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.persistence.dao.taxon;
|
11
|
|
12
|
import java.util.List;
|
13
|
import java.util.Set;
|
14
|
import java.util.UUID;
|
15
|
|
16
|
import org.hibernate.criterion.Criterion;
|
17
|
|
18
|
import eu.etaxonomy.cdm.model.common.DefinedTerm;
|
19
|
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
|
20
|
import eu.etaxonomy.cdm.model.common.MarkerType;
|
21
|
import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
|
22
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
23
|
import eu.etaxonomy.cdm.model.name.Rank;
|
24
|
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
25
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
26
|
import eu.etaxonomy.cdm.model.taxon.Classification;
|
27
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
28
|
import eu.etaxonomy.cdm.model.taxon.SynonymType;
|
29
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
30
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
31
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
32
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
|
33
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
|
34
|
import eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao;
|
35
|
import eu.etaxonomy.cdm.persistence.dao.common.ITitledDao;
|
36
|
import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
|
37
|
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
|
38
|
import eu.etaxonomy.cdm.persistence.query.MatchMode;
|
39
|
import eu.etaxonomy.cdm.persistence.query.NameSearchOrder;
|
40
|
import eu.etaxonomy.cdm.persistence.query.OrderHint;
|
41
|
import eu.etaxonomy.cdm.persistence.query.TaxonTitleType;
|
42
|
|
43
|
/**
|
44
|
* @author a.mueller
|
45
|
*
|
46
|
*/
|
47
|
public interface ITaxonDao extends IIdentifiableDao<TaxonBase>, ITitledDao<TaxonBase> {
|
48
|
|
49
|
/**
|
50
|
* Returns a list of TaxonBase instances where the taxon.titleCache property matches the name parameter,
|
51
|
* and taxon.sec matches the sec parameter.
|
52
|
* @param name
|
53
|
* @param sec
|
54
|
* @return
|
55
|
*/
|
56
|
public List<TaxonBase> getTaxaByName(String name, Reference sec);
|
57
|
|
58
|
/**
|
59
|
* Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
|
60
|
* where the taxonBase.name.nameCache property matches the String queryString, and taxon.sec matches the sec parameter.
|
61
|
* @param name
|
62
|
* @param sec
|
63
|
* @return
|
64
|
*/
|
65
|
public List<TaxonBase> getTaxaByName(String queryString, Boolean accepted, Reference sec);
|
66
|
|
67
|
/**
|
68
|
* Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
|
69
|
* where the taxonBase.name.nameCache property matches the String queryString.
|
70
|
* @param queryString
|
71
|
* @param matchMode
|
72
|
* @param accepted
|
73
|
* @param pageSize
|
74
|
* @param pageNumber
|
75
|
* @return
|
76
|
*/
|
77
|
public List<TaxonBase> getTaxaByName(String queryString, MatchMode matchMode,
|
78
|
Boolean accepted, Integer pageSize, Integer pageNumber);
|
79
|
|
80
|
|
81
|
/**
|
82
|
* Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
|
83
|
* where the taxonBase.name.nameCache property matches the String queryString.
|
84
|
* @param doTaxa
|
85
|
* @param doSynonyms
|
86
|
* @param queryString
|
87
|
* @param classification TODO
|
88
|
* @param matchMode
|
89
|
* @param namedAreas TODO
|
90
|
* @param pageSize
|
91
|
* @param pageNumber
|
92
|
* @param propertyPaths TODO
|
93
|
* @return list of found taxa
|
94
|
*/
|
95
|
public List<TaxonBase> getTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, boolean doCommonNames,
|
96
|
boolean includeAuthors, String queryString, Classification classification,
|
97
|
MatchMode matchMode, Set<NamedArea> namedAreas,
|
98
|
NameSearchOrder order, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
|
99
|
|
100
|
/**
|
101
|
* @param doTaxa
|
102
|
* @param doSynonyms
|
103
|
* @param queryString
|
104
|
* @param classification TODO
|
105
|
* @param matchMode
|
106
|
* @param namedAreas
|
107
|
* @param pageSize
|
108
|
* @param pageNumber
|
109
|
* @param propertyPaths
|
110
|
* @return
|
111
|
*/
|
112
|
public long countTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, boolean doCommonNames,
|
113
|
boolean doIncludeAuthors, String queryString, Classification classification,
|
114
|
MatchMode matchMode, Set<NamedArea> namedAreas);
|
115
|
|
116
|
// /**
|
117
|
// * @param queryString
|
118
|
// * @param matchMode
|
119
|
// * @param accepted
|
120
|
// * @return
|
121
|
// */
|
122
|
// public Integer countTaxaByName(String queryString, MatchMode matchMode,
|
123
|
// Boolean accepted);
|
124
|
|
125
|
// /**
|
126
|
// * Returns a count of TaxonBase instances where the
|
127
|
// * taxon.name properties match the parameters passed.
