1
|
// $Id$
|
2
|
/**
|
3
|
* Copyright (C) 2007 EDIT
|
4
|
* European Distributed Institute of Taxonomy
|
5
|
* http://www.e-taxonomy.eu
|
6
|
*
|
7
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
8
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
9
|
*/
|
10
|
|
11
|
package eu.etaxonomy.cdm.api.service;
|
12
|
|
13
|
import java.util.ArrayList;
|
14
|
import java.util.Comparator;
|
15
|
import java.util.List;
|
16
|
import java.util.Set;
|
17
|
import java.util.UUID;
|
18
|
|
19
|
import org.apache.log4j.Logger;
|
20
|
import org.springframework.beans.factory.annotation.Autowired;
|
21
|
import org.springframework.stereotype.Service;
|
22
|
import org.springframework.transaction.annotation.Propagation;
|
23
|
import org.springframework.transaction.annotation.Transactional;
|
24
|
|
25
|
import eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator;
|
26
|
import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator;
|
27
|
import eu.etaxonomy.cdm.api.service.pager.Pager;
|
28
|
import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
|
29
|
import eu.etaxonomy.cdm.common.IProgressMonitor;
|
30
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
31
|
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
|
32
|
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
|
33
|
import eu.etaxonomy.cdm.model.common.RelationshipBase;
|
34
|
import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
|
35
|
import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
|
36
|
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
|
37
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
38
|
import eu.etaxonomy.cdm.model.media.Media;
|
39
|
import eu.etaxonomy.cdm.model.media.MediaRepresentation;
|
40
|
import eu.etaxonomy.cdm.model.media.MediaUtils;
|
41
|
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
|
42
|
import eu.etaxonomy.cdm.model.name.Rank;
|
43
|
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
44
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
45
|
import eu.etaxonomy.cdm.model.taxon.Classification;
|
46
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
47
|
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
|
48
|
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
|
49
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
50
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
51
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
52
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
|
53
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
|
54
|
import eu.etaxonomy.cdm.persistence.dao.common.IOrderedTermVocabularyDao;
|
55
|
import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;
|
56
|
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
|
57
|
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
|
58
|
import eu.etaxonomy.cdm.persistence.query.MatchMode;
|
59
|
import eu.etaxonomy.cdm.persistence.query.OrderHint;
|
60
|
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
|
61
|
|
62
|
|
63
|
/**
|
64
|
* @author a.kohlbecker
|
65
|
* @date 10.09.2010
|
66
|
*
|
67
|
*/
|
68
|
@Service
|
69
|
@Transactional(propagation = Propagation.SUPPORTS, readOnly = true)
|
70
|
public class TaxonServiceImpl extends IdentifiableServiceBase<TaxonBase,ITaxonDao> implements ITaxonService{
|
71
|
private static final Logger logger = Logger.getLogger(TaxonServiceImpl.class);
|
72
|
|
73
|
@Autowired
|
74
|
private ITaxonNameDao nameDao;
|
75
|
|
76
|
@Autowired
|
77
|
private IOrderedTermVocabularyDao orderedVocabularyDao;
|
78
|
|
79
|
/**
|
80
|
* Constructor
|
81
|
*/
|
82
|
public TaxonServiceImpl(){
|
83
|
if (logger.isDebugEnabled()) { logger.debug("Load TaxonService Bean"); }
|
84
|
}
|
85
|
|
86
|
/**
|
87
|
* FIXME Candidate for harmonization
|
88
|
* rename searchByName ?
|
89
|
*/
|
90
|
public List<TaxonBase> searchTaxaByName(String name, Reference sec) {
|
91
|
return dao.getTaxaByName(name, sec);
|
92
|
}
|
93
|
|
94
|
/**
|
95
|
* FIXME Candidate for harmonization
|
96
|
* list(Synonym.class, ...)
|
97
|
* (non-Javadoc)
|
98
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllSynonyms(int, int)
|
99
|
*/
|
100
|
public List<Synonym> getAllSynonyms(int limit, int start) {
|
101
|
return dao.getAllSynonyms(limit, start);
|
102
|
}
|
103
|
|
104
|
/**
|
105
|
* FIXME Candidate for harmonization
|
106
|
* list(Taxon.class, ...)
|
107
|
* (non-Javadoc)
|
108
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllTaxa(int, int)
|
109
|
*/
|
110
|
public List<Taxon> getAllTaxa(int limit, int start) {
|
111
|
return dao.getAllTaxa(limit, start);
|
112
|
}
|
113
|
|
114
|
/**
|
115
|
* FIXME Candidate for harmonization
|
116
|
* merge with getRootTaxa(Reference sec, ..., ...)
