|
1
|
package eu.etaxonomy.cdm.api.service;
|
|
2
|
|
|
3
|
import java.math.BigDecimal;
|
|
4
|
import java.util.ArrayList;
|
|
5
|
import java.util.Arrays;
|
|
6
|
import java.util.Collection;
|
|
7
|
import java.util.Collections;
|
|
8
|
import java.util.HashMap;
|
|
9
|
import java.util.HashSet;
|
|
10
|
import java.util.List;
|
|
11
|
import java.util.Map;
|
|
12
|
import java.util.Optional;
|
|
13
|
import java.util.Set;
|
|
14
|
import java.util.UUID;
|
|
15
|
import java.util.stream.Collectors;
|
|
16
|
|
|
17
|
import org.apache.logging.log4j.LogManager;
|
|
18
|
import org.apache.logging.log4j.Logger;
|
|
19
|
import org.hibernate.Query;
|
|
20
|
import org.hibernate.Session;
|
|
21
|
import org.springframework.beans.factory.annotation.Autowired;
|
|
22
|
import org.springframework.stereotype.Service;
|
|
23
|
import org.springframework.transaction.annotation.Transactional;
|
|
24
|
|
|
25
|
import eu.etaxonomy.cdm.api.service.UpdateResult.Status;
|
|
26
|
import eu.etaxonomy.cdm.api.service.config.DeleteDescriptiveDataSetConfigurator;
|
|
27
|
import eu.etaxonomy.cdm.api.service.config.IdentifiableServiceConfiguratorImpl;
|
|
28
|
import eu.etaxonomy.cdm.api.service.config.RemoveDescriptionsFromDescriptiveDataSetConfigurator;
|
|
29
|
import eu.etaxonomy.cdm.api.service.dto.CategoricalDataDto;
|
|
30
|
import eu.etaxonomy.cdm.api.service.dto.DescriptionBaseDto;
|
|
31
|
import eu.etaxonomy.cdm.api.service.dto.DescriptionElementDto;
|
|
32
|
import eu.etaxonomy.cdm.api.service.dto.QuantitativeDataDto;
|
|
33
|
import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO;
|
|
34
|
import eu.etaxonomy.cdm.api.service.dto.SpecimenOrObservationDTOFactory;
|
|
35
|
import eu.etaxonomy.cdm.api.service.dto.SpecimenRowWrapperDTO;
|
|
36
|
import eu.etaxonomy.cdm.api.service.dto.StateDataDto;
|
|
37
|
import eu.etaxonomy.cdm.api.service.dto.StatisticalMeasurementValueDto;
|
|
38
|
import eu.etaxonomy.cdm.api.service.dto.TaxonRowWrapperDTO;
|
|
39
|
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
|
|
40
|
import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
|
|
41
|
import eu.etaxonomy.cdm.format.description.DefaultCategoricalDescriptionBuilder;
|
|
42
|
import eu.etaxonomy.cdm.format.description.DefaultQuantitativeDescriptionBuilder;
|
|
43
|
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
|
|
44
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
45
|
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
|
|
46
|
import eu.etaxonomy.cdm.model.common.Language;
|
|
47
|
import eu.etaxonomy.cdm.model.description.CategoricalData;
|
|
48
|
import eu.etaxonomy.cdm.model.description.DescriptionBase;
|
|
49
|
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
|
|
50
|
import eu.etaxonomy.cdm.model.description.DescriptionType;
|
|
51
|
import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
|
|
52
|
import eu.etaxonomy.cdm.model.description.DescriptiveSystemRole;
|
|
53
|
import eu.etaxonomy.cdm.model.description.Feature;
|
|
54
|
import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
|
|
55
|
import eu.etaxonomy.cdm.model.description.MeasurementUnit;
|
|
56
|
import eu.etaxonomy.cdm.model.description.PolytomousKey;
|
|
57
|
import eu.etaxonomy.cdm.model.description.QuantitativeData;
|
|
58
|
import eu.etaxonomy.cdm.model.description.SpecimenDescription;
|
|
59
|
import eu.etaxonomy.cdm.model.description.State;
|
|
60
|
import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
|
|
61
|
import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
