#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

Run Details

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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55.22

/src/main/java/org/w3id/cwl/cwl1_2/CommandOutputBindingImpl.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#CommandOutputBinding</I><BR> <BLOCKQUOTE>
 Describes how to generate an output parameter based on the files produced
 by a CommandLineTool.
 
 The output parameter value is generated by applying these operations in the
 following order:
 
   - glob
   - loadContents
   - outputEval
   - secondaryFiles
  </BLOCKQUOTE>
 */
public class CommandOutputBindingImpl extends SaveableImpl implements CommandOutputBinding {
  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<Boolean> loadContents;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#LoadContents/loadContents</I><BR>
   * <BLOCKQUOTE>
   * Only valid when `type: File` or is an array of `items: File`.
   * 
   * If true, the file (or each file in the array) must be a UTF-8
   * text file 64 KiB or smaller, and the implementation must read
   * the entire contents of the file (or file array) and place it
   * in the `contents` field of the File object for use by
   * expressions.  If the size of the file is greater than 64 KiB,
   * the implementation must raise a fatal error.
   *    * </BLOCKQUOTE>
   */

  public java.util.Optional<Boolean> getLoadContents() {
    return this.loadContents;
  }

  private java.util.Optional<LoadListingEnum> loadListing;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#LoadContents/loadListing</I><BR>
   * <BLOCKQUOTE>
   * Only valid when `type: Directory` or is an array of `items: Directory`.
   * 
   * Specify the desired behavior for loading the `listing` field of
   * a Directory object for use by expressions.
   * 
   * The order of precedence for loadListing is:
   * 
   *   1. `loadListing` on an individual parameter
   *   2. Inherited from `LoadListingRequirement`
   *   3. By default: `no_listing`
   *    * </BLOCKQUOTE>
   */

  public java.util.Optional<LoadListingEnum> getLoadListing() {
    return this.loadListing;
  }

  private Object glob;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#CommandOutputBinding/glob</I><BR>
   * <BLOCKQUOTE>
   * Find files or directories relative to the output directory, using POSIX
   * glob(3) pathname matching.  If an array is provided, find files or
   * directories that match any pattern in the array.  If an expression is
   * provided, the expression must return a string or an array of strings,
   * which will then be evaluated as one or more glob patterns.  Must only
   * match and return files/directories which actually exist.
   * 
   * If the value of glob is a relative path pattern (does not
   * begin with a slash '/') then it is resolved relative to the
   * output directory.  If the value of the glob is an absolute
   * path pattern (it does begin with a slash '/') then it must
   * refer to a path within the output directory.  It is an error
   * if any glob resolves to a path outside the output directory.
   * Specifically this means globs that resolve to paths outside the output
   * directory are illegal.
   * 
   * A glob may match a path within the output directory which is
   * actually a symlink to another file.  In this case, the
   * expected behavior is for the resulting File/Directory object to take the
   * `basename` (and corresponding `nameroot` and `nameext`) of the
   * symlink.  The `location` of the File/Directory is implementation
   * dependent, but logically the File/Directory should have the same content
   * as the symlink target.  Platforms may stage output files/directories to
   * cloud storage that lack the concept of a symlink.  In
   * this case file content and directories may be duplicated, or (to avoid
   * duplication) the File/Directory `location` may refer to the symlink
   * target.
   * 
   * It is an error if a symlink in the output directory (or any
   * symlink in a chain of links) refers to any file or directory
   * that is not under an input or output directory.
   * 
   * Implementations may shut down a container before globbing
   * output, so globs and expressions must not assume access to the
   * container filesystem except for declared input and output.
   *    * </BLOCKQUOTE>
   */