|
117
|
* (non-Javadoc)
|
118
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference, boolean)
|
119
|
*/
|
120
|
public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, boolean onlyWithChildren) {
|
121
|
if (cdmFetch == null){
|
122
|
cdmFetch = CdmFetch.NO_FETCH();
|
123
|
}
|
124
|
return dao.getRootTaxa(sec, cdmFetch, onlyWithChildren, false);
|
125
|
}
|
126
|
|
127
|
|
128
|
/* (non-Javadoc)
|
129
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.name.Rank, eu.etaxonomy.cdm.model.reference.Reference, boolean, boolean)
|
130
|
*/
|
131
|
public List<Taxon> getRootTaxa(Rank rank, Reference sec, boolean onlyWithChildren,boolean withMisapplications, List<String> propertyPaths) {
|
132
|
return dao.getRootTaxa(rank, sec, null, onlyWithChildren, withMisapplications, propertyPaths);
|
133
|
}
|
134
|
|
135
|
/* (non-Javadoc)
|
136
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllRelationships(int, int)
|
137
|
*/
|
138
|
public List<RelationshipBase> getAllRelationships(int limit, int start){
|
139
|
return dao.getAllRelationships(limit, start);
|
140
|
}
|
141
|
|
142
|
/**
|
143
|
* FIXME Candidate for harmonization
|
144
|
* is this the same as termService.getVocabulary(VocabularyEnum.TaxonRelationshipType) ?
|
145
|
*/
|
146
|
@Deprecated
|
147
|
public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary() {
|
148
|
|
149
|
String taxonRelTypeVocabularyId = "15db0cf7-7afc-4a86-a7d4-221c73b0c9ac";
|
150
|
UUID uuid = UUID.fromString(taxonRelTypeVocabularyId);
|
151
|
OrderedTermVocabulary<TaxonRelationshipType> taxonRelTypeVocabulary =
|
152
|
(OrderedTermVocabulary)orderedVocabularyDao.findByUuid(uuid);
|
153
|
return taxonRelTypeVocabulary;
|
154
|
}
|
155
|
|
156
|
|
157
|
|
158
|
/*
|
159
|
* (non-Javadoc)
|
160
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#swapSynonymWithAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym)
|
161
|
*/
|
162
|
@Transactional(readOnly = false)
|
163
|
public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon){
|
164
|
|
165
|
TaxonNameBase synonymName = synonym.getName();
|
166
|
synonymName.removeTaxonBase(synonym);
|
167
|
TaxonNameBase taxonName = acceptedTaxon.getName();
|
168
|
taxonName.removeTaxonBase(acceptedTaxon);
|
169
|
|
170
|
synonym.setName(taxonName);
|
171
|
acceptedTaxon.setName(synonymName);
|
172
|
|
173
|
// the accepted taxon needs a new uuid because the concept has changed
|
174
|
// FIXME this leads to an error "HibernateException: immutable natural identifier of an instance of eu.etaxonomy.cdm.model.taxon.Taxon was altered"
|
175
|
//acceptedTaxon.setUuid(UUID.randomUUID());
|
176
|
}
|
177
|
|
178
|
|
179
|
/* (non-Javadoc)
|
180
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#changeSynonymToAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)
|
181
|
*/
|
182
|
//TODO correct delete handling still needs to be implemented / checked
|
183
|
@Override
|
184
|
@Transactional(readOnly = false)
|
185
|
public Taxon changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, boolean deleteSynonym, boolean copyCitationInfo, Reference citation, String microCitation) throws IllegalArgumentException{
|
186
|
|
187
|
TaxonNameBase acceptedName = acceptedTaxon.getName();
|
188
|
TaxonNameBase synonymName = synonym.getName();
|
189
|
HomotypicalGroup synonymHomotypicGroup = synonymName.getHomotypicalGroup();
|
190
|
if (acceptedName.getHomotypicalGroup().equals(synonymHomotypicGroup)){
|
191
|
String message = "The accepted taxon and the synonym are part of the same homotypical group and therefore can not be both accepted.";
|
192
|
throw new IllegalArgumentException(message);
|
193
|
}
|
194
|
|
195
|
Taxon newAcceptedTaxon = Taxon.NewInstance(synonymName, acceptedTaxon.getSec());
|
196
|
|
197
|
SynonymRelationshipType relType = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF();
|
198
|
List<Synonym> heteroSynonyms = synonymHomotypicGroup.getSynonymsInGroup(acceptedTaxon.getSec());
|
199
|
for (Synonym heteroSynonym : heteroSynonyms){
|
200
|
if (synonym.equals(heteroSynonym)){
|
201
|
acceptedTaxon.removeSynonym(heteroSynonym, false);
|
202
|
}else{
|
203
|
heteroSynonym.replaceAcceptedTaxon(newAcceptedTaxon, relType, copyCitationInfo, citation, microCitation);
|
204
|
}
|
205
|
}
|
206
|
|
207
|
//synonym.getName().removeTaxonBase(synonym);
|
208
|
//TODO correct delete handling still needs to be implemented / checked
|
209
|
if (deleteSynonym){
|
210
|
try {
|
211
|
this.dao.flush();
|
212
|
this.delete(synonym);
|
213
|
|
214
|
} catch (Exception e) {
|
215
|
logger.info("Can't delete old synonym from database");
|
216
|
}
|
217
|
}
|
218
|
|
219
|
|
220
|
return newAcceptedTaxon;
|
221
|
}
|
222
|
|
223
|
public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference citation, String microcitation){
|
224
|
|
225
|
// Get name from synonym
|
226
|
TaxonNameBase<?, ?> synonymName = synonym.getName();
|
227
|
|
228
|
// remove synonym from taxon
|
229
|
toTaxon.removeSynonym(synonym);
|
230
|
|
231
|
// Create a taxon with synonym name
|
232
|
Taxon fromTaxon = Taxon.NewInstance(synonymName, null);
|
233
|
|
234
|
// Add taxon relation
|
235
|
fromTaxon.addTaxonRelation(toTaxon, taxonRelationshipType, citation, microcitation);
|
236
|
|
237
|
// since we are swapping names, we have to detach the name from the synonym completely.
