1
|
/**
|
2
|
* Copyright (C) 2008 EDIT
|
3
|
* European Distributed Institute of Taxonomy
|
4
|
* http://www.e-taxonomy.eu
|
5
|
*/
|
6
|
|
7
|
package eu.etaxonomy.cdm.persistence.dao.hibernate.occurrence;
|
8
|
|
9
|
import java.util.ArrayList;
|
10
|
import java.util.Collection;
|
11
|
import java.util.Collections;
|
12
|
import java.util.HashSet;
|
13
|
import java.util.List;
|
14
|
import java.util.Set;
|
15
|
import java.util.UUID;
|
16
|
|
17
|
import org.apache.log4j.Logger;
|
18
|
import org.hibernate.Criteria;
|
19
|
import org.hibernate.Hibernate;
|
20
|
import org.hibernate.Query;
|
21
|
import org.hibernate.Session;
|
22
|
import org.hibernate.criterion.Disjunction;
|
23
|
import org.hibernate.criterion.ProjectionList;
|
24
|
import org.hibernate.criterion.Projections;
|
25
|
import org.hibernate.criterion.Restrictions;
|
26
|
import org.hibernate.envers.query.AuditEntity;
|
27
|
import org.hibernate.envers.query.AuditQuery;
|
28
|
import org.hibernate.search.FullTextSession;
|
29
|
import org.hibernate.search.Search;
|
30
|
import org.springframework.beans.factory.annotation.Autowired;
|
31
|
import org.springframework.stereotype.Repository;
|
32
|
|
33
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
34
|
import eu.etaxonomy.cdm.model.description.DescriptionBase;
|
35
|
import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
|
36
|
import eu.etaxonomy.cdm.model.media.Media;
|
37
|
import eu.etaxonomy.cdm.model.molecular.DnaSample;
|
38
|
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
|
39
|
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
|
40
|
import eu.etaxonomy.cdm.model.name.TaxonName;
|
41
|
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
|
42
|
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
|
43
|
import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
|
44
|
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
|
45
|
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
|
46
|
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
|
47
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
48
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
49
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
50
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
51
|
import eu.etaxonomy.cdm.model.view.AuditEvent;
|
52
|
import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;
|
53
|
import eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase;
|
54
|
import eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl;
|
55
|
import eu.etaxonomy.cdm.persistence.dao.name.IHomotypicalGroupDao;
|
56
|
import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;
|
57
|
import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
|
58
|
import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
|
59
|
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
|
60
|
import eu.etaxonomy.cdm.persistence.query.MatchMode;
|
61
|
import eu.etaxonomy.cdm.persistence.query.OrderHint;
|
62
|
|
63
|
/**
|
64
|
* @author a.babadshanjan
|
65
|
* @since 01.09.2008
|
66
|
*/
|
67
|
@Repository
|
68
|
public class OccurrenceDaoHibernateImpl
|
69
|
extends IdentifiableDaoBase<SpecimenOrObservationBase>
|
70
|
implements IOccurrenceDao {
|
71
|
|
72
|
@SuppressWarnings("unused")
|
73
|
private static final Logger logger = Logger.getLogger(TaxonDaoHibernateImpl.class);
|
74
|
|
75
|
@Autowired
|
76
|
private IDescriptionDao descriptionDao;
|
77
|
|
78
|
@Autowired
|
79
|
private ITaxonNameDao taxonNameDao;
|
80
|
|
81
|
@Autowired
|
82
|
private IHomotypicalGroupDao homotypicalGroupDao;
|
83
|
|
84
|
public OccurrenceDaoHibernateImpl() {
|
85
|
super(SpecimenOrObservationBase.class);
|
86
|
indexedClasses = new Class[7];
|
87
|
indexedClasses[0] = FieldUnit.class;
|
88
|
indexedClasses[1] = DerivedUnit.class;
|
89
|
indexedClasses[5] = DnaSample.class;
|
90
|
}
|
91
|
|
92
|
@Override
|
93
|
public int countDerivationEvents(SpecimenOrObservationBase occurence) {
|
94
|
checkNotInPriorView("OccurrenceDaoHibernateImpl.countDerivationEvents(SpecimenOrObservationBase occurence)");
|
95
|
Query query = getSession().createQuery("select count(distinct derivationEvent) from DerivationEvent derivationEvent join derivationEvent.originals occurence where occurence = :occurence");
|
96
|
query.setParameter("occurence", occurence);
|
97
|
|
98
|
return ((Long)query.uniqueResult()).intValue();
|
99
|
}
|
100
|
|
101
|
@Override
|
102
|
public int countDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase) {
|
103
|
AuditEvent auditEvent = getAuditEventFromContext();
|
104
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
105
|
Criteria criteria = getSession().createCriteria(DeterminationEvent.class);
|
106
|
if(occurrence != null) {
|
107
|
criteria.add(Restrictions.eq("identifiedUnit",occurrence));
|
108
|
}
|
109
|
|
110
|
if(taxonBase != null) {
|
111
|
criteria.add(Restrictions.eq("taxon",taxonBase));
|
112
|
}
|
113
|
|
114
|
criteria.setProjection(Projections.rowCount());
|
115
|
return ((Number)criteria.uniqueResult()).intValue();
|
116
|
} else {
|
117