|
128
|
// *
|
129
|
// * @param queryString search string
|
130
|
// * @param matchMode way how search string shall be matched: exact, beginning, or anywhere
|
131
|
// * @param selectModel all taxon base, taxa, or synonyms
|
132
|
// */
|
133
|
// public Integer countTaxaByName(String queryString, MatchMode matchMode, SelectMode selectMode);
|
134
|
|
135
|
/**
|
136
|
* Returns a count of TaxonBase instances where the
|
137
|
* taxon.name properties match the parameters passed.
|
138
|
*
|
139
|
* @param doTaxa
|
140
|
* @param doSynonyms
|
141
|
* @param uninomial
|
142
|
* @param infragenericEpithet
|
143
|
* @param specificEpithet
|
144
|
* @param infraspecificEpithet
|
145
|
* @param rank
|
146
|
* @return a count of TaxonBase instances
|
147
|
*/
|
148
|
public int countTaxaByName(Class <? extends TaxonBase> clazz, String uninomial, String infragenericEpithet,String specificEpithet, String infraspecificEpithet, Rank rank);
|
149
|
|
150
|
/**
|
151
|
* Returns a list of TaxonBase instances where the
|
152
|
* taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
|
153
|
* <i>null</i> will search for those taxa with a value of null in that field
|
154
|
* <p>
|
155
|
* Compare with
|
156
|
* {@link #findByName(String, MatchMode, int, int, boolean)}
|
157
|
* which searches for {@link TaxonNameBase}<strong><code>.titleCache</code>
|
158
|
* </strong>
|
159
|
*
|
160
|
* @param doTaxa
|
161
|
* @param doSynonyms
|
162
|
* @param uninomial
|
163
|
* @param infragenericEpithet
|
164
|
* @param specificEpithet
|
165
|
* @param infraspecificEpithet
|
166
|
* @param rank
|
167
|
* @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
|
168
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
169
|
* @return a list of TaxonBase instances
|
170
|
*/
|
171
|
public List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber);
|
172
|
|
173
|
/**
|
174
|
* Find taxa by searching for Taxa and Synonyms where the
|
175
|
* {@link TaxonNameBase}<strong><code>.titleCache</code></strong> matches
|
176
|
* the name specified as queryString <code>taxonName</code>
|
177
|
* <P>
|
178
|
* Compare with
|
179
|
* {@link #findTaxaByName(Class, String, String, String, String, Rank, Integer, Integer)}
|
180
|
* which searches for {@link TaxonNameBase}<strong><code>.nameCache</code>
|
181
|
* </strong>
|
182
|
* @param queryString
|
183
|
* the taqxon Name to search for
|
184
|
* @param classification TODO
|
185
|
* @param matchMode
|
186
|
* @param namedAreas TODO
|
187
|
* @param pageNumber
|
188
|
* @param pageSize
|
189
|
* @param onlyAcccepted
|
190
|
* @return
|
191
|
*/
|
192
|
public List<TaxonBase> findByNameTitleCache(boolean doTaxa, boolean doSynonyms, String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas,
|
193
|
NameSearchOrder order, Integer pageNumber, Integer pageSize, List<String> propertyPaths) ;
|
194
|
|
195
|
/**
|
196
|
* Returns a taxon corresponding to the given uuid
|
197
|
*
|
198
|
* @param uuid
|
199
|
* The uuid of the taxon requested
|
200
|
* @param criteria
|
201
|
* Custom criteria to be added to the default list of applied criteria.