|
238
|
// Otherwise the synonym will still be in the list of typified names.
|
239
|
synonym.getName().removeTaxonBase(synonym);
|
240
|
|
241
|
return fromTaxon;
|
242
|
}
|
243
|
|
244
|
/* (non-Javadoc)
|
245
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#changeHomotypicalGroupOfSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.name.HomotypicalGroup, eu.etaxonomy.cdm.model.taxon.Taxon, boolean, boolean)
|
246
|
*/
|
247
|
@Transactional(readOnly = false)
|
248
|
@Override
|
249
|
public void changeHomotypicalGroupOfSynonym(Synonym synonym, HomotypicalGroup newHomotypicalGroup, Taxon targetTaxon,
|
250
|
boolean removeFromOtherTaxa, boolean setBasionymRelationIfApplicable){
|
251
|
// Get synonym name
|
252
|
TaxonNameBase synonymName = synonym.getName();
|
253
|
HomotypicalGroup oldHomotypicalGroup = synonymName.getHomotypicalGroup();
|
254
|
|
255
|
|
256
|
// Switch groups
|
257
|
oldHomotypicalGroup.removeTypifiedName(synonymName);
|
258
|
newHomotypicalGroup.addTypifiedName(synonymName);
|
259
|
|
260
|
//remove existing basionym relationships
|
261
|
synonymName.removeBasionyms();
|
262
|
|
263
|
//add basionym relationship
|
264
|
if (setBasionymRelationIfApplicable){
|
265
|
Set<TaxonNameBase> basionyms = newHomotypicalGroup.getBasionyms();
|
266
|
for (TaxonNameBase basionym : basionyms){
|
267
|
synonymName.addBasionym(basionym);
|
268
|
}
|
269
|
}
|
270
|
|
271
|
//set synonym relationship correctly
|
272
|
// SynonymRelationship relToTaxon = null;
|
273
|
boolean relToTargetTaxonExists = false;
|
274
|
Set<SynonymRelationship> existingRelations = synonym.getSynonymRelations();
|
275
|
for (SynonymRelationship rel : existingRelations){
|
276
|
Taxon acceptedTaxon = rel.getAcceptedTaxon();
|
277
|
boolean isTargetTaxon = acceptedTaxon != null && acceptedTaxon.equals(targetTaxon);
|
278
|
HomotypicalGroup acceptedGroup = acceptedTaxon.getHomotypicGroup();
|
279
|
boolean isHomotypicToTaxon = acceptedGroup.equals(newHomotypicalGroup);
|
280
|
SynonymRelationshipType newRelationType = isHomotypicToTaxon? SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF() : SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
|
281
|
rel.setType(newRelationType);
|
282
|
//TODO handle citation and microCitation
|
283
|
|
284
|
if (isTargetTaxon){
|
285
|
relToTargetTaxonExists = true;
|
286
|
}else{
|
287
|
if (removeFromOtherTaxa){
|
288
|
acceptedTaxon.removeSynonym(synonym, false);
|
289
|
}else{
|
290
|
//do nothing
|
291
|
}
|
292
|
}
|
293
|
}
|
294
|
if (targetTaxon != null && ! relToTargetTaxonExists ){
|
295
|
Taxon acceptedTaxon = targetTaxon;
|
296
|
HomotypicalGroup acceptedGroup = acceptedTaxon.getHomotypicGroup();
|
297
|
boolean isHomotypicToTaxon = acceptedGroup.equals(newHomotypicalGroup);
|
298
|
SynonymRelationshipType relType = isHomotypicToTaxon? SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF() : SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
|
299
|
//TODO handle citation and microCitation
|
300
|
Reference citation = null;
|
301
|
String microCitation = null;
|
302
|
acceptedTaxon.addSynonym(synonym, relType, citation, microCitation);
|
303
|
}
|
304
|
|
305
|
}
|
306
|
|
307
|
|
308
|
/* (non-Javadoc)
|
309
|
* @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
|
310
|
*/
|
311
|
@Override
|
312
|
public void updateTitleCache(Class<? extends TaxonBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<TaxonBase> cacheStrategy, IProgressMonitor monitor) {
|
313
|
if (clazz == null){
|
314
|
clazz = TaxonBase.class;
|
315
|
}
|
316
|
super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
|
317
|
}
|
318
|
|
319
|
@Autowired
|
320
|
protected void setDao(ITaxonDao dao) {
|
321
|
this.dao = dao;
|
322
|
}
|
323
|
|
324
|
/* (non-Javadoc)
|
325
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaByName(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, java.lang.Integer, java.lang.Integer)
|
326
|
*/
|
327
|
public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
|
328
|
Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank);
|
329
|
|
330
|
List<TaxonBase> results = new ArrayList<TaxonBase>();
|
331
|
if(numberOfResults > 0) { // no point checking again
|
332
|
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber);
|
333
|
}
|
334
|
|
335
|