  public Object getGlob() {
    return this.glob;
  }

  private java.util.Optional<String> outputEval;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#CommandOutputBinding/outputEval</I><BR>
   * <BLOCKQUOTE>
   * Evaluate an expression to generate the output value.  If
   * `glob` was specified, the value of `self` must be an array
   * containing file objects that were matched.  If no files were
   * matched, `self` must be a zero length array; if a single file
   * was matched, the value of `self` is an array of a single
   * element.  The exit code of the process is
   * available in the expression as `runtime.exitCode`.
   * 
   * Additionally, if `loadContents` is true, the file must be a
   * UTF-8 text file 64 KiB or smaller, and the implementation must
   * read the entire contents of the file (or file array) and place
   * it in the `contents` field of the File object for use in
   * `outputEval`.  If the size of the file is greater than 64 KiB,
   * the implementation must raise a fatal error.
   * 
   * If a tool needs to return a large amount of structured data to
   * the workflow, loading the output object from `cwl.output.json`
   * bypasses `outputEval` and is not subject to the 64 KiB
   * `loadContents` limit.
   *    * </BLOCKQUOTE>
   */

  public java.util.Optional<String> getOutputEval() {
    return this.outputEval;
  }

  /**
   * Used by {@link org.w3id.cwl.cwl1_2.utils.RootLoader} to construct instances of CommandOutputBindingImpl.
   *
   * @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 CommandOutputBindingImpl(
      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("CommandOutputBindingImpl 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<Boolean> loadContents;

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

    } else {
      loadContents = null;
    }
    java.util.Optional<LoadListingEnum> loadListing;

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

    } else {
      loadListing = null;
    }
    Object glob;

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

    } else {
      glob = null;
    }
    java.util.Optional<String> outputEval;

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

    } else {
      outputEval = null;
    }
    if (!__errors.isEmpty()) {
      throw new ValidationException("Trying 'RecordField'", __errors);
    }
    this.loadContents = (java.util.Optional<Boolean>) loadContents;
    this.loadListing = (java.util.Optional<LoadListingEnum>) loadListing;
    this.glob = (Object) glob;
    this.outputEval = (java.util.Optional<String>) outputEval;
    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("loadContents", "loadListing", "glob", "outputEval");
}