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(DeterminationEvent.class,auditEvent.getRevisionNumber());
|
118
|
|
119
|
if(occurrence != null) {
|
120
|
query.add(AuditEntity.relatedId("identifiedUnit").eq(occurrence.getId()));
|
121
|
}
|
122
|
|
123
|
if(taxonBase != null) {
|
124
|
query.add(AuditEntity.relatedId("taxon").eq(taxonBase.getId()));
|
125
|
}
|
126
|
query.addProjection(AuditEntity.id().count());
|
127
|
|
128
|
return ((Long)query.getSingleResult()).intValue();
|
129
|
}
|
130
|
}
|
131
|
|
132
|
@Override
|
133
|
public int countMedia(SpecimenOrObservationBase occurence) {
|
134
|
checkNotInPriorView("OccurrenceDaoHibernateImpl.countMedia(SpecimenOrObservationBase occurence)");
|
135
|
Query query = getSession().createQuery("select count(media) from SpecimenOrObservationBase occurence join occurence.media media where occurence = :occurence");
|
136
|
query.setParameter("occurence", occurence);
|
137
|
|
138
|
return ((Long)query.uniqueResult()).intValue();
|
139
|
}
|
140
|
|
141
|
@Override
|
142
|
public List<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
|
143
|
checkNotInPriorView("OccurrenceDaoHibernateImpl.getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber)");
|
144
|
Query query = getSession().createQuery("select distinct derivationEvent from DerivationEvent derivationEvent join derivationEvent.originals occurence where occurence = :occurence");
|
145
|
query.setParameter("occurence", occurence);
|
146
|
|
147
|
if(pageSize != null) {
|
148
|
query.setMaxResults(pageSize);
|
149
|
if(pageNumber != null) {
|
150
|
query.setFirstResult(pageNumber * pageSize);
|
151
|
} else {
|
152
|
query.setFirstResult(0);
|
153
|
}
|
154
|
}
|
155
|
|
156
|
List<DerivationEvent> result = query.list();
|
157
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
158
|
return result;
|
159
|
}
|
160
|
|
161
|
@Override
|
162
|
public List<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
|
163
|
AuditEvent auditEvent = getAuditEventFromContext();
|
164
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
165
|
Criteria criteria = getSession().createCriteria(DeterminationEvent.class);
|
166
|
if(occurrence != null) {
|
167
|
criteria.add(Restrictions.eq("identifiedUnit",occurrence));
|
168
|
}
|
169
|
|
170
|
if(taxonBase != null) {
|
171
|
criteria.add(Restrictions.eq("taxon",taxonBase));
|
172
|
}
|
173
|
|
174
|
if(pageSize != null) {
|
175
|
criteria.setMaxResults(pageSize);
|
176
|
if(pageNumber != null) {
|
177
|
criteria.setFirstResult(pageNumber * pageSize);
|
178
|
} else {
|
179
|
criteria.setFirstResult(0);
|
180
|
}
|
181
|
}
|
182
|
List<DeterminationEvent> result = criteria.list();
|
183
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
184
|
return result;
|
185
|
} else {
|
186
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(DeterminationEvent.class,auditEvent.getRevisionNumber());
|
187
|
if(occurrence != null) {
|
188
|
query.add(AuditEntity.relatedId("identifiedUnit").eq(occurrence.getId()));
|
189
|
}
|
190
|
|
191
|
if(taxonBase != null) {
|
192
|
query.add(AuditEntity.relatedId("taxon").eq(taxonBase.getId()));
|
193
|
}
|
194
|
if(pageSize != null) {
|
195
|
query.setMaxResults(pageSize);
|
196
|
if(pageNumber != null) {
|
197
|
query.setFirstResult(pageNumber * pageSize);
|
198
|
} else {
|
199
|
query.setFirstResult(0);
|
200
|
}
|
201
|
}
|
202
|
List<DeterminationEvent> result = query.getResultList();
|
203
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
204
|
return result;
|
205
|
}
|
206
|
}
|
207
|
|
208
|
@Override
|
209
|
public List<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
|
210
|
checkNotInPriorView("OccurrenceDaoHibernateImpl.getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths)");
|
211
|
Query query = getSession().createQuery("select media from SpecimenOrObservationBase occurence join occurence.media media where occurence = :occurence");
|
212
|
query.setParameter("occurence", occurence);
|
213
|
|
214
|
if(pageSize != null) {
|
215
|
query.setMaxResults(pageSize);
|
216
|
if(pageNumber != null) {
|
217
|
query.setFirstResult(pageNumber * pageSize);
|
218
|
} else {
|
219
|
query.setFirstResult(0);
|
220
|
}
|
221
|
}
|
222
|
|
223
|
List<Media> results = query.list();
|
224
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
225
|
return results;
|
226
|
}
|
227
|
|
228
|
@Override
|
229
|
public void rebuildIndex() {
|
230
|
FullTextSession fullTextSession = Search.getFullTextSession(getSession());
|
231
|
|
232
|
for(SpecimenOrObservationBase<?> occurrence : list(null,null)) { // re-index all taxon base
|
233
|
|
234
|
for(DeterminationEvent determination : occurrence.getDeterminations()) {
|
235
|
Hibernate.initialize(determination.getActor());
|
236
|
Hibernate.initialize(determination.getTaxon());
|
237
|
}
|
238
|
Hibernate.initialize(occurrence.getDefinition());
|
239
|
if(occurrence instanceof DerivedUnit) {
|
240
|
DerivedUnit derivedUnit = (DerivedUnit) occurrence;
|
241
|
Hibernate.initialize(derivedUnit.getCollection());
|
242
|
if(derivedUnit.getCollection() != null) {
|
243
|