return new DefaultPagerImpl<TaxonBase>(pageNumber, numberOfResults, pageSize, results);
|
336
|
}
|
337
|
|
338
|
/* (non-Javadoc)
|
339
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listTaxaByName(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, java.lang.Integer, java.lang.Integer)
|
340
|
*/
|
341
|
public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
|
342
|
Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank);
|
343
|
|
344
|
List<TaxonBase> results = new ArrayList<TaxonBase>();
|
345
|
if(numberOfResults > 0) { // no point checking again
|
346
|
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber);
|
347
|
}
|
348
|
|
349
|
return results;
|
350
|
}
|
351
|
|
352
|
/* (non-Javadoc)
|
353
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listToTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
354
|
*/
|
355
|
public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
|
356
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);
|
357
|
|
358
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
359
|
if(numberOfResults > 0) { // no point checking again
|
360
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedTo);
|
361
|
}
|
362
|
return results;
|
363
|
}
|
364
|
|
365
|
/* (non-Javadoc)
|
366
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#pageToTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
367
|
*/
|
368
|
public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
369
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);
|
370
|
|
371
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
372
|
if(numberOfResults > 0) { // no point checking again
|
373
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedTo);
|
374
|
}
|
375
|
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results);
|
376
|
}
|
377
|
|
378
|
/* (non-Javadoc)
|
379
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listFromTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
380
|
*/
|
381
|
public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
|
382
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom);
|
383
|
|
384
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
385
|
if(numberOfResults > 0) { // no point checking again
|
386
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedFrom);
|
387
|
}
|
388
|
return results;
|
389
|
}
|
390
|
|
391
|
/* (non-Javadoc)
|
392
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#pageFromTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
393
|
*/
|
394
|
public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
395
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom);
|
396
|
|
397
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
398
|
if(numberOfResults > 0) { // no point checking again
|
399
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedFrom);
|
400
|
}
|
401
|
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results);
|
402
|
}
|
403
|
|
404
|
/* (non-Javadoc)
|
405
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getSynonyms(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
406
|
*/
|
407
|
public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
408
|
Integer numberOfResults = dao.countSynonyms(taxon, type);
|
409
|
|
410
|
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
411
|
if(numberOfResults > 0) { // no point checking again
|
412
|
results = dao.getSynonyms(taxon, type, pageSize, pageNumber, orderHints, propertyPaths);
|
413
|
}
|
414
|
|
415
|
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
|
416
|
}
|
417
|
|
418
|
/* (non-Javadoc)
|
419
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getSynonyms(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
420
|
*/
|
421
|
public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
422
|
Integer numberOfResults = dao.countSynonyms(synonym, type);
|
423
|
|
424
|
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
425
|
if(numberOfResults > 0) { // no point checking again
|
426
|
results = dao.getSynonyms(synonym, type, pageSize, pageNumber, orderHints, propertyPaths);
|
427
|
}
|
428
|
|
429
|
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
|
430
|
}
|
431
|
|
432
|
/* (non-Javadoc)
|
433
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getHomotypicSynonymsByHomotypicGroup(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)
