1
|
/**
|
2
|
* Copyright (C) 2007 EDIT
|
3
|
* European Distributed Institute of Taxonomy
|
4
|
* http://www.e-taxonomy.eu
|
5
|
*
|
6
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
7
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
8
|
*/
|
9
|
|
10
|
package eu.etaxonomy.cdm.api.service;
|
11
|
|
12
|
import java.io.IOException;
|
13
|
import java.util.Collection;
|
14
|
import java.util.HashMap;
|
15
|
import java.util.List;
|
16
|
import java.util.Map;
|
17
|
import java.util.Optional;
|
18
|
import java.util.Set;
|
19
|
import java.util.UUID;
|
20
|
|
21
|
import org.hibernate.criterion.Criterion;
|
22
|
|
23
|
import eu.etaxonomy.cdm.api.service.config.DeleteConfiguratorBase;
|
24
|
import eu.etaxonomy.cdm.api.service.config.NameDeletionConfigurator;
|
25
|
import eu.etaxonomy.cdm.api.service.dto.TypeDesignationStatusFilter;
|
26
|
import eu.etaxonomy.cdm.api.service.pager.Pager;
|
27
|
import eu.etaxonomy.cdm.api.service.search.DocumentSearchResult;
|
28
|
import eu.etaxonomy.cdm.api.service.search.LuceneParseException;
|
29
|
import eu.etaxonomy.cdm.api.service.search.SearchResult;
|
30
|
import eu.etaxonomy.cdm.api.util.TaxonNamePartsFilter;
|
31
|
import eu.etaxonomy.cdm.common.URI;
|
32
|
import eu.etaxonomy.cdm.model.common.Language;
|
33
|
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
|
34
|
import eu.etaxonomy.cdm.model.name.HybridRelationship;
|
35
|
import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
|
36
|
import eu.etaxonomy.cdm.model.name.INonViralName;
|
37
|
import eu.etaxonomy.cdm.model.name.NameRelationship;
|
38
|
import eu.etaxonomy.cdm.model.name.NameRelationshipType;
|
39
|
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
|
40
|
import eu.etaxonomy.cdm.model.name.NomenclaturalSource;
|
41
|
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
|
42
|
import eu.etaxonomy.cdm.model.name.Rank;
|
43
|
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
|
44
|
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
|
45
|
import eu.etaxonomy.cdm.model.name.TaxonName;
|
46
|
import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
|
47
|
import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
|
48
|
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
|
49
|
import eu.etaxonomy.cdm.persistence.dao.common.Restriction;
|
50
|
import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
|
51
|
import eu.etaxonomy.cdm.persistence.dto.TaxonNameParts;
|
52
|
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
|
53
|
import eu.etaxonomy.cdm.persistence.query.MatchMode;
|
54
|
import eu.etaxonomy.cdm.persistence.query.OrderHint;
|
55
|
import eu.etaxonomy.cdm.strategy.cache.TaggedText;
|
56
|
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
|
57
|
|
58
|
public interface INameService
|
59
|
extends IIdentifiableEntityService<TaxonName> {
|
60
|
|
61
|
/**
|
62
|
* Deletes a name. Depending on the configurator state links to the name will either be
|
63
|
* deleted or throw exceptions.<BR>
|
64
|
* If name is <code>null</code> this method has no effect.
|
65
|
* @param name
|
66
|
* @param config
|
67
|
*
|
68
|
*/
|
69
|
public DeleteResult delete(UUID nameUUID, NameDeletionConfigurator config);
|
70
|
|
71
|
/**
|
72
|
* Creates specimen duplicate based on the given type specimen which will be assigned as a type
|
73
|
* of the given name.<br>
|
74
|
* The specimen will only differ in accession number, collection and type status and will be attached
|
75
|
* to the same {@link FieldUnit}
|
76
|
* @param name the name where this type designation will be added to
|
77
|
* @param baseDesignation the type specimen of this designation is cloned to create the new specimen
|
78
|
* @param accessionNumber the accession number of the cloned specimen
|
79
|
* @param barcode the barcode of the cloned specimen
|
80
|
* @param catalogNumber the catalog number of the cloned specimen
|
81
|
* @param collectionUuid the collection the cloned specimen belongs to
|
82
|
* @param typeStatus the type status of the cloned specimen
|
83
|
* @return an {@link UpdateResult}
|
84
|
*/
|
85
|
public UpdateResult cloneTypeDesignation(UUID nameUuid, SpecimenTypeDesignation baseDesignation,
|
86
|
String accessionNumber, String barcode, String catalogNumber,
|
87
|
UUID collectionUuid, SpecimenTypeDesignationStatus typeStatus, URI preferredStableUri);
|
88
|
|
89
|
/**
|
90
|
* Removes the given type designation from the given taxon name and deletes it from
|
91
|
* the database if it is not connected to any other name.