Hibernate.initialize(derivedUnit.getCollection().getSuperCollection());
|
244
|
Hibernate.initialize(derivedUnit.getCollection().getInstitute());
|
245
|
}
|
246
|
Hibernate.initialize(derivedUnit.getStoredUnder());
|
247
|
SpecimenOrObservationBase<?> original = derivedUnit.getOriginalUnit();
|
248
|
if(original != null && original.isInstanceOf(FieldUnit.class)) {
|
249
|
FieldUnit fieldUnit = CdmBase.deproxy(original, FieldUnit.class);
|
250
|
Hibernate.initialize(fieldUnit.getGatheringEvent());
|
251
|
if(fieldUnit.getGatheringEvent() != null) {
|
252
|
Hibernate.initialize(fieldUnit.getGatheringEvent().getActor());
|
253
|
}
|
254
|
}
|
255
|
}
|
256
|
fullTextSession.index(occurrence);
|
257
|
}
|
258
|
fullTextSession.flushToIndexes();
|
259
|
}
|
260
|
|
261
|
@Override
|
262
|
public int count(Class<? extends SpecimenOrObservationBase> clazz, TaxonName determinedAs) {
|
263
|
|
264
|
Criteria criteria = null;
|
265
|
if(clazz == null) {
|
266
|
criteria = getSession().createCriteria(type);
|
267
|
} else {
|
268
|
criteria = getSession().createCriteria(clazz);
|
269
|
}
|
270
|
|
271
|
criteria.createCriteria("determinations").add(Restrictions.eq("taxonName", determinedAs));
|
272
|
criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));
|
273
|
return ((Number)criteria.uniqueResult()).intValue();
|
274
|
}
|
275
|
|
276
|
@Override
|
277
|
public List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> clazz, TaxonName determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
278
|
Criteria criteria = null;
|
279
|
if(clazz == null) {
|
280
|
criteria = getSession().createCriteria(type);
|
281
|
} else {
|
282
|
criteria = getSession().createCriteria(clazz);
|
283
|
}
|
284
|
|
285
|
criteria.createCriteria("determinations").add(Restrictions.eq("taxonName", determinedAs));
|
286
|
|
287
|
if(limit != null) {
|
288
|
if(start != null) {
|
289
|
criteria.setFirstResult(start);
|
290
|
} else {
|
291
|
criteria.setFirstResult(0);
|
292
|
}
|
293
|
criteria.setMaxResults(limit);
|
294
|
}
|
295
|
|
296
|
addOrder(criteria,orderHints);
|
297
|
|
298
|
@SuppressWarnings("unchecked")
|
299
|
List<SpecimenOrObservationBase> results = criteria.list();
|
300
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
301
|
return results;
|
302
|
}
|
303
|
|
304
|
@Override
|
305
|
public int count(Class<? extends SpecimenOrObservationBase> clazz, TaxonBase determinedAs) {
|
306
|
|
307
|
Criteria criteria = null;
|
308
|
if(clazz == null) {
|
309
|
criteria = getSession().createCriteria(type);
|
310
|
} else {
|
311
|
criteria = getSession().createCriteria(clazz);
|
312
|
}
|
313
|
|
314
|
criteria.createCriteria("determinations").add(Restrictions.eq("taxon", determinedAs));
|
315
|
criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));
|
316
|
return ((Number)criteria.uniqueResult()).intValue();
|
317
|
}
|
318
|
|
319
|
@Override
|
320
|
public List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> clazz, TaxonBase determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
321
|
Criteria criteria = null;
|
322
|
if(clazz == null) {
|
323
|
criteria = getSession().createCriteria(type);
|
324
|
} else {
|
325
|
criteria = getSession().createCriteria(clazz);
|
326
|
}
|
327
|
|
328
|
criteria.createCriteria("determinations").add(Restrictions.eq("taxon", determinedAs));
|
329
|
|
330
|
if(limit != null) {
|
331
|
if(start != null) {
|
332
|
criteria.setFirstResult(start);
|
333
|
} else {
|
334
|
criteria.setFirstResult(0);
|
335
|
}
|
336
|
criteria.setMaxResults(limit);
|
337
|
}
|
338
|
|
339
|
addOrder(criteria,orderHints);
|
340
|
|
341
|
@SuppressWarnings("unchecked")
|
342
|
List<SpecimenOrObservationBase> results = criteria.list();
|
343
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
344
|
return results;
|
345
|
}
|
346
|
|
347
|
@Override
|
348
|
public <T extends SpecimenOrObservationBase> List<UuidAndTitleCache<SpecimenOrObservationBase>> findOccurrencesUuidAndTitleCache(
|
349
|
Class<T> clazz, String queryString, String significantIdentifier, SpecimenOrObservationType recordBasis,
|
350
|
Taxon associatedTaxon, TaxonName associatedTaxonName, MatchMode matchmode, Integer limit, Integer start,
|
351
|
List<OrderHint> orderHints) {
|
352
|
Criteria criteria = createFindOccurrenceCriteria(clazz, queryString, significantIdentifier, recordBasis,
|
353
|
associatedTaxon, associatedTaxonName, matchmode, limit, start, orderHints, null);
|
354
|
if(criteria!=null){
|
355
|
ProjectionList projectionList = Projections.projectionList();
|
356
|
projectionList.add(Projections.property("uuid"));
|
357
|
projectionList.add(Projections.property("id"));
|
358
|
projectionList.add(Projections.property("titleCache"));
|
359
|
criteria.setProjection(projectionList);
|
360
|
|
361
|
@SuppressWarnings("unchecked")
|
362
|
List<Object[]> result = criteria.list();
|
363
|
List<UuidAndTitleCache<SpecimenOrObservationBase>> uuidAndTitleCacheList = new ArrayList<>();
|
364
|
for(Object[] object : result){
|
365
|
uuidAndTitleCacheList.add(new UuidAndTitleCache<>((UUID) object[0],(Integer) object[1], (String) object[2]));