|
|
62
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
|
63
|
import eu.etaxonomy.cdm.model.description.TextData;
|
|
64
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
|
65
|
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
|
|
66
|
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
|
|
67
|
import eu.etaxonomy.cdm.model.reference.CdmLinkSource;
|
|
68
|
import eu.etaxonomy.cdm.model.taxon.Classification;
|
|
69
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
|
70
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
|
71
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
|
72
|
import eu.etaxonomy.cdm.model.term.DefinedTermBase;
|
|
73
|
import eu.etaxonomy.cdm.persistence.dao.description.IDescriptiveDataSetDao;
|
|
74
|
import eu.etaxonomy.cdm.persistence.dao.term.IDefinedTermDao;
|
|
75
|
import eu.etaxonomy.cdm.persistence.dto.DescriptiveDataSetBaseDto;
|
|
76
|
import eu.etaxonomy.cdm.persistence.dto.MergeResult;
|
|
77
|
import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
|
|
78
|
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
|
|
79
|
import eu.etaxonomy.cdm.persistence.dto.TermDto;
|
|
80
|
import eu.etaxonomy.cdm.persistence.dto.TermTreeDto;
|
|
81
|
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
|
|
82
|
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
|
|
83
|
import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGenerator;
|
|
84
|
import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGeneratorConfigurator;
|
|
85
|
|
|
86
|
@Service
|
|
87
|
@Transactional(readOnly=true)
|
|
88
|
public class DescriptiveDataSetService
|
|
89
|
extends IdentifiableServiceBase<DescriptiveDataSet, IDescriptiveDataSetDao>
|
|
90
|
implements IDescriptiveDataSetService {
|
|
91
|
|
|
92
|
private static Logger logger = LogManager.getLogger(DescriptiveDataSetService.class);
|
|
93
|
|
|
94
|
@Autowired
|
|
95
|
private IOccurrenceService occurrenceService;
|
|
96
|
|
|
97
|
@Autowired
|
|
98
|
private ITaxonService taxonService;
|
|
99
|
|
|
100
|
@Autowired
|
|
101
|
private IPolytomousKeyService polytomousKeyService;
|
|
102
|
|
|
103
|
@Autowired
|
|
104
|
private IDefinedTermDao termDao;
|
|
105
|
|
|
106
|
@Autowired
|
|
107
|
private IDescriptionService descriptionService;
|
|
108
|
|
|
109
|
@Autowired
|
|
110
|
private ITaxonNodeService taxonNodeService;
|
|
111
|
|
|
112
|
@Override
|
|
113
|
@Autowired
|
|
114
|
protected void setDao(IDescriptiveDataSetDao dao) {
|
|
115
|
this.dao = dao;
|
|
116
|
}
|
|
117
|
|
|
118
|
@Override
|
|
119
|
public Map<DescriptionBase, Set<DescriptionElementBase>> getDescriptionElements(DescriptiveDataSet descriptiveDataSet, Set<Feature> features, Integer pageSize, Integer pageNumber,
|
|
120
|
List<String> propertyPaths) {
|
|
121
|
return dao.getDescriptionElements(descriptiveDataSet, features, pageSize, pageNumber, propertyPaths);
|
|
122
|
}
|
|
123
|
|
|
124
|
@Override
|
|
125
|
public <T extends DescriptionElementBase> Map<UuidAndTitleCache, Map<UUID, Set<T>>> getTaxonFeatureDescriptionElementMap(
|
|
126
|
Class<T> clazz, UUID descriptiveDataSetUuid, DescriptiveSystemRole role) {
|
|
127
|
return dao.getTaxonFeatureDescriptionElementMap(clazz, descriptiveDataSetUuid, role);
|
|
128
|
}
|
|
129
|
|
|
130
|
@Override
|
|
131
|
public List<UuidAndTitleCache<DescriptiveDataSet>> getDescriptiveDataSetUuidAndTitleCache(Integer limitOfInitialElements, String pattern) {
|
|
132
|
return dao.getDescriptiveDataSetUuidAndTitleCache( limitOfInitialElements, pattern);