|
434
|
*/
|
435
|
public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths){
|
436
|
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
|
437
|
return t.getHomotypicSynonymsByHomotypicGroup();
|
438
|
}
|
439
|
|
440
|
/* (non-Javadoc)
|
441
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getHeterotypicSynonymyGroups(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)
|
442
|
*/
|
443
|
public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths){
|
444
|
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
|
445
|
List<HomotypicalGroup> hsgl = t.getHeterotypicSynonymyGroups();
|
446
|
List<List<Synonym>> heterotypicSynonymyGroups = new ArrayList<List<Synonym>>(hsgl.size());
|
447
|
for(HomotypicalGroup hsg : hsgl){
|
448
|
heterotypicSynonymyGroups.add(hsg.getSynonymsInGroup(t.getSec()));
|
449
|
}
|
450
|
return heterotypicSynonymyGroups;
|
451
|
}
|
452
|
|
453
|
public List<UuidAndTitleCache<TaxonBase>> findTaxaAndNamesForEditor(ITaxonServiceConfigurator configurator){
|
454
|
|
455
|
List<UuidAndTitleCache<TaxonBase>> result = new ArrayList<UuidAndTitleCache<TaxonBase>>();
|
456
|
Class<? extends TaxonBase> clazz = null;
|
457
|
if ((configurator.isDoTaxa() && configurator.isDoSynonyms())) {
|
458
|
clazz = TaxonBase.class;
|
459
|
//propertyPath.addAll(configurator.getTaxonPropertyPath());
|
460
|
//propertyPath.addAll(configurator.getSynonymPropertyPath());
|
461
|
} else if(configurator.isDoTaxa()) {
|
462
|
clazz = Taxon.class;
|
463
|
//propertyPath = configurator.getTaxonPropertyPath();
|
464
|
} else if (configurator.isDoSynonyms()) {
|
465
|
clazz = Synonym.class;
|
466
|
//propertyPath = configurator.getSynonymPropertyPath();
|
467
|
}
|
468
|
|
469
|
|
470
|
result = dao.getTaxaByNameForEditor(clazz, configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas());
|
471
|
return result;
|
472
|
}
|
473
|
/* (non-Javadoc)
|
474
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaAndNames(eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator)
|
475
|
*/
|
476
|
public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator) {
|
477
|
|
478
|
List<IdentifiableEntity> results = new ArrayList<IdentifiableEntity>();
|
479
|
int numberOfResults = 0; // overall number of results (as opposed to number of results per page)
|
480
|
List<TaxonBase> taxa = null;
|
481
|
|
482
|
// Taxa and synonyms
|
483
|
long numberTaxaResults = 0L;
|
484
|
|
485
|
Class<? extends TaxonBase> clazz = null;
|
486
|
List<String> propertyPath = new ArrayList<String>();
|
487
|
if(configurator.getTaxonPropertyPath() != null){
|
488
|
propertyPath.addAll(configurator.getTaxonPropertyPath());
|
489
|
}
|
490
|
if ((configurator.isDoTaxa() && configurator.isDoSynonyms())) {
|
491
|
clazz = TaxonBase.class;
|
492
|
//propertyPath.addAll(configurator.getTaxonPropertyPath());
|
493
|
//propertyPath.addAll(configurator.getSynonymPropertyPath());
|
494
|
} else if(configurator.isDoTaxa()) {
|
495
|
clazz = Taxon.class;
|
496
|
//propertyPath = configurator.getTaxonPropertyPath();
|
497
|
} else if (configurator.isDoSynonyms()) {
|
498
|
clazz = Synonym.class;
|
499
|
//propertyPath = configurator.getSynonymPropertyPath();
|
500
|
}
|
501
|
|
502
|
if(clazz != null){
|
503
|
if(configurator.getPageSize() != null){ // no point counting if we need all anyway
|
504
|
numberTaxaResults =
|
505
|
dao.countTaxaByName(clazz,
|
506
|
configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(),
|
507
|
configurator.getNamedAreas());
|
508
|
}
|
509
|
|
510
|
if(configurator.getPageSize() == null || numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){ // no point checking again if less results
|
511
|
taxa = dao.getTaxaByName(clazz,
|
512
|
configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(),
|
513
|
configurator.getNamedAreas(), configurator.getPageSize(),
|
514
|
configurator.getPageNumber(), propertyPath);
|
515
|
}
|
516
|
}
|
517
|
|
518
|
if (logger.isDebugEnabled()) { logger.debug(numberTaxaResults + " matching taxa counted"); }
|
519
|
|
520
|
if(taxa != null){
|
521
|
results.addAll(taxa);
|
522
|
}
|
523
|
|
524
|
numberOfResults += numberTaxaResults;
|
525
|
|
526
|
// Names without taxa
|
527
|
if (configurator.isDoNamesWithoutTaxa()) {
|
528
|
int numberNameResults = 0;
|
529
|
|
530
|