|
92
|
* If <code>typeDesignation</code> is <code>null</code> all type designations are deleted
|
93
|
* from the given taxon name. If <code>name</code> is <code>null</code> all names are removed from
|
94
|
* the given type designation. If both are <code>null</code> nothing happens.
|
95
|
* @param typeDesignation
|
96
|
* @param name
|
97
|
* @return
|
98
|
*/
|
99
|
public DeleteResult deleteTypeDesignation(TaxonName name, TypeDesignationBase<?> typeDesignation);
|
100
|
|
101
|
/**
|
102
|
* Removes the given type designation from the given taxon name and deletes it from
|
103
|
* the database if it is not connected to any other name.
|
104
|
* If <code>typeDesignation</code> is <code>null</code> all type designations are deleted
|
105
|
* from the given taxon name. If <code>name</code> is <code>null</code> all names are removed from
|
106
|
* the given type designation. If both are <code>null</code> nothing happens.
|
107
|
* @param typeDesignation
|
108
|
* @param name
|
109
|
* @return
|
110
|
*/
|
111
|
public DeleteResult deleteTypeDesignation(UUID nameUuid, UUID typeDesignationUuid);
|
112
|
|
113
|
|
114
|
/**
|
115
|
* Saves the given type designations.
|
116
|
* @param typeDesignationCollection
|
117
|
* @return
|
118
|
*/
|
119
|
public Map<UUID, TypeDesignationBase<?>> saveTypeDesignationAll(Collection<TypeDesignationBase<?>> typeDesignationCollection);
|
120
|
|
121
|
/**
|
122
|
* Saves the given homotypical groups.
|
123
|
* @param homotypicalGroups
|
124
|
* @return
|
125
|
*/
|
126
|
public Map<UUID, HomotypicalGroup> saveAllHomotypicalGroups(Collection<HomotypicalGroup> homotypicalGroups);
|
127
|
|
128
|
/**
|
129
|
* Returns all nomenclatural status.
|
130
|
* @param limit
|
131
|
* @param start
|
132
|
* @return
|
133
|
*/
|
134
|
public List<NomenclaturalStatus> getAllNomenclaturalStatus(int limit, int start);
|
135
|
|
136
|
/**
|
137
|
* Returns all type designations.
|
138
|
* @param limit
|
139
|
* @param start
|
140
|
* @return
|
141
|
*/
|
142
|
public List<TypeDesignationBase<?>> getAllTypeDesignations(int limit, int start);
|
143
|
|
144
|
public TypeDesignationBase<?> loadTypeDesignation(int id, List<String> propertyPaths);
|
145
|
|
146
|
public TypeDesignationBase<?> loadTypeDesignation(UUID uuid, List<String> propertyPaths);
|
147
|
|
148
|
public List<TypeDesignationBase<?>> loadTypeDesignations(List<UUID> uuids, List<String> propertyPaths);
|
149
|
|
150
|
/**
|
151
|
* Returns all NonViralNames with a name cache that matches the given string
|
152
|
* @param name
|
153
|
* @return
|
154
|
*/
|
155
|
public List<TaxonName> getNamesByNameCache(String nameCache);
|
156
|
|
157
|
/**
|
158
|
* Returns all NonViralNames with a title cache that matches the given string
|
159
|
* using the given match mode and initialization strategy
|
160
|
*
|
161
|
* @param name
|
162
|
* @param matchMode must not be <code>NULL</code>
|
163
|
* @param propertyPaths
|
164
|
* @return
|
165
|
*/
|
166
|
public List<TaxonName> findNamesByTitleCache(String titleCache, MatchMode matchMode, List<String> propertyPaths);
|
167
|
|
168
|
/**
|
169
|
* Supports using wildcards in the query parameters.