|
366
|
}
|
367
|
return uuidAndTitleCacheList;
|
368
|
}
|
369
|
return Collections.emptyList();
|
370
|
}
|
371
|
|
372
|
@Override
|
373
|
public <T extends SpecimenOrObservationBase> List<T> findOccurrences(Class<T> clazz, String queryString,
|
374
|
String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon, TaxonName associatedTaxonName,
|
375
|
MatchMode matchmode, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
376
|
|
377
|
Criteria criteria = createFindOccurrenceCriteria(clazz, queryString, significantIdentifier, recordBasis,
|
378
|
associatedTaxon, associatedTaxonName, matchmode, limit, start, orderHints, propertyPaths);
|
379
|
if(criteria!=null){
|
380
|
@SuppressWarnings("unchecked")
|
381
|
List<T> results = criteria.list();
|
382
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
383
|
return results;
|
384
|
}
|
385
|
return Collections.emptyList();
|
386
|
}
|
387
|
|
388
|
private <T extends SpecimenOrObservationBase> Criteria createFindOccurrenceCriteria(Class<T> clazz, String queryString,
|
389
|
String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon, TaxonName associatedTaxonName, MatchMode matchmode, Integer limit,
|
390
|
Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
391
|
Criteria criteria = null;
|
392
|
|
393
|
if(clazz == null) {
|
394
|
criteria = getSession().createCriteria(type);
|
395
|
} else {
|
396
|
criteria = getSession().createCriteria(clazz);
|
397
|
}
|
398
|
|
399
|
//queryString
|
400
|
if (queryString != null) {
|
401
|
if(matchmode == null) {
|
402
|
matchmode = MatchMode.ANYWHERE;
|
403
|
criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString)));
|
404
|
} else if(matchmode == MatchMode.BEGINNING) {
|
405
|
criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.START));
|
406
|
} else if(matchmode == MatchMode.END) {
|
407
|
criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.END));
|
408
|
} else if(matchmode == MatchMode.EXACT) {
|
409
|
criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.EXACT));
|
410
|
} else {
|
411
|
criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.ANYWHERE));
|
412
|
}
|
413
|
}
|
414
|
|
415
|
//significant identifier
|
416
|
if (significantIdentifier != null) {
|
417
|
criteria.add(Restrictions.or(Restrictions.ilike("accessionNumber", significantIdentifier),
|
418
|
Restrictions.ilike("catalogNumber", significantIdentifier), Restrictions.ilike("barcode", significantIdentifier)));
|
419
|
}
|
420
|
|
421
|
//recordBasis/SpecimenOrObservationType
|
422
|
Set<SpecimenOrObservationType> typeAndSubtypes = new HashSet<SpecimenOrObservationType>();
|
423
|
if(recordBasis==null){
|
424
|
//add all types
|
425
|
SpecimenOrObservationType[] values = SpecimenOrObservationType.values();
|
426
|
for (SpecimenOrObservationType specimenOrObservationType : values) {
|
427
|
typeAndSubtypes.add(specimenOrObservationType);
|
428
|
}
|
429
|
}
|
430
|
else{
|
431
|
typeAndSubtypes = recordBasis.getGeneralizationOf(true);
|
432
|
typeAndSubtypes.add(recordBasis);
|
433
|
}
|
434
|
criteria.add(Restrictions.in("recordBasis", typeAndSubtypes));
|
435
|
|
436
|
Set<UUID> associationUuids = new HashSet<UUID>();
|
437
|
//taxon associations
|
438
|
if(associatedTaxon!=null){
|
439
|
List<UuidAndTitleCache<SpecimenOrObservationBase>> associatedTaxaList = listUuidAndTitleCacheByAssociatedTaxon(clazz, associatedTaxon, limit, start, orderHints);
|
440
|
if(associatedTaxaList!=null){
|
441
|
for (UuidAndTitleCache<SpecimenOrObservationBase> uuidAndTitleCache : associatedTaxaList) {
|
442
|
associationUuids.add(uuidAndTitleCache.getUuid());
|
443
|
}
|
444
|
}
|
445
|
}
|
446
|
//taxon name associations
|
447
|
else if(associatedTaxonName!=null){
|
448
|
List<? extends SpecimenOrObservationBase> associatedTaxaList = listByAssociatedTaxonName(clazz, associatedTaxonName, limit, start, orderHints, propertyPaths);
|
449
|
if(associatedTaxaList!=null){
|
450
|
for (SpecimenOrObservationBase specimenOrObservationBase : associatedTaxaList) {
|
451
|
associationUuids.add(specimenOrObservationBase.getUuid());
|
452
|
}
|
453
|
}
|
454
|
}
|
455
|
if(associatedTaxon!=null || associatedTaxonName!=null){
|
456
|
if(!associationUuids.isEmpty()){
|
457
|
criteria.add(Restrictions.in("uuid", associationUuids));
|
458
|
}
|
459
|
else{
|
460
|
return null;
|
461
|
}
|
462
|
}
|
463
|
if(limit != null) {
|
464
|
if(start != null) {
|
465
|
criteria.setFirstResult(start);
|
466
|
} else {
|
467
|
criteria.setFirstResult(0);
|
468
|
}
|
469
|
criteria.setMaxResults(limit);
|
470
|
}
|
471
|
|
472
|
if(orderHints!=null){
|
473
|
addOrder(criteria,orderHints);
|
474
|
}
|
475
|
return criteria;
|
476
|
}
|
477
|
|
478
|
|
479
|
@Override
|
480
|
public <T extends SpecimenOrObservationBase> int countOccurrences(Class<T> clazz, String queryString,
|
481
|
String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon, TaxonName associatedTaxonName,
|
482
|
MatchMode matchmode, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
483
|
Criteria criteria = createFindOccurrenceCriteria(clazz, queryString, significantIdentifier, recordBasis,