List<? extends TaxonNameBase<?,?>> names =
|
531
|
nameDao.findByName(configurator.getTitleSearchStringSqlized(), configurator.getMatchMode(),
|
532
|
configurator.getPageSize(), configurator.getPageNumber(), null, configurator.getTaxonNamePropertyPath());
|
533
|
if (logger.isDebugEnabled()) { logger.debug(names.size() + " matching name(s) found"); }
|
534
|
if (names.size() > 0) {
|
535
|
for (TaxonNameBase<?,?> taxonName : names) {
|
536
|
if (taxonName.getTaxonBases().size() == 0) {
|
537
|
results.add(taxonName);
|
538
|
numberNameResults++;
|
539
|
}
|
540
|
}
|
541
|
if (logger.isDebugEnabled()) { logger.debug(numberNameResults + " matching name(s) without taxa found"); }
|
542
|
numberOfResults += numberNameResults;
|
543
|
}
|
544
|
}
|
545
|
|
546
|
// Taxa from common names
|
547
|
|
548
|
if (configurator.isDoTaxaByCommonNames()) {
|
549
|
taxa = null;
|
550
|
numberTaxaResults = 0;
|
551
|
if(configurator.getPageSize() != null){// no point counting if we need all anyway
|
552
|
numberTaxaResults = dao.countTaxaByCommonName(configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas());
|
553
|
}
|
554
|
if(configurator.getPageSize() == null || numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){
|
555
|
taxa = dao.getTaxaByCommonName(configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas(), configurator.getPageSize(), configurator.getPageNumber(), configurator.getTaxonPropertyPath());
|
556
|
}
|
557
|
if(taxa != null){
|
558
|
results.addAll(taxa);
|
559
|
}
|
560
|
numberOfResults += numberTaxaResults;
|
561
|
|
562
|
}
|
563
|
|
564
|
return new DefaultPagerImpl<IdentifiableEntity>
|
565
|
(configurator.getPageNumber(), numberOfResults, configurator.getPageSize(), results);
|
566
|
}
|
567
|
|
568
|
public List<UuidAndTitleCache<TaxonBase>> getTaxonUuidAndTitleCache(){
|
569
|
return dao.getUuidAndTitleCache();
|
570
|
}
|
571
|
|
572
|
/* (non-Javadoc)
|
573
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllMedia(eu.etaxonomy.cdm.model.taxon.Taxon, int, int, int, java.lang.String[])
|
574
|
*/
|
575
|
public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes){
|
576
|
List<MediaRepresentation> medRep = new ArrayList<MediaRepresentation>();
|
577
|
taxon = (Taxon)dao.load(taxon.getUuid());
|
578
|
Set<TaxonDescription> descriptions = taxon.getDescriptions();
|
579
|
for (TaxonDescription taxDesc: descriptions){
|
580
|
Set<DescriptionElementBase> elements = taxDesc.getElements();
|
581
|
for (DescriptionElementBase descElem: elements){
|
582
|
for(Media media : descElem.getMedia()){
|
583
|
|
584
|
//find the best matching representation
|
585
|
medRep.add(MediaUtils.findBestMatchingRepresentation(media, null, size, height, widthOrDuration, mimeTypes));
|
586
|
|
587
|
}
|
588
|
}
|
589
|
}
|
590
|
return medRep;
|
591
|
}
|
592
|
|
593
|
/* (non-Javadoc)
|
594
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaByID(java.util.Set)
|
595
|
*/
|
596
|
public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs) {
|
597
|
return this.dao.findById(listOfIDs);
|
598
|
}
|
599
|
|
600
|
/* (non-Javadoc)
|
601
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#countAllRelationships()
|
602
|
*/
|
603
|
public int countAllRelationships() {
|
604
|
return this.dao.countAllRelationships();
|
605
|
}
|
606
|
|
607
|
/* (non-Javadoc)
|
608
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#createAllInferredSynonyms(eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.model.taxon.Taxon)
|
609
|
*/
|
610
|
public List<Synonym> createAllInferredSynonyms(Classification tree,
|
611
|
Taxon taxon) {
|
612
|
|
613
|
return this.dao.createAllInferredSynonyms(taxon, tree);
|
614
|
}
|
615
|
|
616
|
/* (non-Javadoc)
|
617
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#createInferredSynonyms(eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType)
|
618
|
*/
|
619
|
public List<Synonym> createInferredSynonyms(Classification tree, Taxon taxon, SynonymRelationshipType type) {
|
620
|
|
621
|
return this.dao.createInferredSynonyms(taxon, tree, type);
|
622
|
}
|
623
|
|
624
|
/* (non-Javadoc)
|
625
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNames(java.util.List)
|
626
|
*/
|
627
|
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath) {
|
628
|
|
629
|
return this.dao.findIdenticalTaxonNames(propertyPath);