|
170
|
* If a name part passed to the method contains the asterisk character ('*') it will be translated into '%' the related field is search with a LIKE clause.
|
171
|
* <p>
|
172
|
* A query parameter which is passed as <code>NULL</code> value will be ignored. A parameter passed as {@link Optional} object containing a <code>NULL</code> value will be used
|
173
|
* to filter select taxon names where the according field is <code>null</code>.
|
174
|
*
|
175
|
* @param filter
|
176
|
* @param infraGenericEpithet
|
177
|
* @param specificEpithet
|
178
|
* @param infraSpecificEpithet
|
179
|
* @param rank
|
180
|
* Only names having the specified rank are taken into account.
|
181
|
* @param excludedNamesUuids
|
182
|
* Names to be excluded from the result set
|
183
|
* @return
|
184
|
*/
|
185
|
public Pager<TaxonNameParts> findTaxonNameParts(Optional<String> genusOrUninomial,
|
186
|
Optional<String> infraGenericEpithet, Optional<String> specificEpithet,
|
187
|
Optional<String> infraSpecificEpithet, Rank rank, Set<UUID> excludedNamesUuids,
|
188
|
Integer pageSize, Integer pageIndex, List<OrderHint> orderHints);
|
189
|
|
190
|
/**
|
191
|
* <b>This method behaves differently compared to {@link #findTaxonNameParts(Optional, Optional, Optional, Optional, Rank, Integer, Integer, List)}!</b>
|
192
|
* <p>
|
193
|
* The {@link TaxonNamePartsFilter} defines the rank and fixed name parts for the search process.
|
194
|
* For example: In case the <code>rank</code> is "genus", the <code>genusOrUninomial</code> will be used as search parameter which needs to match exactly.
|
195
|
* The <code>namePartQueryString</code> will be used to do a wildcard search on the specificEpithet.
|
196
|
* <p>
|
197
|
* For name part lookup purposes the <code>TaxonNameParts</code> in the result list can be asked to return the relavant name part by
|
198
|
* calling {@link TaxonNameParts#nameRankSpecificNamePart(TaxonName)}
|
199
|
*
|
200
|
*
|
201
|
* @param filter
|
202
|
* @return
|
203
|
*/
|
204
|
public Pager<TaxonNameParts> findTaxonNameParts(TaxonNamePartsFilter filter, String namePartQueryString, Integer pageSize, Integer pageIndex, List<OrderHint> orderHints);
|
205
|
|
206
|
/**
|
207
|
* Returns all NonViralNames with a name cache that matches the given string
|
208
|
* using the given match mode and initialization strategy
|
209
|
*
|
210
|
* @param name
|
211
|
* @param matchMode
|
212
|
* @param propertyPaths
|
213
|
* @return
|
214
|
*/
|
215
|
public List<TaxonName> findNamesByNameCache(String nameCache, MatchMode matchMode, List<String> propertyPaths);
|
216
|
|
217
|
/**
|
218
|
* Fuzzy matching for the taxon name elements. The input name is first atomised using the {@link NonViralNameParserImpl}
|
219
|
* into its separate parts (genusOrUninomial,infraGenericEpithet,specificEpithet,infraGenericEpithet,authorshipCache).
|
220
|
* Each field is then matched separately with the same accuracy parameter.
|
221
|
*
|
222
|
* @param name taxon name to fuzzy match
|
223
|
* @param accuracy value > 0.0 and < 1.0 which determines the accuracy of the result.
