk.cwl1_1.utils.SaveableImpl;
21	import org.commonwl.cwlsdk.cwl1_1.utils.ValidationException;
22
23	/**
24	* Auto-generated class implementation for <I>https://w3id.org/cwl/cwl#SecondaryFileSchema</I><BR>
25	*/
26	public class SecondaryFileSchemaImpl extends SaveableImpl implements SecondaryFileSchema {
27	private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();	1✔
28	private java.util.Map<String, Object> extensionFields_ =	1✔
29	new java.util.HashMap<String, Object>();
30	public LoadingOptions getLoadingOptions() {
NEW 31	return this.loadingOptions_;	×
32	}
33	public java.util.Map<String, Object> getExtensionFields() {
NEW 34	return this.extensionFields_;	×
35	}
36
37	private Object pattern;
38
39	/**
40	* Getter for property <I>https://w3id.org/cwl/cwl#SecondaryFileSchema/pattern</I><BR>
41	* <BLOCKQUOTE>
42	* Provides a pattern or expression specifying files or directories that
43	* should be included alongside the primary file.
44	*
45	* If the value is an expression, the value of `self` in the expression
46	* must be the primary input or output File object to which this binding
47	* applies. The `basename`, `nameroot` and `nameext` fields must be
48	* present in `self`. For `CommandLineTool` outputs the `path` field must
49	* also be present. The expression must return a filename string relative
50	* to the path to the primary File, a File or Directory object with either
51	* `path` or `location` and `basename` fields set, or an array consisting
52	* of strings or File or Directory objects. It is legal to reference an
53	* unchanged File or Directory object taken from input as a secondaryFile.
54	* The expression may return "null" in which case there is no secondaryFile
55	* from that expression.
56	*
57	* To work on non-filename-preserving storage systems, portable tool
58	* descriptions should avoid constructing new values from `location`, but
59	* should construct relative references using `basename` or `nameroot`
60	* instead.
61	*
62	* If a value in `secondaryFiles` is a string that is not an expression,
63	* it specifies that the following pattern should be applied to the path
64	* of the primary file to yield a filename relative to the primary File:
65	*
66	* 1. If string ends with `?` character, remove the last `?` and mark
67	* the resulting secondary file as optional.
68	* 2. If string begins with one or more caret `^` characters, for each
69	* caret, remove the last file extension from the path (the last
70	* period `.` and all following characters). If there are no file
71	* extensions, the path is unchanged.
72	* 3. Append the remainder of the string to the end of the file path.
73	* * </BLOCKQUOTE>
74	*/
75
76	public Object getPattern() {
77	return this.pattern;	1✔
78	}
79
80	private Object required;
81
82	/**
83	* Getter for property <I>https://w3id.org/cwl/cwl#SecondaryFileSchema/required</I><BR>
84	* <BLOCKQUOTE>
85	* An implementation must not fail workflow execution if `required` is
86	* set to `false` and the expected secondary file does not exist.
87	* Default value for `required` field is `true` for secondary files on
88	* input and `false` for secondary files on output.
89	* * </BLOCKQUOTE>
90	*/
91
92	public Object getRequired() {
93	return this.required;	1✔
94	}
95
96	/**
97	* Used by {@link org.commonwl.cwlsdk.cwl1_1.utils.RootLoader} to construct instances of SecondaryFileSchemaImpl.
98	*
99	* @param __doc_ Document fragment to load this record object from (presumably a
100	{@link java.util.Map}).
101	* @param __baseUri_ Base URI to generate child document IDs against.
102	* @param __loadingOptions Context for loading URIs and populating objects.
103	* @param __docRoot_ ID at this position in the document (if available) (maybe?)
104	* @throws ValidationException If the document fragment is not a {@link java.util.Map}
105	* or validation of fields fails.
106	*/
107	public SecondaryFileSchemaImpl(
108	final Object __doc_,
109	final String __baseUri_,
110	LoadingOptions __loadingOptions,
111	final String __docRoot_) {
112	super(__doc_, __baseUri_, __loadingOptions, __docRoot_);	1✔
113	// Prefix plumbing variables with '__' to reduce likelihood of collision with
114	// generated names.
115	String __baseUri = __baseUri_;	1✔
116	String __docRoot = __docRoot_;	1✔
117	if (!(__doc_ instanceof java.util.Map)) {	1✔
NEW 118	throw new ValidationException("SecondaryFileSchemaImpl called on non-map");	×
119	}
120	final java.util.Map<String, Object> __doc = (java.util.Map<String, Object>) __doc_;	1✔
121	final java.util.List<ValidationException> __errors =	1✔
122	new java.util.ArrayList<ValidationException>();
123	if (__loadingOptions != null) {	1✔
124	this.loadingOptions_ = __loadingOptions;	1✔
125	}
126	Object pattern;
127	try {
128	pattern =	1✔
129	LoaderInstances
130	.union_of_StringInstance_or_ExpressionLoader
131	.loadField(__doc.get("pattern"), __baseUri, __loadingOptions);	1✔
NEW 132	} catch (ValidationException e) {	×
NEW 133	pattern = null; // won't be used but prevents compiler from complaining.	×
NEW 134	final String __message = "the `pattern` field is not valid because:";	×
NEW 135	__errors.add(new ValidationException(__message, e));	×
136	}	1✔
137	Object required;
138
139	if (__doc.containsKey("required")) {	1✔
140	try {
141	required =	1✔
142	LoaderInstances
143	.union_of_NullInstance_or_BooleanInstance_or_ExpressionLoader
144	.loadField(__doc.get("required"), __baseUri, __loadingOptions);	1✔
NEW 145	} catch (ValidationException e) {	×
NEW 146	required = null; // won't be used but prevents compiler from complaining.	×
NEW 147	final String __message = "the `required` field is not valid because:";	×
NEW 148	__errors.add(new ValidationException(__message, e));	×
149	}	1✔
150
151	} else {
152	required = null;	1✔
153	}
154	if (!__errors.isEmpty()) {	1✔
NEW 155	throw new ValidationException("Trying 'RecordField'", __errors);	×
156	}
157	this.pattern = (Object) pattern;	1✔
158	this.required = (Object) required;	1✔
159	for (String field:__doc.keySet()) {	1✔
160	if (!attrs.contains(field)) {	1✔
NEW 161	if (field.contains(":")) {	×
NEW 162	String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null);	×
NEW 163	extensionFields_.put(expanded_field, __doc.get(field));	×
164	}
165	}
166	}	1✔
167	}	1✔
168	private java.util.List<String> attrs = java.util.Arrays.asList("pattern", "required");	1✔
169	}

common-workflow-language / cwljava / #394

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