|
630
|
}
|
631
|
|
632
|
/* (non-Javadoc)
|
633
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNameIds(java.util.List)
|
634
|
*/
|
635
|
public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath) {
|
636
|
|
637
|
return this.dao.findIdenticalNamesNew(propertyPath);
|
638
|
}
|
639
|
|
640
|
/* (non-Javadoc)
|
641
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getPhylumName(eu.etaxonomy.cdm.model.name.TaxonNameBase)
|
642
|
*/
|
643
|
public String getPhylumName(TaxonNameBase name){
|
644
|
return this.dao.getPhylumName(name);
|
645
|
}
|
646
|
|
647
|
/* (non-Javadoc)
|
648
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#deleteSynonymRelationships(eu.etaxonomy.cdm.model.taxon.Synonym)
|
649
|
*/
|
650
|
public long deleteSynonymRelationships(Synonym syn) {
|
651
|
|
652
|
return dao.deleteSynonymRelationships(syn);
|
653
|
}
|
654
|
|
655
|
|
656
|
/* (non-Javadoc)
|
657
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listSynonymRelationships(eu.etaxonomy.cdm.model.taxon.TaxonBase, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction)
|
658
|
*/
|
659
|
public List<SynonymRelationship> listSynonymRelationships(
|
660
|
TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber,
|
661
|
List<OrderHint> orderHints, List<String> propertyPaths, Direction direction) {
|
662
|
Integer numberOfResults = dao.countSynonymRelationships(taxonBase, type, direction);
|
663
|
|
664
|
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
665
|
if(numberOfResults > 0) { // no point checking again
|
666
|
results = dao.getSynonymRelationships(taxonBase, type, pageSize, pageNumber, orderHints, propertyPaths, direction);
|
667
|
}
|
668
|
return results;
|
669
|
}
|
670
|
|
671
|
/* (non-Javadoc)
|
672
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findBestMatchingTaxon(java.lang.String)
|
673
|
*/
|
674
|
@Override
|
675
|
public Taxon findBestMatchingTaxon(String taxonName) {
|
676
|
MatchingTaxonConfigurator config = MatchingTaxonConfigurator.NewInstance();
|
677
|
config.setTaxonNameTitle(taxonName);
|
678
|
return findBestMatchingTaxon(config);
|
679
|
}
|
680
|
|
681
|
|
682
|
|
683
|
@Override
|
684
|
public Taxon findBestMatchingTaxon(MatchingTaxonConfigurator config) {
|
685
|
|
686
|
Taxon bestCandidate = null;
|
687
|
try{
|
688
|
// 1. search for acceptet taxa
|
689
|
List<TaxonBase> taxonList = dao.findByNameTitleCache(Taxon.class, config.getTaxonNameTitle(), null, MatchMode.EXACT, null, 0, null, null);
|
690
|
boolean bestCandidateMatchesSecUuid = false;
|
691
|
boolean bestCandidateIsInClassification = false;
|
692
|
int countEqualCandidates = 0;
|
693
|
for(TaxonBase taxonBaseCandidate : taxonList){
|
694
|
if(taxonBaseCandidate instanceof Taxon){
|
695
|
Taxon newCanditate = CdmBase.deproxy(taxonBaseCandidate, Taxon.class);
|
696
|
boolean newCandidateMatchesSecUuid = isMatchesSecUuid(newCanditate, config);
|
697
|
if (! newCandidateMatchesSecUuid && config.isOnlyMatchingSecUuid() ){
|
698
|
continue;
|
699
|
}else if(newCandidateMatchesSecUuid && ! bestCandidateMatchesSecUuid){
|
700
|
bestCandidate = newCanditate;
|
701
|
countEqualCandidates = 1;
|
702
|
bestCandidateMatchesSecUuid = true;
|
703
|
continue;
|
704
|
}
|
705
|
|
706
|
boolean newCandidateInClassification = isInClassification(newCanditate, config);
|
707
|
if (! newCandidateInClassification && config.isOnlyMatchingClassificationUuid()){
|
708
|
continue;
|
709
|
}else if (newCandidateInClassification && ! bestCandidateIsInClassification){
|
710
|
bestCandidate = newCanditate;
|
711
|
countEqualCandidates = 1;
|
712
|
bestCandidateIsInClassification = true;
|
713
|
continue;
|
714
|
}
|
715
|
if (bestCandidate == null){
|
716
|
bestCandidate = newCanditate;
|
717
|
countEqualCandidates = 1;
|
718
|
continue;
|
719
|
}
|
720
|
|
721
|
}else{ //not Taxon.class
|
722
|
continue;
|
723
|
}
|
724
|
countEqualCandidates++;
|
725
|
|
726
|
}
|
727
|
if (bestCandidate != null){
|
728
|
if(countEqualCandidates > 1){
|
729
|
logger.info(countEqualCandidates + " equally matching TaxonBases found, using first accepted Taxon: " + bestCandidate.getTitleCache());
|
730
|
return bestCandidate;
|
731
|
} else {
|
732
|
logger.info("using accepted Taxon: " + bestCandidate.getTitleCache());
|
733
|
return bestCandidate;