|
202
|
* @param propertyPaths
|
203
|
*
|
204
|
* @return
|
205
|
*/
|
206
|
public TaxonBase findByUuid(UUID uuid, List<Criterion> criteria, List<String> propertyPaths);
|
207
|
|
208
|
/**
|
209
|
* Returns a list of Taxon entities corresponding to the given uuid list.
|
210
|
* @param uuids
|
211
|
* @param criteria
|
212
|
* @param propertyPaths
|
213
|
* @return
|
214
|
*/
|
215
|
public List<? extends TaxonBase> findByUuids(List<UUID> uuids, List<Criterion> criteria, List<String> propertyPaths);
|
216
|
|
217
|
/**
|
218
|
* @param queryString
|
219
|
* @param classification
|
220
|
* @param matchMode
|
221
|
* @param namedAreas
|
222
|
* @param pageSize
|
223
|
* @param pageNumber
|
224
|
* @param propertyPaths
|
225
|
* @return A List matching Taxa
|
226
|
*/
|
227
|
public List<Taxon> getTaxaByCommonName(String queryString, Classification classification,
|
228
|
MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize,
|
229
|
Integer pageNumber, List<String> propertyPaths);
|
230
|
|
231
|
/**
|
232
|
* TODO necessary?
|
233
|
* @param pagesize max maximum number of returned taxa
|
234
|
* @param page page to start, with 0 being first page
|
235
|
* @return
|
236
|
*/
|
237
|
public List<TaxonBase> getAllTaxonBases(Integer pagesize, Integer page);
|
238
|
|
239
|
|
240
|
/**
|
241
|
* @param limit
|
242
|
* @param start
|
243
|
* @return
|
244
|
*/
|
245
|
public List<Taxon> getAllTaxa(Integer limit, Integer start);
|
246
|
|
247
|
/**
|
248
|
* @param limit
|
249
|
* @param start
|
250
|
* @return
|
251
|
*/
|
252
|
public List<Synonym> getAllSynonyms(Integer limit, Integer start);
|
253
|
|
254
|
/**
|
255
|
* Counts the number of synonyms
|
256
|
* @param onlyAttachedToTaxon if <code>true</code> only those synonyms being attached to
|
257
|
* an accepted taxon are counted
|
258
|
* @return the number of synonyms
|
259
|
*/
|
260
|
public int countSynonyms(boolean onlyAttachedToTaxon);
|
261
|
|
262
|
/**
|
263
|
* @param queryString
|
264
|
* @param matchMode
|
265
|
* @param onlyAcccepted
|
266
|
* @return
|
267
|
*/
|
268
|
public int countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted);
|
269
|
|
270
|
/**
|
271
|
* @param queryString
|
272
|
* @param matchMode
|
273
|
* @param onlyAcccepted
|
274
|
* @param criteria
|
275
|
* @return
|
276
|
*/
|
277
|
public int countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted, List<Criterion> criteria);
|
278
|
|
279
|
/**
|
280
|
* Returns a count of the TaxonRelationships (of where relationship.type ==
|
281
|
* type, if this argument is supplied) where the supplied taxon either is
|
282
|
* relatedFrom or relatedTo depending on the <code>direction</code>
|
283
|
* parameter.
|
284
|
*
|
285
|
* @param taxon
|
286
|
* The taxon that is relatedFrom
|
287
|
* @param type
|
288
|
* The type of TaxonRelationship (can be null)
|
289
|
* @param direction
|
290
|
* specifies the direction of the relationship
|
291
|
* @return the number of TaxonRelationship instances
|
292
|
*/
|
293
|
public int countTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
|
294
|
Direction direction);
|
295
|
|
296
|
/**
|
297
|
* Returns the TaxonRelationships (of where relationship.type == type, if
|
298
|
* this argument is supplied) where the supplied taxon either is
|
299
|
* relatedFrom or relatedTo depending on the <code>direction</code>
|
300
|
* parameter.