|
484
|
associatedTaxon, associatedTaxonName, matchmode, limit, start, orderHints, propertyPaths);
|
485
|
|
486
|
if(criteria!=null){
|
487
|
|
488
|
criteria.setProjection(Projections.rowCount());
|
489
|
|
490
|
return ((Number)criteria.uniqueResult()).intValue();
|
491
|
}
|
492
|
return 0;
|
493
|
}
|
494
|
|
495
|
@Override
|
496
|
public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache(Integer limit, String pattern) {
|
497
|
List<UuidAndTitleCache<DerivedUnit>> list = new ArrayList<>();
|
498
|
Session session = getSession();
|
499
|
Query query;
|
500
|
if (pattern != null){
|
501
|
query = session.createQuery("select uuid, id, titleCache from " + type.getSimpleName() + " where NOT dtype = " + FieldUnit.class.getSimpleName() +" AND titleCache like :pattern");
|
502
|
pattern = pattern.replace("*", "%");
|
503
|
pattern = pattern.replace("?", "_");
|
504
|
pattern = pattern + "%";
|
505
|
query.setParameter("pattern", pattern);
|
506
|
} else {
|
507
|
query = session.createQuery("select uuid, id, titleCache from " + type.getSimpleName() +" where NOT dtype = " + FieldUnit.class.getSimpleName());
|
508
|
}
|
509
|
if (limit != null){
|
510
|
query.setMaxResults(limit);
|
511
|
}
|
512
|
|
513
|
@SuppressWarnings("unchecked")
|
514
|
List<Object[]> result = query.list();
|
515
|
|
516
|
for(Object[] object : result){
|
517
|
list.add(new UuidAndTitleCache<DerivedUnit>(DerivedUnit.class, (UUID) object[0], (Integer)object[1], (String) object[2]));
|
518
|
}
|
519
|
|
520
|
return list;
|
521
|
}
|
522
|
|
523
|
@Override
|
524
|
public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
|
525
|
List<UuidAndTitleCache<FieldUnit>> list = new ArrayList<UuidAndTitleCache<FieldUnit>>();
|
526
|
Session session = getSession();
|
527
|
|
528
|
Query query = session.createQuery("select uuid, id, titleCache from " + type.getSimpleName() + " where dtype = " + FieldUnit.class.getSimpleName());
|
529
|
|
530
|
@SuppressWarnings("unchecked")
|
531
|
List<Object[]> result = query.list();
|
532
|
|
533
|
for(Object[] object : result){
|
534
|
list.add(new UuidAndTitleCache<FieldUnit>(FieldUnit.class, (UUID) object[0], (Integer)object[1], (String) object[2]));
|
535
|
}
|
536
|
|
537
|
return list;
|
538
|
}
|
539
|
|
540
|
@Override
|
541
|
public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxonName(Class<T> type,
|
542
|
TaxonName associatedTaxonName, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
543
|
Set<SpecimenOrObservationBase> setOfAll = new HashSet<>();
|
544
|
|
545
|
// A Taxon name may be referenced by the DeterminationEvent of the SpecimenOrObservationBase
|
546
|
List<SpecimenOrObservationBase> byDetermination = list(type, associatedTaxonName, null, 0, null, null);
|
547
|
setOfAll.addAll(byDetermination);
|
548
|
|
549
|
if(setOfAll.size() == 0){
|
550
|
// no need querying the data base
|
551
|
return new ArrayList<T>();
|
552
|
}
|
553
|
|
554
|
String queryString =
|
555
|
"select sob " +
|
556
|
" from SpecimenOrObservationBase sob" +
|
557
|
" where sob in (:setOfAll)";
|
558
|
|
559
|
if(type != null && !type.equals(SpecimenOrObservationBase.class)){
|
560
|
queryString += " and sob.class = :type";
|
561
|
}
|
562
|
|
563
|
if(orderHints != null && orderHints.size() > 0){
|
564
|
queryString += " order by ";
|
565
|
String orderStr = "";
|
566
|
for(OrderHint orderHint : orderHints){
|
567
|
if(orderStr.length() > 0){
|
568
|
orderStr += ", ";
|
569
|
}
|
570
|
queryString += "sob." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
|
571
|
}
|
572
|
queryString += orderStr;
|
573
|
}
|
574
|
|
575
|
Query query = getSession().createQuery(queryString);
|
576
|
query.setParameterList("setOfAll", setOfAll);
|
577
|
|
578
|
if(type != null && !type.equals(SpecimenOrObservationBase.class)){
|
579
|
query.setParameter("type", type.getSimpleName());
|
580
|
}
|
581
|
|
582
|
if(limit != null) {
|
583
|
if(start != null) {
|
584
|
query.setFirstResult(start);
|
585
|
} else {
|
586
|
query.setFirstResult(0);
|
587
|
}
|
588
|
query.setMaxResults(limit);
|
589
|
}
|
590
|
|
591
|
|
592
|
@SuppressWarnings("unchecked")
|
593
|
List<T> results = query.list();
|
594
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
595
|
return results;
|
596
|
}
|
597
|
|
598
|
private List<SpecimenNodeWrapper> querySpecimen(
|
599
|
Query query, List<UUID> taxonNodeUuids,
|
600
|
Integer limit, Integer start){
|
601
|
query.setParameterList("taxonNodeUuids", taxonNodeUuids);
|
602
|
|
603
|
if(limit != null) {
|
604
|
if(start != null) {
|
605
|
query.setFirstResult(start);
|
606
|
} else {
|
607
|
query.setFirstResult(0);
|
608
|
}
|
609
|
query.setMaxResults(limit);
|
610
|
}
|
611
|
|
612
|
List<SpecimenNodeWrapper> list = new ArrayList<>();
|
613
|
@SuppressWarnings("unchecked")
|
614
|
List<Object[]> result = query.list();
|
615
|
for(Object[] object : result){
|
616
|
list.add(new SpecimenNodeWrapper(
|
617
|
new UuidAndTitleCache<>(
|
618
|
(UUID) object[0],
|
619
|
(Integer) object[1],
|
620
|
(String) object[2]),
|
621
|
(TaxonNode)object[3]));
|
622
|
}
|
623
|