|
224
|
* @param languages list of languages to consider when matching (currently not used)
|
225
|
* @param highlightFragments
|
226
|
* @param propertyPaths
|
227
|
* @param maxNoOfResults
|
228
|
* @return
|
229
|
* @throws IOException
|
230
|
* @throws LuceneParseException
|
231
|
*/
|
232
|
public List<SearchResult<TaxonName>> findByNameFuzzySearch(
|
233
|
String name,
|
234
|
float accuracy,
|
235
|
List<Language> languages,
|
236
|
boolean highlightFragments,
|
237
|
List<String> propertyPaths,
|
238
|
int maxNoOfResults) throws IOException, LuceneParseException;
|
239
|
|
240
|
/**
|
241
|
* Fuzzy matching for the taxon name elements using only the lucene index.
|
242
|
*
|
243
|
* The input name is first atomised using the {@link NonViralNameParserImpl}
|
244
|
* into its separate parts (genusOrUninomial,infraGenericEpithet,specificEpithet,infraGenericEpithet,authorshipCache).
|
245
|
* Each field is then matched separately with the same accuracy parameter.
|
246
|
*
|
247
|
* @param name taxon name to fuzzy match
|
248
|
* @param accuracy value > 0.0 and < 1.0 which determines the accuracy of the result.
|
249
|
* @param languages list of languages to consider when matching (currently not used)
|
250
|
* @param highlightFragments
|
251
|
* @param maxNoOfResults
|
252
|
* @return
|
253
|
* @throws IOException
|
254
|
* @throws LuceneParseException
|
255
|
*/
|
256
|
public List<DocumentSearchResult> findByNameFuzzySearch(
|
257
|
String name,
|
258
|
float accuracy,
|
259
|
List<Language> languages,
|
260
|
boolean highlightFragments,
|
261
|
int maxNoOfResults) throws IOException, LuceneParseException;
|
262
|
|
263
|
/**
|
264
|
* Fuzzy matching against the name cache using only the lucene index.
|
265
|
*
|
266
|
*
|
267
|
* @param name taxon name to fuzzy match
|
268
|
* @param accuracy value > 0.0 and < 1.0 which determines the accuracy of the result.
|
269
|
* @param languages list of languages to consider when matching (currently not used)
|
270
|
* @param highlightFragments
|
271
|
* @param maxNoOfResults
|
272
|
* @return
|
273
|
* @throws IOException
|
274
|
* @throws LuceneParseException
|
275
|
*/
|
276
|
public List<DocumentSearchResult> findByFuzzyNameCacheSearch(
|
277
|
String name,
|
278
|
float accuracy,
|
279
|
List<Language> languages,
|
280
|
boolean highlightFragments,
|
281
|
int maxNoOfResults) throws IOException, LuceneParseException;
|
282
|
|
283
|
/**
|
284
|
* Exact matching for the taxon name elements using only the lucene index.
|
285
|
*
|
286
|
* The input name is first atomised using the {@link NonViralNameParserImpl}
|
287
|
* into its separate parts (genusOrUninomial,infraGenericEpithet,specificEpithet,infraGenericEpithet,authorshipCache).
|
288
|
* Each field is then matched separately with the same accuracy parameter.
|
289
|
*
|
290
|
* @param name taxon name to fuzzy match
|
291
|
* @param wildcard boolean flag to indicate whether a wildcard '*' should be added at the end of the query
|
292
|
* @param languages list of languages to consider when matching (currently not used)
|
293
|
* @param highlightFragments
|
294
|
* @param maxNoOfResults
|
295
|
* @return
|
296
|
* @throws IOException
|
297
|
* @throws LuceneParseException
|
298
|
*/
|
299
|
|
300
|
public List<DocumentSearchResult> findByNameExactSearch(
|
301
|
String name,
|
302
|
boolean wildcard,
|
303
|
List<Language> languages,
|
304
|
boolean highlightFragments,
|
305
|
int maxNoOfResults) throws IOException, LuceneParseException;
|
306
|
|
307
|
// TODO: Remove getNamesByName() methods. Use findNamesByTitle() instead.
|
308
|
|
309
|
public List<HomotypicalGroup> getAllHomotypicalGroups(int limit, int start);
|
310
|
|
311
|
/**
|
312
|
* Returns all or a page of all original spellings in the database.
