#352

Committed 07 Apr 2025 10:22AM UTC coverage: 59.538% (-0.6%) from 60.167%

Build # #352

Build Type

Pull #193

github

Committed by

web-flow

Commit Message

Merge d636f9333 into 46536cad2

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

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/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 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;
  }
}

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

common-workflow-language / cwljava / #352

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