return list;
|
624
|
}
|
625
|
|
626
|
private List<SpecimenNodeWrapper> queryIndividualAssociatedSpecimen(List<UUID> taxonNodeUuids,
|
627
|
Integer limit, Integer start){
|
628
|
String queryString = "SELECT "
|
629
|
+ "de.associatedSpecimenOrObservation.uuid, "
|
630
|
+ "de.associatedSpecimenOrObservation.id, "
|
631
|
+ "de.associatedSpecimenOrObservation.titleCache, "
|
632
|
+ "tn "
|
633
|
+ "FROM DescriptionElementBase AS de "
|
634
|
+ "LEFT JOIN de.inDescription AS d "
|
635
|
+ "LEFT JOIN d.taxon AS t "
|
636
|
+ "JOIN t.taxonNodes AS tn "
|
637
|
+ "WHERE d.class = 'TaxonDescription' "
|
638
|
+ "AND tn.uuid in (:taxonNodeUuids) "
|
639
|
;
|
640
|
Query query = getSession().createQuery(queryString);
|
641
|
return querySpecimen(query, taxonNodeUuids, limit, start);
|
642
|
}
|
643
|
|
644
|
private List<SpecimenNodeWrapper> queryTypeSpecimen(List<UUID> taxonNodeUuids,
|
645
|
Integer limit, Integer start){
|
646
|
String queryString = "SELECT "
|
647
|
+ "td.typeSpecimen.uuid, "
|
648
|
+ "td.typeSpecimen.id, "
|
649
|
+ "td.typeSpecimen.titleCache, "
|
650
|
+ "tn "
|
651
|
+ "FROM SpecimenTypeDesignation AS td "
|
652
|
+ "LEFT JOIN td.typifiedNames AS tn "
|
653
|
+ "LEFT JOIN tn.taxonBases AS t "
|
654
|
+ "JOIN t.taxonNodes AS tn "
|
655
|
+ "WHERE tn.uuid in (:taxonNodeUuids) "
|
656
|
;
|
657
|
Query query = getSession().createQuery(queryString);
|
658
|
return querySpecimen(query, taxonNodeUuids, limit, start);
|
659
|
}
|
660
|
|
661
|
private List<SpecimenNodeWrapper> queryTaxonDeterminations(List<UUID> taxonNodeUuids,
|
662
|
Integer limit, Integer start){
|
663
|
String queryString = "SELECT "
|
664
|
+ "det.identifiedUnit.uuid, "
|
665
|
+ "det.identifiedUnit.id, "
|
666
|
+ "det.identifiedUnit.titleCache, "
|
667
|
+ "tn "
|
668
|
+ "FROM DeterminationEvent AS det "
|
669
|
+ "LEFT JOIN det.taxon AS t "
|
670
|
+ "JOIN t.taxonNodes AS tn "
|
671
|
+ "WHERE tn.uuid in (:taxonNodeUuids) "
|
672
|
;
|
673
|
Query query = getSession().createQuery(queryString);
|
674
|
return querySpecimen(query, taxonNodeUuids, limit, start);
|
675
|
}
|
676
|
|
677
|
private List<SpecimenNodeWrapper> queryTaxonNameDeterminations(List<UUID> taxonNodeUuids,
|
678
|
Integer limit, Integer start){
|
679
|
String queryString = "SELECT "
|
680
|
+ "det.identifiedUnit.uuid, "
|
681
|
+ "det.identifiedUnit.id, "
|
682
|
+ "det.identifiedUnit.titleCache, "
|
683
|
+ "tn "
|
684
|
+ "FROM DeterminationEvent AS det "
|
685
|
+ "LEFT JOIN det.taxonName AS n "
|
686
|
+ "LEFT JOIN n.taxonBases AS t "
|
687
|
+ "JOIN t.taxonNodes AS tn "
|
688
|
+ "WHERE tn.uuid in (:taxonNodeUuids) "
|
689
|
;
|
690
|
Query query = getSession().createQuery(queryString);
|
691
|
return querySpecimen(query, taxonNodeUuids, limit, start);
|
692
|
}
|
693
|
|
694
|
@Override
|
695
|
public Collection<SpecimenNodeWrapper> listUuidAndTitleCacheByAssociatedTaxon(List<UUID> taxonNodeUuids,
|
696
|
Integer limit, Integer start){
|
697
|
|
698
|
Collection<SpecimenNodeWrapper> wrappers = new HashSet<>();
|
699
|
wrappers.addAll(queryIndividualAssociatedSpecimen(taxonNodeUuids, limit, start));
|
700
|
wrappers.addAll(queryTaxonDeterminations(taxonNodeUuids, limit, start));
|
701
|
wrappers.addAll(queryTaxonNameDeterminations(taxonNodeUuids, limit, start));
|
702
|
wrappers.addAll(queryTypeSpecimen(taxonNodeUuids, limit, start));
|
703
|
|
704
|
return wrappers;
|
705
|
}
|
706
|
|
707
|
@Override
|
708
|
public <T extends SpecimenOrObservationBase> List<UuidAndTitleCache<SpecimenOrObservationBase>> listUuidAndTitleCacheByAssociatedTaxon(Class<T> clazz, Taxon associatedTaxon,
|
709
|
Integer limit, Integer start, List<OrderHint> orderHints){
|
710
|
Query query = createSpecimenQuery("sob.uuid, sob.id, sob.titleCache", clazz, associatedTaxon, limit, start, orderHints, null);
|
711
|
if(query==null){
|
712
|
return Collections.emptyList();
|
713
|
}
|
714
|
List<UuidAndTitleCache<SpecimenOrObservationBase>> list = new ArrayList<>();
|
715
|
@SuppressWarnings("unchecked")
|
716
|
List<Object[]> result = query.list();
|
717
|
for(Object[] object : result){
|
718
|
list.add(new UuidAndTitleCache<>((UUID) object[0],(Integer) object[1], (String) object[2]));
|
719
|
}
|
720
|
return list;
|
721
|
}
|
722
|
|
723
|
@Override
|
724
|
public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> clazz,
|
725
|
Taxon associatedTaxon, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
726
|
Query query = createSpecimenQuery("sob", clazz, associatedTaxon, limit, start, orderHints, propertyPaths);
|
727
|
if(query==null){
|
728
|
return Collections.emptyList();
|
729
|
}
|
730
|
@SuppressWarnings("unchecked")
|
731
|
List<T> results = query.list();
|
732
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
733
|
return results;
|
734
|
}
|
735
|
|
736
|
private <T extends SpecimenOrObservationBase> Query createSpecimenQuery(String select, Class<T> clazz,
|
737
|
Taxon associatedTaxon, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths){
|
738
|
Set<SpecimenOrObservationBase> setOfAll = new HashSet<>();
|
739
|
Set<Integer> setOfAllIds = new HashSet<>();