|
313
|
* As original spellings are
|
314
|
*
|
315
|
* @param pageSize the page size
|
316
|
* @param pageStart the number of the page
|
317
|
* @param orderHints the order hints
|
318
|
* @param propertyPaths the property path to initialize the resulting objects
|
319
|
* @return list of nomenclatural the filter criteria
|
320
|
*/
|
321
|
public List<NomenclaturalSource> listOriginalSpellings(Integer pageSize,
|
322
|
Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
323
|
|
324
|
/**
|
325
|
* Returns all or a page of all taxon name relationships in the database.
|
326
|
* The result can be filtered by relationship types.
|
327
|
* It does NOT contain hybrid relationships
|
328
|
* (see {@link #listHybridRelationships(Set, Integer, Integer, List, List)})
|
329
|
*
|
330
|
* @param types The name relationship type filter, if <code>null</code> no filter is set, if empty the result will also be empty
|
331
|
* @param pageSize the page size
|
332
|
* @param pageStart the number of the page
|
333
|
* @param orderHints the order hints
|
334
|
* @param propertyPaths the property path to initialize the resulting objects
|
335
|
* @return list of name relationships matching the filter criteria
|
336
|
*/
|
337
|
public List<NameRelationship> listNameRelationships(Set<NameRelationshipType> types,
|
338
|
Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
339
|
|
340
|
/**
|
341
|
* Returns all or a page of all hybrid relationships in the database.
|
342
|
* The result can be filtered by relationship types.
|
343
|
* It does NOT contain ordinary name relationships
|
344
|
* (see {@link #listNameRelationships(Set, Integer, Integer, List, List)})
|
345
|
*
|
346
|
* @param types The hybrid relationship type filter, if <code>null</code> no filter is set, if empty the result will also be empty
|
347
|
* @param pageSize the page size
|
348
|
* @param pageStart the number of the page
|
349
|
* @param orderHints the order hints
|
350
|
* @param propertyPaths the property path to initialize the resulting objects
|
351
|
* @return list of hybrid relationships matching the filter criteria
|
352
|
*/
|
353
|
public List<HybridRelationship> listHybridRelationships(Set<HybridRelationshipType> types,
|
354
|
Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
355
|
|
356
|
/**
|
357
|
* Return a List of name relationships in which this name is related to
|
358
|
* another name, optionally filtered by relationship type
|
359
|
*
|
360
|
* @param name
|
361
|
* the name on either the <i>"from side"</i> or on the
|
362
|
* <i>"to side"</i> of the relationship, depending on the
|
363
|
* <code>direction</code> of the relationship.
|
364
|
* @param direction
|
365
|
* the direction of the NameRelationship, may be null to return all relationships
|
366
|
* @param type
|
367
|
* the relationship type (or null to return all relationships)
|
368
|
* @param pageSize
|
369
|
* The maximum number of relationships returned (can be null for
|
370
|
* all relationships)
|
371
|
* @param pageNumber
|
372
|
* The offset (in pageSize chunks) from the start of the result
|
373
|
* set (0 - based)
|
374
|
* @param orderHints
|
375
|
* may be null
|
376
|
* @param propertyPaths
|
377
|
* properties to initialize - see
|
378
|
* {@link IBeanInitializer#initialize(Object, List)}
|
379
|
* @return a Pager of NameRelationship instances
|
380
|
*/
|
381
|
public List<NameRelationship> listNameRelationships(TaxonName name, NameRelationship.Direction direction, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
382
|
|
383
|
/**
|
384
|
* Return a List of name relationships in which this name is related to another name, optionally filtered
|
385
|
* by relationship type
|
386
|
*
|
387
|
* @param name the name on the <i>"from side"</i> of the relationship
|
388
|
* @param direction the direction of the NameRelationship
|
389
|
* @param type the relationship type (or null to return all relationships)
|
390
|
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
|
391
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
392
|
* @param orderHints may be null
|
393
|
* @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
|
394
|
* @return a Pager of NameRelationship instances
|
395
|
*/
|
396
|
public Pager<NameRelationship> pageNameRelationships(TaxonName name, NameRelationship.Direction direction, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
397
|
|
398
|
/**
|
399
|
* Return a List of relationships in which this name is related to another name, optionally filtered
|
400
|
* by relationship type
|
401
|
*
|
402
|
* @param name the name on the <i>"from side"</i> of the relationship
|
403
|
* @param type the relationship type (or null to return all relationships)
|
404
|
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
|
405
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