|
301
|
*
|
302
|
* @param taxon
|
303
|
* The taxon that is relatedTo
|
304
|
* @param type
|
305
|
* The type of TaxonRelationship (can be null)
|
306
|
* @param pageSize
|
307
|
* The maximum number of relationships returned (can be null for
|
308
|
* all relationships)
|
309
|
* @param pageNumber
|
310
|
* The offset (in pageSize chunks) from the start of the result
|
311
|
* set (0 - based)
|
312
|
* @param orderHints
|
313
|
* Properties to order by
|
314
|
* @param propertyPaths
|
315
|
* Properties to initialize in the returned entities, following
|
316
|
* the syntax described in
|
317
|
* {@link IBeanInitializer#initialize(Object, List)}
|
318
|
* @param direction
|
319
|
* specifies the direction of the relationship
|
320
|
* @return a List of TaxonRelationship instances
|
321
|
*/
|
322
|
public List<TaxonRelationship> getTaxonRelationships(Taxon taxon,
|
323
|
TaxonRelationshipType type, Integer pageSize, Integer pageNumber,
|
324
|
List<OrderHint> orderHints, List<String> propertyPaths,
|
325
|
Direction direction);
|
326
|
|
327
|
/**
|
328
|
* Returns a count of the Synonyms (where relationship.type == type,
|
329
|
* if this argument is supplied) where the supplied taxon is relatedTo.
|
330
|
*
|
331
|
* @param taxon The taxon that is relatedTo
|
332
|
* @param type The type of Synonym (can be null)
|
333
|
* @return the number of Synonym instances
|
334
|
*/
|
335
|
public long countSynonyms(Taxon taxon, SynonymType type);
|
336
|
|
337
|
/**
|
338
|
* Returns the Synonyms (of where relationship.type == type, if this argument is supplied)
|
339
|
* that do have the supplied taxon as accepted taxon.
|
340
|
*
|
341
|
* @param taxon The accepted taxon
|
342
|
* @param type The type of synonym (can be null)
|
343
|
* @param pageSize The maximum number of synonyms returned (can be null for all synonyms)
|
344
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
345
|
* * @param orderHints Properties to order by
|
346
|
* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
|
347
|
* @return a {@link List} of {@link Synonym} instances
|
348
|
*/
|
349
|
public List<Synonym> getSynonyms(Taxon taxon, SynonymType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
350
|
|
351
|
/**
|
352
|
* Returns a count of the synonyms (where relationship.type == type,
|
353
|
* if this argument is supplied) which do have an accepted taxon.
|
354
|
*
|
355
|
* @param synonym The synonym that is relatedFrom
|
356
|
* @param type The type of Synonym (can be null)
|
357
|
* @return the number of Synonym instances
|
358
|
*/
|
359
|
public int countSynonyms(Synonym synonym, SynonymType type);
|
360
|
|
361
|
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath);
|
362
|
|
363
|
public long countTaxaByCommonName(String searchString,
|
364
|
Classification classification, MatchMode matchMode,
|
365
|
Set<NamedArea> namedAreas);
|
366
|
|
367
|
public List<UUID> findIdenticalTaxonNameIds(List<String> propertyPath);
|
368
|
|
369
|
public List<TaxonNameBase> findIdenticalNamesNew(List <String> propertyPaths);
|
370
|
|
371
|
public List<UuidAndTitleCache<IdentifiableEntity>> getTaxaByNameForEditor(boolean doTaxa, boolean doSynonyms, boolean doNamesWithoutTaxa,
|
372
|
boolean doMisappliedNames, boolean doCommonNames,
|
373
|
String queryString, Classification classification,
|
374
|
MatchMode matchMode, Set<NamedArea> namedAreas);
|
375
|
|
376
|
public List<String> taxaByNameNotInDB(List<String> taxonNames);
|
377
|
|
378
|
/**
|
379
|
* This method was originally required when synonyms still had a synonym relationship
|
380
|
* to taxa and could belong to multiple taxa. Now the method might be obsolete.