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#CommandOutputBinding</I><BR> <BLOCKQUOTE>
25	Describes how to generate an output parameter based on the files produced
26	by a CommandLineTool.
27
28	The output parameter value is generated by applying these operations in the
29	following order:
30
31	- glob
32	- loadContents
33	- outputEval
34	- secondaryFiles
35	</BLOCKQUOTE>
36	*/
37	public class CommandOutputBindingImpl extends SaveableImpl implements CommandOutputBinding {
38	private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();	1✔
39	private java.util.Map<String, Object> extensionFields_ =	1✔
40	new java.util.HashMap<String, Object>();
41	public LoadingOptions getLoadingOptions() {
NEW 42	return this.loadingOptions_;	×
43	}
44	public java.util.Map<String, Object> getExtensionFields() {
45	return this.extensionFields_;	×
46	}
47
48	private java.util.Optional<Boolean> loadContents;
49
50	/**
51	* Getter for property <I>https://w3id.org/cwl/cwl#LoadContents/loadContents</I><BR>
52	* <BLOCKQUOTE>
53	* Only valid when `type: File` or is an array of `items: File`.
54	*
55	* If true, the file (or each file in the array) must be a UTF-8
56	* text file 64 KiB or smaller, and the implementation must read
57	* the entire contents of the file (or file array) and place it
58	* in the `contents` field of the File object for use by
59	* expressions. If the size of the file is greater than 64 KiB,
60	* the implementation must raise a fatal error.
61	* * </BLOCKQUOTE>
62	*/
63
64	public java.util.Optional<Boolean> getLoadContents() {
65	return this.loadContents;	×
66	}
67
68	private java.util.Optional<LoadListingEnum> loadListing;
69
70	/**
71	* Getter for property <I>https://w3id.org/cwl/cwl#LoadContents/loadListing</I><BR>
72	* <BLOCKQUOTE>
73	* Only valid when `type: Directory` or is an array of `items: Directory`.
74	*
75	* Specify the desired behavior for loading the `listing` field of
76	* a Directory object for use by expressions.
77	*
78	* The order of precedence for loadListing is:
79	*
80	* 1. `loadListing` on an individual parameter
81	* 2. Inherited from `LoadListingRequirement`
82	* 3. By default: `no_listing`
83	* * </BLOCKQUOTE>
84	*/
85
86	public java.util.Optional<LoadListingEnum> getLoadListing() {
87	return this.loadListing;	×
88	}
89
90	private Object glob;
91
92	/**
93	* Getter for property <I>https://w3id.org/cwl/cwl#CommandOutputBinding/glob</I><BR>
94	* <BLOCKQUOTE>
95	* Find files or directories relative to the output directory, using POSIX
96	* glob(3) pathname matching. If an array is provided, find files or
97	* directories that match any pattern in the array. If an expression is
98	* provided, the expression must return a string or an array of strings,
99	* which will then be evaluated as one or more glob patterns. Must only
100	* match and return files/directories which actually exist.
101	*
102	* If the value of glob is a relative path pattern (does not
103	* begin with a slash '/') then it is resolved relative to the
104	* output directory. If the value of the glob is an absolute
105	* path pattern (it does begin with a slash '/') then it must
106	* refer to a path within the output directory. It is an error
107	* if any glob resolves to a path outside the output directory.
108	* Specifically this means globs that resolve to paths outside the output
109	* directory are illegal.
110	*
111	* A glob may match a path within the output directory which is
112	* actually a symlink to another file. In this case, the
113	* expected behavior is for the resulting File/Directory object to take the
114	* `basename` (and corresponding `nameroot` and `nameext`) of the
115	* symlink. The `location` of the File/Directory is implementation
116	* dependent, but logically the File/Directory should have the same content
117	* as the symlink target. Platforms may stage output files/directories to
118	* cloud storage that lack the concept of a symlink. In
119	* this case file content and directories may be duplicated, or (to avoid
120	* duplication) the File/Directory `location` may refer to the symlink
121	* target.
122	*
123	* It is an error if a symlink in the output directory (or any
124	* symlink in a chain of links) refers to any file or directory
125	* that is not under an input or output directory.
126	*
127	* Implementations may shut down a container before globbing
128	* output, so globs and expressions must not assume access to the
129	* container filesystem except for declared input and output.
130	* * </BLOCKQUOTE>
131	*/
132
133	public Object getGlob() {
134	return this.glob;	×
135	}
136
137	private java.util.Optional<String> outputEval;
138
139	/**
140	* Getter for property <I>https://w3id.org/cwl/cwl#CommandOutputBinding/outputEval</I><BR>
141	* <BLOCKQUOTE>
142	* Evaluate an expression to generate the output value. If
143	* `glob` was specified, the value of `self` must be an array
144	* containing file objects that were matched. If no files were
145	* matched, `self` must be a zero length array; if a single file
146	* was matched, the value of `self` is an array of a single
147	* element. The exit code of the process is
148	* available in the expression as `runtime.exitCode`.
149	*
150	* Additionally, if `loadContents` is true, the file must be a