406
|
* @param orderHints may be null
|
407
|
* @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
|
408
|
* @return a Pager of NameRelationship instances
|
409
|
* @deprecated use {@link #listNameRelationships(TaxonName, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction, NameRelationshipType, Integer, Integer, List, List)} instead
|
410
|
*/
|
411
|
@Deprecated
|
412
|
public List<NameRelationship> listFromNameRelationships(TaxonName name, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
413
|
|
414
|
/**
|
415
|
* Return a List of relationships in which this name is related to another name, optionally filtered
|
416
|
* by relationship type
|
417
|
*
|
418
|
* @param name the name on the <i>"from side"</i> of the relationship
|
419
|
* @param type the relationship type (or null to return all relationships)
|
420
|
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
|
421
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
422
|
* @param orderHints may be null
|
423
|
* @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
|
424
|
* @return a Pager of NameRelationship instances
|
425
|
* @deprecated use {@link #pageNameRelationships(TaxonName, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction, NameRelationshipType, Integer, Integer, List, List)} instead
|
426
|
*/
|
427
|
@Deprecated
|
428
|
public Pager<NameRelationship> pageFromNameRelationships(TaxonName name, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
429
|
|
430
|
/**
|
431
|
* Return a List of relationships in which another name is related to this name, optionally filtered
|
432
|
* by relationship type
|
433
|
*
|
434
|
* @param name the name on the <i>"to side"</i> of the relationship
|
435
|
* @param type the relationship type (or null to return all relationships)
|
436
|
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
|
437
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
438
|
* @param orderHints may be null
|
439
|
* @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
|
440
|
* @return a Pager of NameRelationship instances
|
441
|
* @deprecated use {@link #listNameRelationships(TaxonName, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction, NameRelationshipType, Integer, Integer, List, List)} instead
|
442
|
*/
|
443
|
@Deprecated
|
444
|
public List<NameRelationship> listToNameRelationships(TaxonName name, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
445
|
|
446
|
/**
|
447
|
* Return a List of relationships in which another name is related to this name, optionally filtered
|
448
|
* by relationship type
|
449
|
*
|
450
|
* @param name the name on the <i>"to side"</i> of the relationship
|
451
|
* @param type the relationship type (or null to return all relationships)
|
452
|
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
|
453
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
454
|
* @param orderHints may be null
|
455
|
* @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
|
456
|
* @return a Pager of NameRelationship instances
|
457
|
* @deprecated use {@link #pageNameRelationships(TaxonName, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction, NameRelationshipType, Integer, Integer, List, List)} instead
|
458
|
*/
|
459
|
@Deprecated
|
460
|
public Pager<NameRelationship> pageToNameRelationships(TaxonName name, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
461
|
|
462
|
|
463
|
/**
|
464
|
* Return a List of hybrids related to this name, optionally filtered
|
465
|
* by hybrid relationship type
|
466
|
*
|
467
|
* @param name the name
|
468
|
* @param type the hybrid relationship type (or null to return all hybrids)
|
469
|
* @param pageSize The maximum number of hybrid relationships returned (can be null for all relationships)
|
470
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
471
|
* @param orderHints may be null
|
472
|
* @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
|
473
|
* @return a Pager of HybridRelationship instances
|
474
|
*/
|
475
|
public Pager<HybridRelationship> getHybridNames(INonViralName name, HybridRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
476
|
|
477
|
/**
|
478
|
* Return a List of types related to this name, optionally filtered
|
479
|
* by type designation status
|
480
|
*
|
481
|
* @param name the name
|
482
|
* @param status the type designation status (or null to return all types)
|
483
|
* @param pageSize The maximum number of types returned (can be null for all types)
|
484
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
485
|
* @return a Pager of TypeDesignationBase instances
|
486
|
*/
|
487
|
public Pager<TypeDesignationBase> getTypeDesignations(TaxonName name,
|
488
|
SpecimenTypeDesignationStatus status, Integer pageSize, Integer pageNumber);
|
489
|
|
490
|
public Pager<TypeDesignationBase> getTypeDesignations(TaxonName name,