|
734
|
}
|
735
|
}
|
736
|
|
737
|
|
738
|
// 2. search for synonyms
|
739
|
if (config.isIncludeSynonyms()){
|
740
|
List<TaxonBase> synonymList = dao.findByNameTitleCache(Synonym.class, config.getTaxonNameTitle(), null, MatchMode.EXACT, null, 0, null, null);
|
741
|
for(TaxonBase taxonBase : synonymList){
|
742
|
if(taxonBase instanceof Synonym){
|
743
|
Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
|
744
|
Set<Taxon> acceptetdCandidates = synonym.getAcceptedTaxa();
|
745
|
if(!acceptetdCandidates.isEmpty()){
|
746
|
bestCandidate = acceptetdCandidates.iterator().next();
|
747
|
if(acceptetdCandidates.size() == 1){
|
748
|
logger.info(acceptetdCandidates.size() + " Accepted taxa found for synonym " + taxonBase.getTitleCache() + ", using first one: " + bestCandidate.getTitleCache());
|
749
|
return bestCandidate;
|
750
|
} else {
|
751
|
logger.info("using accepted Taxon " + bestCandidate.getTitleCache() + "for synonym " + taxonBase.getTitleCache());
|
752
|
return bestCandidate;
|
753
|
}
|
754
|
//TODO extend method: search using treeUUID, using SecUUID, first find accepted then include synonyms until a matching taxon is found
|
755
|
}
|
756
|
}
|
757
|
}
|
758
|
}
|
759
|
|
760
|
} catch (Exception e){
|
761
|
logger.error(e);
|
762
|
}
|
763
|
|
764
|
return bestCandidate;
|
765
|
}
|
766
|
|
767
|
private boolean isInClassification(Taxon taxon, MatchingTaxonConfigurator config) {
|
768
|
UUID configClassificationUuid = config.getClassificationUuid();
|
769
|
if (configClassificationUuid == null){
|
770
|
return false;
|
771
|
}
|
772
|
for (TaxonNode node : taxon.getTaxonNodes()){
|
773
|
UUID classUuid = node.getClassification().getUuid();
|
774
|
if (configClassificationUuid.equals(classUuid)){
|
775
|
return true;
|
776
|
}
|
777
|
}
|
778
|
return false;
|
779
|
}
|
780
|
|
781
|
private boolean isMatchesSecUuid(Taxon taxon, MatchingTaxonConfigurator config) {
|
782
|
UUID configSecUuid = config.getSecUuid();
|
783
|
if (configSecUuid == null){
|
784
|
return false;
|
785
|
}
|
786
|
UUID taxonSecUuid = (taxon.getSec() == null)? null : taxon.getSec().getUuid();
|
787
|
return configSecUuid.equals(taxonSecUuid);
|
788
|
}
|
789
|
|
790
|
/* (non-Javadoc)
|
791
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findBestMatchingSynonym(java.lang.String)
|
792
|
*/
|
793
|
@Override
|
794
|
public Synonym findBestMatchingSynonym(String taxonName) {
|
795
|
List<TaxonBase> synonymList = dao.findByNameTitleCache(Synonym.class, taxonName, null, MatchMode.EXACT, null, 0, null, null);
|
796
|
if(! synonymList.isEmpty()){
|
797
|
Synonym result = CdmBase.deproxy(synonymList.iterator().next(), Synonym.class);
|
798
|
if(synonymList.size() == 1){
|
799
|
logger.info(synonymList.size() + " Synonym found " + result.getTitleCache() );
|
800
|
return result;
|
801
|
} else {
|
802
|
logger.info("Several matching synonyms found. Using first: " + result.getTitleCache());
|
803
|
return result;
|
804
|
}
|
805
|
}
|
806
|
return null;
|
807
|
}
|
808
|
|
809
|
/* (non-Javadoc)
|
810
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#moveSynonymToAnotherTaxon(eu.etaxonomy.cdm.model.taxon.SynonymRelationship, eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)
|
811
|
*/
|
812
|
@Override
|
813
|
public Taxon moveSynonymToAnotherTaxon(SynonymRelationship synonymRelation,
|
814
|
Taxon toTaxon, SynonymRelationshipType synonymRelationshipType, Reference reference, String referenceDetail) {
|
815
|
Taxon fromTaxon = synonymRelation.getAcceptedTaxon();
|
816
|
|
817
|
toTaxon.addSynonym(synonymRelation.getSynonym(), synonymRelationshipType, reference, referenceDetail);
|
818
|
|
819
|
fromTaxon.removeSynonymRelation(synonymRelation);
|
820
|
|
821
|
return toTaxon;
|
822
|
}
|
823
|
|
824
|
/* (non-Javadoc)
|
825
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheTaxon()
|
826
|
*/
|
827
|
@Override
|
828
|
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheTaxon() {
|
829
|
return dao.getUuidAndTitleCacheTaxon();
|
830
|
}
|
831
|
|
832
|
/* (non-Javadoc)
|
833
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheSynonym()
|
834
|
*/
|
835
|
@Override
|
836
|
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheSynonym() {
|
837
|
return dao.getUuidAndTitleCacheSynonym();
|
838
|
}
|
839
|
|
840
|
|
841
|
}
|