|
740
|
|
741
|
Criteria criteria = null;
|
742
|
if(clazz == null) {
|
743
|
criteria = getSession().createCriteria(type, "specimen");
|
744
|
} else {
|
745
|
criteria = getSession().createCriteria(clazz, "specimen");
|
746
|
}
|
747
|
|
748
|
Disjunction determinationOr = Restrictions.disjunction();
|
749
|
|
750
|
// A Taxon may be referenced by the DeterminationEvent of the SpecimenOrObservationBase
|
751
|
Criteria determinationsCriteria = criteria.createCriteria("determinations");
|
752
|
|
753
|
determinationOr.add(Restrictions.eq("taxon", associatedTaxon));
|
754
|
//check also for synonyms
|
755
|
for (Synonym synonym : associatedTaxon.getSynonyms()) {
|
756
|
determinationOr.add(Restrictions.eq("taxon", synonym));
|
757
|
}
|
758
|
|
759
|
//check also for name determinations
|
760
|
determinationOr.add(Restrictions.eq("taxonName", associatedTaxon.getName()));
|
761
|
for (TaxonName synonymName : associatedTaxon.getSynonymNames()) {
|
762
|
determinationOr.add(Restrictions.eq("taxonName", synonymName));
|
763
|
}
|
764
|
|
765
|
determinationsCriteria.add(determinationOr);
|
766
|
|
767
|
if(limit != null) {
|
768
|
if(start != null) {
|
769
|
criteria.setFirstResult(start);
|
770
|
} else {
|
771
|
criteria.setFirstResult(0);
|
772
|
}
|
773
|
criteria.setMaxResults(limit);
|
774
|
}
|
775
|
criteria.setProjection(Projections.property("id"));
|
776
|
|
777
|
addOrder(criteria,orderHints);
|
778
|
|
779
|
@SuppressWarnings("unchecked")
|
780
|
List<Integer> detResults = criteria.list();
|
781
|
setOfAllIds.addAll(detResults);
|
782
|
|
783
|
// The IndividualsAssociation elements in a TaxonDescription contain DerivedUnits
|
784
|
setOfAllIds.addAll(descriptionDao.getIndividualAssociationSpecimenIDs(
|
785
|
associatedTaxon.getUuid(), null, null, 0, null));
|
786
|
|
787
|
|
788
|
// SpecimenTypeDesignations may be associated with the TaxonName.
|
789
|
setOfAllIds.addAll(taxonNameDao.getTypeSpecimenIdsForTaxonName(
|
790
|
associatedTaxon.getName(), null, null, null));
|
791
|
|
792
|
// SpecimenTypeDesignations may be associated with any HomotypicalGroup related to the specific Taxon.
|
793
|
//TODO adapt to set of ids
|
794
|
for(HomotypicalGroup homotypicalGroup : associatedTaxon.getHomotypicSynonymyGroups()) {
|
795
|
List<SpecimenTypeDesignation> byHomotypicalGroup = homotypicalGroupDao.getTypeDesignations(homotypicalGroup, SpecimenTypeDesignation.class, null, null, 0, null);
|
796
|
for (SpecimenTypeDesignation specimenTypeDesignation : byHomotypicalGroup) {
|
797
|
setOfAll.add(specimenTypeDesignation.getTypeSpecimen());
|
798
|
}
|
799
|
}
|
800
|
|
801
|
if(setOfAllIds.size() == 0){
|
802
|
// no need querying the data base
|
803
|
return null;
|
804
|
}
|
805
|
|
806
|
String queryString =
|
807
|
"select "+select+
|
808
|
" from SpecimenOrObservationBase sob" +
|
809
|
" where sob.id in (:setOfAllIds)";
|
810
|
|
811
|
if(clazz != null && !clazz.equals(SpecimenOrObservationBase.class)){
|
812
|
queryString += " and sob.class = :type ";
|
813
|
}
|
814
|
|
815
|
if(orderHints != null && orderHints.size() > 0){
|
816
|
queryString += " order by ";
|
817
|
String orderStr = "";
|
818
|
for(OrderHint orderHint : orderHints){
|
819
|
if(orderStr.length() > 0){
|
820
|
orderStr += ", ";
|
821
|
}
|
822
|
queryString += "sob." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
|
823
|
}
|
824
|
queryString += orderStr;
|
825
|
}
|
826
|
|
827
|
Query query = getSession().createQuery(queryString);
|
828
|
query.setParameterList("setOfAllIds", setOfAllIds);
|
829
|
|
830
|
if(clazz != null && !clazz.equals(SpecimenOrObservationBase.class)){
|
831
|
query.setParameter("type", clazz.getSimpleName());
|
832
|
}
|
833
|
|
834
|
if(limit != null) {
|
835
|
if(start != null) {
|
836
|
query.setFirstResult(start);
|
837
|
} else {
|
838
|
query.setFirstResult(0);
|
839
|
}
|
840
|
query.setMaxResults(limit);
|
841
|
}
|
842
|
|
843
|
return query;
|
844
|
}
|
845
|
|
846
|
@Override
|
847
|
public Collection<SpecimenOrObservationBase> listBySpecimenOrObservationType(SpecimenOrObservationType type, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
848
|
String queryString = "FROM SpecimenOrObservationBase specimens "
|
849
|
+ " WHERE specimens.recordBasis = :type ";
|
850
|
|
851
|
queryString += orderByClause(orderHints, "specimens");
|
852
|
|
853
|
Query query = getSession().createQuery(queryString);
|
854
|
query.setParameter("type", type);
|
855
|
|
856
|
if(limit != null) {
|
857
|
if(start != null) {
|
858
|
query.setFirstResult(start);
|
859
|
} else {
|
860
|
query.setFirstResult(0);
|
861
|
}
|
862
|
query.setMaxResults(limit);
|
863
|
}
|
864
|
|
865
|
@SuppressWarnings({ "unchecked", "rawtypes" })
|
866
|
List<SpecimenOrObservationBase> results = query.list();
|
867
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
868
|
return results;
|
869
|
}
|
870
|
|
871
|
|
872
|
@Override
|
873
|
public Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
874
|
String queryString = "FROM DeterminationEvent determination "
|
875
|
+ " WHERE determination.identifiedUnit = :specimen";