|
491
|
SpecimenTypeDesignationStatus status, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
|
492
|
|
493
|
public List<TypeDesignationBase> getTypeDesignationsInHomotypicalGroup(UUID nameUuid, Integer pageSize,
|
494
|
Integer pageNumber, List<String> propertyPaths);
|
495
|
|
496
|
|
497
|
/**
|
498
|
* Returns a List of TaxonName instances that match the properties passed
|
499
|
*
|
500
|
* @param uninomial
|
501
|
* @param infraGenericEpithet
|
502
|
* @param specificEpithet
|
503
|
* @param infraspecificEpithet
|
504
|
* @param rank
|
505
|
* @param pageSize The maximum number of names returned (can be null for all names)
|
506
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
507
|
* @param orderHints may be null
|
508
|
* @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
|
509
|
* @return a Pager of TaxonName instances
|
510
|
*/
|
511
|
public Pager<TaxonName> searchNames(String uninomial, String infraGenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
512
|
|
513
|
/**
|
514
|
* Returns a Paged List of TaxonName instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
|
515
|
*
|
516
|
* @param clazz filter the results by class (or pass null to return all TaxonName instances)
|
517
|
* @param queryString
|
518
|
* @param pageSize The maximum number of names returned (can be null for all matching names)
|
519
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
520
|
* @param orderHints
|
521
|
* Supports path like <code>orderHints.propertyNames</code> which
|
522
|
* include *-to-one properties like createdBy.username or
|
523
|
* authorTeam.persistentTitleCache
|
524
|
* @param propertyPaths properties to be initialized
|
525
|
* @return a Pager TaxonName instances
|
526
|
* @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>
|
527
|
*/
|
528
|
@Override
|
529
|
public Pager<TaxonName> search(Class<? extends TaxonName> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
530
|
|
531
|
/**
|
532
|
* Returns a map that holds uuid, titleCache pairs of all names in the current database
|
533
|
*
|
534
|
* @return
|
535
|
* a <code>Map</code> containing uuid and titleCache of names
|
536
|
*/
|
537
|
public List<UuidAndTitleCache> getUuidAndTitleCacheOfNames(Integer limit, String pattern);
|
538
|
|
539
|
/**
|
540
|
* Returns a list of names belonging to the synonymy of the taxon
|
541
|
* @param limit
|
542
|
* @param taxonUuid
|
543
|
* @return a list containing uuid and titleCache of names of the synonymy of the given taxon
|
544
|
*/
|
545
|
public List<UuidAndTitleCache> getUuidAndTitleCacheOfSynonymy(Integer limit, UUID taxonUuid);
|
546
|
|
547
|
/**
|
548
|
* Return a Pager of names matching the given query string, optionally filtered by class, optionally with a particular MatchMode
|
549
|
*
|
550
|
* @param clazz filter by class - can be null to include all instances of type T
|
551
|
* @param queryString the query string to filter by
|
552
|
* @param matchmode use a particular type of matching (can be null - defaults to exact matching)
|
553
|
* @param criteria additional criteria to filter by
|
554
|
* @param pageSize The maximum number of objects returned (can be null for all objects)
|
555
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
556
|
* @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
|
557
|
* @param orderHints
|
558
|
* Supports path like <code>orderHints.propertyNames</code> which
|
559
|
* include *-to-one properties like createdBy.username or
|
560
|
* authorTeam.persistentTitleCache
|
561
|
* @return a paged list of instances of type T matching the queryString
|
562
|
*/
|
563
|
public Pager<TaxonName> findByName(Class<TaxonName> clazz, String queryString, MatchMode matchmode,
|
564
|
List<Criterion> criteria, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
565
|
|
566
|
/**
|
567
|
* Returns a homotypical group with the given UUID or null if not homotypical group exists with that UUID
|
568
|
*
|
569
|
* @param uuid the uuid of the homotypical group
|
570
|
* @return a homotypical group
|
571
|
*/
|
572
|
public HomotypicalGroup findHomotypicalGroup(UUID uuid);
|
573
|
|
574
|
/**
|
575
|
* @param uuid
|
576
|
* @return
|
577
|
*/
|
578
|
public List<TaggedText> getTaggedName(UUID uuid);
|
579
|
|
580
|
/**
|
581
|
* @param nameUuid
|
582
|
* @return
|
583
|
*/
|
584
|
public UpdateResult setAsGroupsBasionym(UUID nameUuid);
|
585
|
|
586
|
public List<HashMap<String, String>> getNameRecords();
|
587
|
|
588
|
/**
|
589
|
* @param name
|
590
|
* @param config
|
591
|
* @return
|
592
|
*/
|
593
|
DeleteResult delete(TaxonName name, NameDeletionConfigurator config);
|
594
|
|
595
|
List<TypeDesignationStatusBase> getTypeDesignationStatusInUse();
|
596
|
|
597
|
/**
|
598
|
* Provides a collection of the TypeDesignationStatusBase terms which are in use.