151	* UTF-8 text file 64 KiB or smaller, and the implementation must
152	* read the entire contents of the file (or file array) and place
153	* it in the `contents` field of the File object for use in
154	* `outputEval`. If the size of the file is greater than 64 KiB,
155	* the implementation must raise a fatal error.
156	*
157	* If a tool needs to return a large amount of structured data to
158	* the workflow, loading the output object from `cwl.output.json`
159	* bypasses `outputEval` and is not subject to the 64 KiB
160	* `loadContents` limit.
161	* * </BLOCKQUOTE>
162	*/
163
164	public java.util.Optional<String> getOutputEval() {
165	return this.outputEval;	×
166	}
167
168	/**
169	* Used by {@link org.w3id.cwl.cwl1_2.utils.RootLoader} to construct instances of CommandOutputBindingImpl.
170	*
171	* @param __doc_ Document fragment to load this record object from (presumably a
172	{@link java.util.Map}).
173	* @param __baseUri_ Base URI to generate child document IDs against.
174	* @param __loadingOptions Context for loading URIs and populating objects.
175	* @param __docRoot_ ID at this position in the document (if available) (maybe?)
176	* @throws ValidationException If the document fragment is not a {@link java.util.Map}
177	* or validation of fields fails.
178	*/
179	public CommandOutputBindingImpl(
180	final Object __doc_,
181	final String __baseUri_,
182	LoadingOptions __loadingOptions,
183	final String __docRoot_) {
184	super(__doc_, __baseUri_, __loadingOptions, __docRoot_);	1✔
185	// Prefix plumbing variables with '__' to reduce likelihood of collision with
186	// generated names.
187	String __baseUri = __baseUri_;	1✔
188	String __docRoot = __docRoot_;	1✔
189	if (!(__doc_ instanceof java.util.Map)) {	1✔
190	throw new ValidationException("CommandOutputBindingImpl called on non-map");	×
191	}
192	final java.util.Map<String, Object> __doc = (java.util.Map<String, Object>) __doc_;	1✔
193	final java.util.List<ValidationException> __errors =	1✔
194	new java.util.ArrayList<ValidationException>();
195	if (__loadingOptions != null) {	1✔
196	this.loadingOptions_ = __loadingOptions;	1✔
197	}
198	java.util.Optional<Boolean> loadContents;
199
200	if (__doc.containsKey("loadContents")) {	1✔
201	try {
202	loadContents =	1✔
203	LoaderInstances
204	.optional_BooleanInstance
205	.loadField(__doc.get("loadContents"), __baseUri, __loadingOptions);	1✔
206	} catch (ValidationException e) {	×
207	loadContents = null; // won't be used but prevents compiler from complaining.	×
208	final String __message = "the `loadContents` field is not valid because:";	×
209	__errors.add(new ValidationException(__message, e));	×
210	}	1✔
211
212	} else {
213	loadContents = null;	1✔
214	}
215	java.util.Optional<LoadListingEnum> loadListing;
216
217	if (__doc.containsKey("loadListing")) {	1✔
218	try {
219	loadListing =	×
220	LoaderInstances
221	.optional_LoadListingEnum
222	.loadField(__doc.get("loadListing"), __baseUri, __loadingOptions);	×
223	} catch (ValidationException e) {	×
224	loadListing = null; // won't be used but prevents compiler from complaining.	×
225	final String __message = "the `loadListing` field is not valid because:";	×
226	__errors.add(new ValidationException(__message, e));	×
227	}	×
228
229	} else {
230	loadListing = null;	1✔
231	}
232	Object glob;
233
234	if (__doc.containsKey("glob")) {	1✔
235	try {
236	glob =	1✔
237	LoaderInstances
238	.union_of_NullInstance_or_StringInstance_or_ExpressionLoader_or_array_of_StringInstance
239	.loadField(__doc.get("glob"), __baseUri, __loadingOptions);	1✔
240	} catch (ValidationException e) {	×
241	glob = null; // won't be used but prevents compiler from complaining.	×
242	final String __message = "the `glob` field is not valid because:";	×
243	__errors.add(new ValidationException(__message, e));	×
244	}	1✔
245
246	} else {
247	glob = null;	1✔
248	}
249	java.util.Optional<String> outputEval;
250
251	if (__doc.containsKey("outputEval")) {	1✔
252	try {
253	outputEval =	1✔
254	LoaderInstances
255	.optional_ExpressionLoader
256	.loadField(__doc.get("outputEval"), __baseUri, __loadingOptions);	1✔
257	} catch (ValidationException e) {	×
258	outputEval = null; // won't be used but prevents compiler from complaining.	×
259	final String __message = "the `outputEval` field is not valid because:";	×
260	__errors.add(new ValidationException(__message, e));	×
261	}	1✔
262
263	} else {
264	outputEval = null;	1✔
265	}
266	if (!__errors.isEmpty()) {	1✔
267	throw new ValidationException("Trying 'RecordField'", __errors);	×
268	}
269	this.loadContents = (java.util.Optional<Boolean>) loadContents;	1✔
270	this.loadListing = (java.util.Optional<LoadListingEnum>) loadListing;	1✔
271	this.glob = (Object) glob;	1✔
272	this.outputEval = (java.util.Optional<String>) outputEval;	1✔
273	for (String field:__doc.keySet()) {	1✔
274	if (!attrs.contains(field)) {	1✔
NEW 275	if (field.contains(":")) {	×
NEW 276	String expanded_field = __loadingOptions.expandUrl(field, "", false, false, null);	×
NEW 277	extensionFields_.put(expanded_field, __doc.get(field));	×
278	}
279	}
280	}	1✔
281	}	1✔
282	private java.util.List<String> attrs = java.util.Arrays.asList("loadContents", "loadListing", "glob", "outputEval");	1✔
283	}

common-workflow-language / cwljava / #388

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