#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_1/DirectoryImpl.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_1;

import org.w3id.cwl.cwl1_1.utils.LoaderInstances;
import org.w3id.cwl.cwl1_1.utils.LoadingOptions;
import org.w3id.cwl.cwl1_1.utils.LoadingOptionsBuilder;
import org.w3id.cwl.cwl1_1.utils.SaveableImpl;
import org.w3id.cwl.cwl1_1.utils.ValidationException;

/**
* Auto-generated class implementation for <I>https://w3id.org/cwl/cwl#Directory</I><BR> <BLOCKQUOTE>
 Represents a directory to present to a command line tool.
 
 Directories are represented as objects with `class` of `Directory`.  Directory objects have
 a number of properties that provide metadata about the directory.
 
 The `location` property of a Directory is a URI that uniquely identifies
 the directory.  Implementations must support the file:// URI scheme and may
 support other schemes such as http://.  Alternately to `location`,
 implementations must also accept the `path` property on Directory, which
 must be a filesystem path available on the same host as the CWL runner (for
 inputs) or the runtime environment of a command line tool execution (for
 command line tool outputs).
 
 A Directory object may have a `listing` field.  This is a list of File and
 Directory objects that are contained in the Directory.  For each entry in
 `listing`, the `basename` property defines the name of the File or
 Subdirectory when staged to disk.  If `listing` is not provided, the
 implementation must have some way of fetching the Directory listing at
 runtime based on the `location` field.
 
 If a Directory does not have `location`, it is a Directory literal.  A
 Directory literal must provide `listing`.  Directory literals must be
 created on disk at runtime as needed.
 
 The resources in a Directory literal do not need to have any implied
 relationship in their `location`.  For example, a Directory listing may
 contain two files located on different hosts.  It is the responsibility of
 the runtime to ensure that those files are staged to disk appropriately.
 Secondary files associated with files in `listing` must also be staged to
 the same Directory.
 
 When executing a CommandLineTool, Directories must be recursively staged
 first and have local values of `path` assigend.
 
 Directory objects in CommandLineTool output must provide either a
 `location` URI or a `path` property in the context of the tool execution
 runtime (local to the compute node, or within the executing container).
 
 An ExpressionTool may forward file references from input to output by using
 the same value for `location`.
 
 Name conflicts (the same `basename` appearing multiple times in `listing`
 or in any entry in `secondaryFiles` in the listing) is a fatal error.
  </BLOCKQUOTE>
 */
public class DirectoryImpl extends SaveableImpl implements Directory {
  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 Directory_class class_;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#Directory/class</I><BR>
   * <BLOCKQUOTE>
   * Must be `Directory` to indicate this object describes a Directory.   * </BLOCKQUOTE>
   */

  public Directory_class getClass_() {
    return this.class_;
  }

  private java.util.Optional<String> location;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#Directory/location</I><BR>
   * <BLOCKQUOTE>
   * An IRI that identifies the directory resource.  This may be a relative
   * reference, in which case it must be resolved using the base IRI of the
   * document.  The location may refer to a local or remote resource.  If
   * the `listing` field is not set, the implementation must use the
   * location IRI to retrieve directory listing.  If an implementation is
   * unable to retrieve the directory listing stored at a remote resource (due to
   * unsupported protocol, access denied, or other issue) it must signal an
   * error.
   * 
   * If the `location` field is not provided, the `listing` field must be
   * provided.  The implementation must assign a unique identifier for
   * the `location` field.
   * 
   * If the `path` field is provided but the `location` field is not, an
   * implementation may assign the value of the `path` field to `location`,
   * then follow the rules above.
   *    * </BLOCKQUOTE>
   */

  public java.util.Optional<String> getLocation() {
    return this.location;
  }

  private java.util.Optional<String> path;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#path</I><BR>
   * <BLOCKQUOTE>
   * The local path where the Directory is made available prior to executing a
   * CommandLineTool.  This must be set by the implementation.  This field
   * must not be used in any other context.  The command line tool being
   * executed must be able to to access the directory at `path` using the POSIX
   * `opendir(2)` syscall.
   * 
   * If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
   * (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
   * `<space>`, `<tab>`, and `<newline>`) or characters
   * [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
   * for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
   * then implementations may terminate the process with a
   * `permanentFailure`.
   *    * </BLOCKQUOTE>
   */

  public java.util.Optional<String> getPath() {
    return this.path;
  }

  private java.util.Optional<String> basename;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#Directory/basename</I><BR>
   * <BLOCKQUOTE>
   * The base name of the directory, that is, the name of the file without any
   * leading directory path.  The base name must not contain a slash `/`.
   * 
   * If not provided, the implementation must set this field based on the
   * `location` field by taking the final path component after parsing
   * `location` as an IRI.  If `basename` is provided, it is not required to
   * match the value from `location`.
   * 
   * When this file is made available to a CommandLineTool, it must be named
   * with `basename`, i.e. the final component of the `path` field must match
   * `basename`.
   *    * </BLOCKQUOTE>
   */

  public java.util.Optional<String> getBasename() {
    return this.basename;
  }

  private java.util.Optional<java.util.List<Object>> listing;