|
599
|
* Terms having the same label are merged into one filter item.
|
600
|
*
|
601
|
* @param preferredLanguage
|
602
|
* @return
|
603
|
*/
|
604
|
Collection<TypeDesignationStatusFilter> getTypeDesignationStatusFilterTerms(List<Language> preferredLanguages);
|
605
|
|
606
|
/**
|
607
|
* @param uuid
|
608
|
* @param propertyPaths
|
609
|
* @return
|
610
|
*/
|
611
|
NomenclaturalStatus loadNomenclaturalStatus(UUID uuid, List<String> propertyPaths);
|
612
|
|
613
|
/**
|
614
|
* @param clazz
|
615
|
* @param restrictions
|
616
|
* @param pageSize
|
617
|
* @param pageIndex
|
618
|
* @param orderHints
|
619
|
* @param propertyPaths
|
620
|
* @param includeUnpublished
|
621
|
* @return
|
622
|
*/
|
623
|
public <S extends TaxonName> Pager<S> page(Class<S> clazz, List<Restriction<?>> restrictions, Integer pageSize, Integer pageIndex,
|
624
|
List<OrderHint> orderHints, List<String> propertyPaths, boolean includeUnpublished);
|
625
|
|
626
|
/**
|
627
|
* @param clazz
|
628
|
* @param queryString
|
629
|
* @param matchmode
|
630
|
* @param criteria
|
631
|
* @param pageSize
|
632
|
* @param pageNumber
|
633
|
* @param orderHints
|
634
|
* @param propertyPaths
|
635
|
* @return
|
636
|
*/
|
637
|
public List<TaxonName> findByFullTitle(Class<TaxonName> clazz, String queryString, MatchMode matchmode,
|
638
|
List<Criterion> criteria, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
639
|
List<String> propertyPaths);
|
640
|
|
641
|
|
642
|
/**
|
643
|
* Parses a name string and returns a parsed name. If deduplicate is <code>true</code>
|
644
|
* the parsed parts like nomenclatural reference and authors are deduplicated against the
|
645
|
* database.
|
646
|
*
|
647
|
* @param taxonNameString
|
648
|
* @param code the nomenclatural code to use
|
649
|
* @param preferredRank the preferred rank to use if rank is not clearly defined by the taxon name
|
650
|
* @param doDeduplicate if <code>true</code> the name parts are deduplicated against the database,
|
651
|
* but the name itself is NOT deduplicated (this may change in future)
|
652
|
* @return
|
653
|
*/
|
654
|
public UpdateResult parseName(String taxonNameString, NomenclaturalCode code, Rank preferredRank, boolean doDeduplicate);
|
655
|
|
656
|
public UpdateResult parseName(TaxonName nameToBeFilled, String stringToBeParsed, Rank preferredRank, boolean doEmpty, boolean doDeduplicate);
|
657
|
|
658
|
/**
|
659
|
* checks whether the name can be deleted if the taxon with taxonUuid will be deleted, too
|
660
|
* @param name
|
661
|
* @param config
|
662
|
* @param taxonUuid
|
663
|
* @return
|
664
|
*/
|
665
|
DeleteResult isDeletable(UUID nameUuid, DeleteConfiguratorBase config, UUID taxonUuid);
|
666
|
|
667
|
}
|