|
876
|
|
877
|
queryString += orderByClause(orderHints, "determination");
|
878
|
|
879
|
Query query = getSession().createQuery(queryString);
|
880
|
query.setParameter("specimen", specimen);
|
881
|
|
882
|
if(limit != null) {
|
883
|
if(start != null) {
|
884
|
query.setFirstResult(start);
|
885
|
} else {
|
886
|
query.setFirstResult(0);
|
887
|
}
|
888
|
query.setMaxResults(limit);
|
889
|
}
|
890
|
|
891
|
@SuppressWarnings("unchecked")
|
892
|
List<DeterminationEvent> results = query.list();
|
893
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
894
|
return results;
|
895
|
}
|
896
|
|
897
|
@Override
|
898
|
public Collection<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
899
|
String queryString = "FROM SpecimenTypeDesignation designations "
|
900
|
+ " WHERE designations.typeSpecimen = :specimen";
|
901
|
|
902
|
queryString += orderByClause(orderHints, "designations");
|
903
|
|
904
|
Query query = getSession().createQuery(queryString);
|
905
|
query.setParameter("specimen", specimen);
|
906
|
|
907
|
if(limit != null) {
|
908
|
if(start != null) {
|
909
|
query.setFirstResult(start);
|
910
|
} else {
|
911
|
query.setFirstResult(0);
|
912
|
}
|
913
|
query.setMaxResults(limit);
|
914
|
}
|
915
|
|
916
|
@SuppressWarnings("unchecked")
|
917
|
List<SpecimenTypeDesignation> results = query.list();
|
918
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
919
|
return results;
|
920
|
}
|
921
|
|
922
|
@Override
|
923
|
public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
924
|
//DISTINCT is necessary if more than one description exists for a taxon because we create the cross product of all taxon descriptions and description elements
|
925
|
String queryString = "FROM IndividualsAssociation associations WHERE associations.associatedSpecimenOrObservation = :specimen";
|
926
|
|
927
|
queryString += orderByClause(orderHints, "associations");
|
928
|
|
929
|
Query query = getSession().createQuery(queryString);
|
930
|
query.setParameter("specimen", specimen);
|
931
|
|
932
|
if(limit != null) {
|
933
|
if(start != null) {
|
934
|
query.setFirstResult(start);
|
935
|
} else {
|
936
|
query.setFirstResult(0);
|
937
|
}
|
938
|
query.setMaxResults(limit);
|
939
|
}
|
940
|
|
941
|
@SuppressWarnings("unchecked")
|
942
|
List<IndividualsAssociation> results = query.list();
|
943
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
944
|
return results;
|
945
|
}
|
946
|
|
947
|
@Override
|
948
|
public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
949
|
//DISTINCT is necessary if more than one description exists for a taxon because we create the cross product of all taxon descriptions and description elements
|
950
|
String queryString = "FROM DescriptionBase descriptions "
|
951
|
+ " WHERE descriptions.describedSpecimenOrObservation = :specimen";
|
952
|
|
953
|
queryString += orderByClause(orderHints, "descriptions");
|
954
|
|
955
|
Query query = getSession().createQuery(queryString);
|
956
|
query.setParameter("specimen", specimen);
|
957
|
|
958
|
if(limit != null) {
|
959
|
if(start != null) {
|
960
|
query.setFirstResult(start);
|
961
|
} else {
|
962
|
query.setFirstResult(0);
|
963
|
}
|
964
|
query.setMaxResults(limit);
|
965
|
}
|
966
|
|
967
|
@SuppressWarnings("unchecked")
|
968
|
List<DescriptionBase<?>> results = query.list();
|
969
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
970
|
return results;
|
971
|
}
|
972
|
|
973
|
/**
|
974
|
* {@inheritDoc}
|
975
|
*/
|
976
|
@Override
|
977
|
public List<FieldUnit> getFieldUnitsForGatheringEvent(UUID gatheringEventUuid, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
978
|
String queryString = "FROM SpecimenOrObservationBase sob "
|
979
|
+ "WHERE sob.gatheringEvent.uuid = :gatheringEventUuid";
|
980
|
|
981
|
queryString += orderByClause(orderHints, "sob");
|
982
|
|
983
|
Query query = getSession().createQuery(queryString);
|
984
|
query.setParameter("gatheringEventUuid", gatheringEventUuid);
|
985
|
|
986
|
if(limit != null) {
|
987
|
if(start != null) {
|
988
|
query.setFirstResult(start);
|
989
|
} else {
|
990
|
query.setFirstResult(0);
|
991
|
}
|
992
|
query.setMaxResults(limit);
|
993
|
}
|
994
|
|
995
|
@SuppressWarnings("unchecked")
|
996
|
List<FieldUnit> results = query.list();
|
997
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
998
|
return results;
|
999
|
}
|
1000
|
|
1001
|
/**
|
1002
|
* {@inheritDoc}
|
1003
|
*/
|
1004
|
@Override
|
1005
|
public List<DerivedUnit> getByGeneticAccessionNumber(String accessionNumberString, List<String> propertyPaths) {
|
1006
|
String queryString = "SELECT dnaSample FROM DnaSample dnaSample join dnaSample.sequences sequence WHERE sequence.geneticAccessionNumber LIKE :accessionNumberString";
|
1007
|
Query query = getSession().createQuery(queryString);
|
1008
|
query.setParameter("accessionNumberString", accessionNumberString);
|
1009
|
@SuppressWarnings("unchecked")
|
1010
|
List<DerivedUnit> results = query.list();
|
1011
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
1012
|
return results;
|
1013
|
}
|
1014
|
|
1015
|
}
|