  /**
   * Getter for property <I>https://w3id.org/cwl/cwl#listing</I><BR>
   * <BLOCKQUOTE>
   * List of files or subdirectories contained in this directory.  The name
   * of each file or subdirectory is determined by the `basename` field of
   * each `File` or `Directory` object.  It is an error if a `File` shares a
   * `basename` with any other entry in `listing`.  If two or more
   * `Directory` object share the same `basename`, this must be treated as
   * equivalent to a single subdirectory with the listings recursively
   * merged.
   *    * </BLOCKQUOTE>
   */

  public java.util.Optional<java.util.List<Object>> getListing() {
    return this.listing;
  }

  /**
   * Used by {@link org.w3id.cwl.cwl1_1.utils.RootLoader} to construct instances of DirectoryImpl.
   *
   * @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 DirectoryImpl(
      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("DirectoryImpl 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;
    }
    Directory_class class_;
    try {
      class_ =
          LoaderInstances
              .uri_Directory_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> location;

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

    } else {
      location = null;
    }
    java.util.Optional<String> path;

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

    } else {
      path = null;
    }
    java.util.Optional<String> basename;

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

    } else {
      basename = null;
    }
    java.util.Optional<java.util.List<Object>> listing;

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

    } else {
      listing = null;
    }
    if (!__errors.isEmpty()) {
      throw new ValidationException("Trying 'RecordField'", __errors);
    }
    this.class_ = (Directory_class) class_;
    this.location = (java.util.Optional<String>) location;
    this.path = (java.util.Optional<String>) path;
    this.basename = (java.util.Optional<String>) basename;
    this.listing = (java.util.Optional<java.util.List<Object>>) listing;
  }
}