|
|
133
|
}
|
|
134
|
|
|
135
|
@Override
|
|
136
|
public List<RowWrapperDTO<?>> getRowWrapper(UUID descriptiveDataSetUuid, IProgressMonitor monitor) {
|
|
137
|
DescriptiveDataSetBaseDto datasetDto = dao.getDescriptiveDataSetDtoByUuid(descriptiveDataSetUuid);
|
|
138
|
// DescriptiveDataSet descriptiveDataSet = load(descriptiveDataSetUuid);
|
|
139
|
monitor.beginTask("Load row wrapper", datasetDto.getDescriptionUuids().size());
|
|
140
|
List<RowWrapperDTO<?>> wrappers = new ArrayList<>();
|
|
141
|
Set<UUID> descriptions = datasetDto.getDescriptionUuids();
|
|
142
|
for (UUID description : descriptions) {
|
|
143
|
if(monitor.isCanceled()){
|
|
144
|
return new ArrayList<>();
|
|
145
|
}
|
|
146
|
DescriptionBaseDto descDto = descriptionService.loadDto(description);
|
|
147
|
RowWrapperDTO<?> rowWrapper = null;
|
|
148
|
if (descDto != null && descDto.getTaxonDto() != null &&
|
|
149
|
(descDto.getTypes().contains(DescriptionType.DEFAULT_VALUES_FOR_AGGREGATION)
|
|
150
|
|| descDto.getTypes().contains(DescriptionType.AGGREGATED_STRUC_DESC)
|
|
151
|
|| descDto.getTypes().contains(DescriptionType.SECONDARY_DATA)
|
|
152
|
)){
|
|
153
|
rowWrapper = createTaxonRowWrapper(descDto, datasetDto.getUuid());
|
|
154
|
}
|
|
155
|
else if (descDto != null &&descDto.getSpecimenDto() != null && (descDto.getTypes() == null ||
|
|
156
|
!descDto.getTypes().contains(DescriptionType.CLONE_FOR_SOURCE))){
|
|
157
|
rowWrapper = createSpecimenRowWrapper(descDto, descriptiveDataSetUuid);
|
|
158
|
}
|
|
159
|
if(rowWrapper!=null){
|
|
160
|
wrappers.add(rowWrapper);
|
|
161
|
}
|
|
162
|
monitor.worked(1);
|
|
163
|
}
|
|
164
|
return wrappers;
|
|
165
|
}
|
|
166
|
|
|
167
|
@Override
|
|
168
|
public Collection<SpecimenNodeWrapper> loadSpecimens(DescriptiveDataSet descriptiveDataSet){
|
|
169
|
List<UUID> filteredNodes = findFilteredTaxonNodes(descriptiveDataSet);
|
|
170
|
if(filteredNodes.isEmpty()){
|
|
171
|
return Collections.emptySet();
|
|
172
|
}
|
|
173
|
Collection<SpecimenNodeWrapper> result = occurrenceService.listUuidAndTitleCacheByAssociatedTaxon(filteredNodes, null, null);
|
|
174
|
|
|
175
|
return result;
|
|
176
|
}
|
|
177
|
|
|
178
|
@Override
|
|
179
|
public Collection<SpecimenNodeWrapper> loadSpecimens(UUID descriptiveDataSetUuid){
|
|
180
|
DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);
|
|
181
|
return loadSpecimens(dataSet);
|
|
182
|
}
|
|
183
|
|
|
184
|
|
|
185
|
@Override
|
|
186
|
public List<UUID> findFilteredTaxonNodes(DescriptiveDataSet descriptiveDataSet){
|
|
187
|
TaxonNodeFilter filter = TaxonNodeFilter.NewRankInstance(descriptiveDataSet.getMinRank(), descriptiveDataSet.getMaxRank());
|
|
188
|
descriptiveDataSet.getGeoFilter().forEach(area -> filter.orArea(area.getUuid()));
|
|
189
|
descriptiveDataSet.getTaxonSubtreeFilter().forEach(node -> filter.orSubtree(node));
|
|
190
|
filter.setIncludeUnpublished(true);
|
|
191
|
|
|
192
|
return taxonNodeService.uuidList(filter);
|
|
193
|
}
|
|
194
|
|
|
195
|
@Override
|
|
196
|
public List<TaxonNode> loadFilteredTaxonNodes(DescriptiveDataSet descriptiveDataSet, List<String> propertyPaths){
|
|
197
|
return taxonNodeService.load(findFilteredTaxonNodes(descriptiveDataSet), propertyPaths);
|
|
198
|
}
|
|
199
|
|
|
200
|
@Override
|
|
201
|
public DescriptionBaseDto findDefaultDescription(UUID specimenDescriptionUuid, UUID dataSetUuid){
|
|
202
|
DescriptionBaseDto specimenDescription = descriptionService.loadDto(specimenDescriptionUuid);
|
|
203
|