|
381
|
* @param synonym
|
382
|
* @param classificationFilter
|
383
|
* @param propertyPaths
|
384
|
* @see #countAcceptedTaxonFor(Synonym, Classification)
|
385
|
*/
|
386
|
public Taxon acceptedTaxonFor(Synonym synonym, Classification classificationFilter, List<String> propertyPaths);
|
387
|
|
388
|
/**
|
389
|
* This method was originally required when synonyms still had a synonym relationship
|
390
|
* to taxa and could belong to multiple taxa. Now the method might be obsolete.@param synonym
|
391
|
* @param classificationFilter
|
392
|
*
|
393
|
* @see #acceptedTaxonFor(Synonym, Classification, Integer, Integer, List, List)
|
394
|
*/
|
395
|
public long countAcceptedTaxonFor(Synonym synonym, Classification classificationFilter);
|
396
|
|
397
|
public List<UuidAndTitleCache<IdentifiableEntity>> getTaxaByCommonNameForEditor(
|
398
|
String titleSearchStringSqlized, Classification classification,
|
399
|
MatchMode matchMode, Set namedAreas);
|
400
|
|
401
|
public <S extends TaxonBase> List<Object[]> findByIdentifier(Class<S> clazz, String identifier,
|
402
|
DefinedTerm identifierType, TaxonNode subtreeFilter, MatchMode matchmode,
|
403
|
boolean includeEntity, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
|
404
|
|
405
|
/**
|
406
|
* Counts all taxa which match the given identifier (identifier type, identifier string and match mode).
|
407
|
* Optionally a subtreefilter can be defined.
|
408
|
*
|
409
|
* @param clazz optional, the TaxonBase subclass
|
410
|
* @param identifier the identifier string
|
411
|
* @param identifierType the identifier type
|
412
|
* @param matchmode the match mode for the identifier string
|
413
|
* @param subtreeFilter the subtree filter as taxon node
|
414
|
* @return
|
415
|
*/
|
416
|
public <S extends TaxonBase> int countByIdentifier(Class<S> clazz,
|
417
|
String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter, MatchMode matchmode);
|
418
|
|
419
|
/**
|
420
|
* Counts all taxa which have the given marker of type markerType and with value markerValue.
|
421
|
* Additionally an optional subtreefilter can be defined.
|
422
|
*
|
423
|
* @param clazz
|
424
|
* @param markerType
|
425
|
* @param markerValue
|
426
|
* @param subtreeFilter
|
427
|
* @return
|
428
|
*/
|
429
|
public <S extends TaxonBase> long countByMarker(Class<S> clazz, MarkerType markerType,
|
430
|
Boolean markerValue, TaxonNode subtreeFilter);
|
431
|
|
432
|
/**
|
433
|
* @param clazz
|
434
|
* @param markerType
|
435
|
* @param markerValue
|
436
|
* @param subtreeFilter
|
437
|
* @param includeEntity
|
438
|
* @param pageSize
|
439
|
* @param pageNumber
|
440
|
* @param propertyPaths
|
441
|
* @return
|
442
|
*/
|
443
|
public <S extends TaxonBase> List<Object[]> findByMarker(Class<S> clazz, MarkerType markerType,
|
444
|
Boolean markerValue, TaxonNode subtreeFilter, boolean includeEntity, TaxonTitleType titleType,
|
445
|
Integer pageSize, Integer pageNumber, List<String> propertyPaths);
|
446
|
|
447
|
/**
|
448
|
* @param classification
|
449
|
* @param excludeUuid
|
450
|
* @param limit
|
451
|
* @param pattern
|
452
|
* @return
|
453
|
*/
|
454
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
455
|
Classification classification, Integer limit, String pattern);
|
456
|
|
457
|
/**
|
458
|
* @param types
|
459
|
* @return
|
460
|
*/
|
461
|
public long countTaxonRelationships(Set<TaxonRelationshipType> types);
|
462
|
|
463
|
/**
|
464
|
* @param types
|
465
|
* @param pageSize
|
466
|
* @param pageNumber
|
467
|
* @param orderHints
|
468
|
* @param propertyPaths
|
469
|
* @return
|
470
|
*/
|
471
|
public List<TaxonRelationship> getTaxonRelationships(Set<TaxonRelationshipType> types,
|
472
|
Integer pageSize, Integer pageNumber,
|
473
|
List<OrderHint> orderHints, List<String> propertyPaths);
|
474
|
|
475
|
}
|