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_1;
16
17	import org.w3id.cwl.cwl1_1.utils.LoaderInstances;
18	import org.w3id.cwl.cwl1_1.utils.LoadingOptions;
19	import org.w3id.cwl.cwl1_1.utils.LoadingOptionsBuilder;
20	import org.w3id.cwl.cwl1_1.utils.SaveableImpl;
21	import org.w3id.cwl.cwl1_1.utils.ValidationException;
22
23	/**
24	* Auto-generated class implementation for <I>https://w3id.org/cwl/cwl#Directory</I><BR> <BLOCKQUOTE>
25	Represents a directory to present to a command line tool.
26
27	Directories are represented as objects with `class` of `Directory`. Directory objects have
28	a number of properties that provide metadata about the directory.
29
30	The `location` property of a Directory is a URI that uniquely identifies
31	the directory. Implementations must support the file:// URI scheme and may
32	support other schemes such as http://. Alternately to `location`,
33	implementations must also accept the `path` property on Directory, which
34	must be a filesystem path available on the same host as the CWL runner (for
35	inputs) or the runtime environment of a command line tool execution (for
36	command line tool outputs).
37
38	A Directory object may have a `listing` field. This is a list of File and
39	Directory objects that are contained in the Directory. For each entry in
40	`listing`, the `basename` property defines the name of the File or
41	Subdirectory when staged to disk. If `listing` is not provided, the
42	implementation must have some way of fetching the Directory listing at
43	runtime based on the `location` field.
44
45	If a Directory does not have `location`, it is a Directory literal. A
46	Directory literal must provide `listing`. Directory literals must be
47	created on disk at runtime as needed.
48
49	The resources in a Directory literal do not need to have any implied
50	relationship in their `location`. For example, a Directory listing may
51	contain two files located on different hosts. It is the responsibility of
52	the runtime to ensure that those files are staged to disk appropriately.
53	Secondary files associated with files in `listing` must also be staged to
54	the same Directory.
55
56	When executing a CommandLineTool, Directories must be recursively staged
57	first and have local values of `path` assigend.
58
59	Directory objects in CommandLineTool output must provide either a
60	`location` URI or a `path` property in the context of the tool execution
61	runtime (local to the compute node, or within the executing container).
62
63	An ExpressionTool may forward file references from input to output by using
64	the same value for `location`.
65
66	Name conflicts (the same `basename` appearing multiple times in `listing`
67	or in any entry in `secondaryFiles` in the listing) is a fatal error.
68	</BLOCKQUOTE>
69	*/
70	public class DirectoryImpl extends SaveableImpl implements Directory {
71	private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();	1✔
72	private java.util.Map<String, Object> extensionFields_ =	1✔
73	new java.util.HashMap<String, Object>();
74	public java.util.Map<String, Object> getExtensionFields() {
NEW 75	return this.extensionFields_;	×
76	}
77
78	private Directory_class class_;
79
80	/**
81	* Getter for property <I>https://w3id.org/cwl/cwl#Directory/class</I><BR>
82	* <BLOCKQUOTE>
83	* Must be `Directory` to indicate this object describes a Directory. * </BLOCKQUOTE>
84	*/
85
86	public Directory_class getClass_() {
87	return this.class_;	×
88	}
89
90	private java.util.Optional<String> location;
91
92	/**
93	* Getter for property <I>https://w3id.org/cwl/cwl#Directory/location</I><BR>
94	* <BLOCKQUOTE>
95	* An IRI that identifies the directory resource. This may be a relative
96	* reference, in which case it must be resolved using the base IRI of the
97	* document. The location may refer to a local or remote resource. If
98	* the `listing` field is not set, the implementation must use the
99	* location IRI to retrieve directory listing. If an implementation is
100	* unable to retrieve the directory listing stored at a remote resource (due to
101	* unsupported protocol, access denied, or other issue) it must signal an
102	* error.
103	*
104	* If the `location` field is not provided, the `listing` field must be
105	* provided. The implementation must assign a unique identifier for
106	* the `location` field.
107	*
108	* If the `path` field is provided but the `location` field is not, an
109	* implementation may assign the value of the `path` field to `location`,
110	* then follow the rules above.
111	* * </BLOCKQUOTE>
112	*/
113
114	public java.util.Optional<String> getLocation() {
115	return this.location;	×
116	}
117
118	private java.util.Optional<String> path;
119
120	/**
121	* Getter for property <I>https://w3id.org/cwl/cwl#path</I><BR>
122	* <BLOCKQUOTE>
123	* The local path where the Directory is made available prior to executing a
124	* CommandLineTool. This must be set by the implementation. This field
125	* must not be used in any other context. The command line tool being
126	* executed must be able to to access the directory at `path` using the POSIX
127	* `opendir(2)` syscall.
128	*
129	* If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
130	* (`\|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
131	* `<space>`, `<tab>`, and `<newline>`) or characters
132	* [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
133	* for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
134	* then implementations may terminate the process with a
135	* `permanentFailure`.
136	* * </BLOCKQUOTE>
137	*/
138
139	public java.util.Optional<String> getPath() {
140	return this.path;	×
141	}
142
143	private java.util.Optional<String> basename;
144
145	/**
146	* Getter for property <I>https://w3id.org/cwl/cwl#Directory/basename</I><BR>
147	* <BLOCKQUOTE>
148	* The base name of the directory, that is, the name of the file without any
149	* leading directory path. The base name must not contain a slash `/`.
150	*
151	* If not provided, the implementation must set this field based on the
152	* `location` field by taking the final path component after parsing
153	* `location` as an IRI. If `basename` is provided, it is not required to
154	* match the value from `location`.
155	*
156	* When this file is made available to a CommandLineTool, it must be named
157	* with `basename`, i.e. the final component of the `path` field must match
158	* `basename`.
159	* * </BLOCKQUOTE>
160	*/
161
162	public java.util.Optional<String> getBasename() {
163	return this.basename;	×
164	}
165
166	private java.util.Optional<java.util.List<Object>> listing;
167
168	/**
169	* Getter for property <I>https://w3id.org/cwl/cwl#listing</I><BR>
170	* <BLOCKQUOTE>
171	* List of files or subdirectories contained in this directory. The name
172	* of each file or subdirectory is determined by the `basename` field of
173	* each `File` or `Directory` object. It is an error if a `File` shares a
174	* `basename` with any other entry in `listing`. If two or more
175	* `Directory` object share the same `basename`, this must be treated as
176	* equivalent to a single subdirectory with the listings recursively
177	* merged.
178	* * </BLOCKQUOTE>
179	*/
180
181	public java.util.Optional<java.util.List<Object>> getListing() {
182	return this.listing;	×
183	}
184
185	/**
186	* Used by {@link org.w3id.cwl.cwl1_1.utils.RootLoader} to construct instances of DirectoryImpl.
187	*
188	* @param __doc_ Document fragment to load this record object from (presumably a
189	{@link java.util.Map}).
190	* @param __baseUri_ Base URI to generate child document IDs against.
191	* @param __loadingOptions Context for loading URIs and populating objects.
192	* @param __docRoot_ ID at this position in the document (if available) (maybe?)
193	* @throws ValidationException If the document fragment is not a {@link java.util.Map}
194	* or validation of fields fails.
195	*/
196	public DirectoryImpl(
197	final Object __doc_,
198	final String __baseUri_,
199	LoadingOptions __loadingOptions,
200	final String __docRoot_) {
201	super(__doc_, __baseUri_, __loadingOptions, __docRoot_);	1✔
202	// Prefix plumbing variables with '__' to reduce likelihood of collision with
203	// generated names.
204	String __baseUri = __baseUri_;	1✔
205	String __docRoot = __docRoot_;	1✔
206	if (!(__doc_ instanceof java.util.Map)) {	1✔
207	throw new ValidationException("DirectoryImpl called on non-map");	×
208	}
209	final java.util.Map<String, Object> __doc = (java.util.Map<String, Object>) __doc_;	1✔
210	final java.util.List<ValidationException> __errors =	1✔
211	new java.util.ArrayList<ValidationException>();
212	if (__loadingOptions != null) {	1✔
213	this.loadingOptions_ = __loadingOptions;	1✔
214	}
215	Directory_class class_;
216	try {
217	class_ =	1✔
218	LoaderInstances
219	.uri_Directory_class_False_True_None_None
220	.loadField(__doc.get("class"), __baseUri, __loadingOptions);	×
221	} catch (ValidationException e) {	1✔
222	class_ = null; // won't be used but prevents compiler from complaining.	1✔
223	final String __message = "the `class` field is not valid because:";	1✔
224	__errors.add(new ValidationException(__message, e));	1✔
225	}	×
226	java.util.Optional<String> location;
227
228	if (__doc.containsKey("location")) {	1✔
229	try {
230	location =	×
231	LoaderInstances
232	.uri_optional_StringInstance_False_False_None_None
233	.loadField(__doc.get("location"), __baseUri, __loadingOptions);	×
234	} catch (ValidationException e) {	×
235	location = null; // won't be used but prevents compiler from complaining.	×
236	final String __message = "the `location` field is not valid because:";	×
237	__errors.add(new ValidationException(__message, e));	×
238	}	×
239
240	} else {
241	location = null;	1✔
242	}
243	java.util.Optional<String> path;
244
245	if (__doc.containsKey("path")) {	1✔
246	try {
247	path =	×
248	LoaderInstances
249	.uri_optional_StringInstance_False_False_None_None
250	.loadField(__doc.get("path"), __baseUri, __loadingOptions);	×
251	} catch (ValidationException e) {	×
252	path = null; // won't be used but prevents compiler from complaining.	×
253	final String __message = "the `path` field is not valid because:";	×
254	__errors.add(new ValidationException(__message, e));	×
255	}	×
256
257	} else {
258	path = null;	1✔
259	}
260	java.util.Optional<String> basename;
261
262	if (__doc.containsKey("basename")) {	1✔
263	try {
264	basename =	×
265	LoaderInstances
266	.optional_StringInstance
267	.loadField(__doc.get("basename"), __baseUri, __loadingOptions);	×
268	} catch (ValidationException e) {	×
269	basename = null; // won't be used but prevents compiler from complaining.	×
270	final String __message = "the `basename` field is not valid because:";	×
271	__errors.add(new ValidationException(__message, e));	×
272	}	×
273
274	} else {
275	basename = null;	1✔
276	}
277	java.util.Optional<java.util.List<Object>> listing;
278
279	if (__doc.containsKey("listing")) {	1✔
280	try {
281	listing =	×
282	LoaderInstances
283	.optional_array_of_union_of_File_or_Directory
284	.loadField(__doc.get("listing"), __baseUri, __loadingOptions);	×
285	} catch (ValidationException e) {	×
286	listing = null; // won't be used but prevents compiler from complaining.	×
287	final String __message = "the `listing` field is not valid because:";	×
288	__errors.add(new ValidationException(__message, e));	×
289	}	×
290
291	} else {
292	listing = null;	1✔
293	}
294	if (!__errors.isEmpty()) {	1✔
295	throw new ValidationException("Trying 'RecordField'", __errors);	1✔
296	}
297	this.class_ = (Directory_class) class_;	×
298	this.location = (java.util.Optional<String>) location;	×
299	this.path = (java.util.Optional<String>) path;	×
300	this.basename = (java.util.Optional<String>) basename;	×
301	this.listing = (java.util.Optional<java.util.List<Object>>) listing;	×
302	}	×
303	}

common-workflow-language / cwljava / #352

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