DescriptiveDataSetBaseDto dataSet = dao.getDescriptiveDataSetDtoByUuid(dataSetUuid);
|
|
204
|
TaxonNodeDto node = findTaxonNodeForDescription(specimenDescription, dataSet);
|
|
205
|
return recurseDefaultDescription(node, dataSet);
|
|
206
|
}
|
|
207
|
|
|
208
|
private DescriptionBaseDto recurseDefaultDescription(TaxonNodeDto node, DescriptiveDataSetBaseDto dataSet){
|
|
209
|
DescriptionBaseDto defaultDescription = null;
|
|
210
|
if(node!=null && node.getTaxonUuid()!=null){
|
|
211
|
defaultDescription = getTaxonDescriptionForDescriptiveDataSetAndType(dataSet, node.getTaxonUuid(), DescriptionType.DEFAULT_VALUES_FOR_AGGREGATION);
|
|
212
|
if(defaultDescription==null && node.getParentUUID()!=null){
|
|
213
|
defaultDescription = recurseDefaultDescription(taxonNodeService.dto(node.getParentUUID()), dataSet);
|
|
214
|
}
|
|
215
|
}
|
|
216
|
return defaultDescription;
|
|
217
|
}
|
|
218
|
|
|
219
|
private TaxonNodeDto findTaxonNodeForDescription(DescriptionBaseDto description, DescriptiveDataSetBaseDto descriptiveDataSet){
|
|
220
|
UuidAndTitleCache<SpecimenOrObservationBase> specimen = description.getSpecimenDto();
|
|
221
|
//get taxon node
|
|
222
|
|
|
223
|
|
|
224
|
return descriptionService.findTaxonNodeDtoForIndividualAssociation(specimen.getUuid(), descriptiveDataSet.getSubTreeFilter().iterator().next().getClassificationUUID());
|
|
225
|
//NOTE: don't remove cast as it does not compile on some systems
|
|
226
|
// List<DescriptionBaseDto> descDtos = descriptionService.loadDtos(descriptiveDataSet.getDescriptionUuids());
|
|
227
|
// descriptionService.
|
|
228
|
// Set<IndividualsAssociation> associations = descDtos
|
|
229
|
// .stream()
|
|
230
|
// .flatMap(desc->desc.getElements().stream())// put all description element in one stream
|
|
231
|
// .filter(element->element.get)
|
|
232
|
// .map(ia->(IndividualsAssociation)ia)
|
|
233
|
// .collect(Collectors.toSet());
|
|
234
|
// UUID classification = descriptiveDataSet.getSubTreeFilter().iterator().next().getClassificationUUID();
|
|
235
|
// for (IndividualsAssociation individualsAssociation : associations) {
|
|
236
|
// if(individualsAssociation.getAssociatedSpecimenOrObservation().equals(specimen)){
|
|
237
|
// return ((TaxonDescription) individualsAssociation.getInDescription()).getTaxon().getTaxonNode(classification);
|
|
238
|
// }
|
|
239
|
// }
|
|
240
|
// return null;
|
|
241
|
}
|
|
242
|
|
|
243
|
@Override
|
|
244
|
public TaxonRowWrapperDTO createTaxonRowWrapper(UUID taxonDescriptionUuid, UUID descriptiveDataSetUuid) {
|
|
245
|
DescriptionBaseDto description = descriptionService.loadDto(taxonDescriptionUuid);
|
|
246
|
return createTaxonRowWrapper(description, descriptiveDataSetUuid);
|
|
247
|
}
|
|
248
|
|
|
249
|
@Override
|
|
250
|
@Transactional(readOnly=false)
|
|
251
|
public UpdateResult addRowWrapperToDataset(Collection<SpecimenRowWrapperDTO> wrappers, UUID datasetUuid, boolean addDatasetSource){
|
|
252
|
UpdateResult result = new UpdateResult();
|
|
253
|
DescriptiveDataSet dataSet = load(datasetUuid);
|
|
254
|
result.setCdmEntity(dataSet);
|
|
255
|
|
|
256
|
List<UUID> taxonUuids = wrappers.stream().map(wrapper->wrapper.getTaxonNode().getTaxonUuid()).collect(Collectors.toList());
|
|
257
|
List<TaxonBase> taxa = taxonService.load(taxonUuids, Arrays.asList(new String[]{"descriptions"}));
|
|
258
|
|
|
259
|
for (SpecimenRowWrapperDTO wrapper : wrappers) {
|
|
260
|
Optional<TaxonBase> findAny = taxa.stream().filter(taxon->taxon.getUuid().equals(wrapper.getTaxonNode().getTaxonUuid())).findAny();
|
|
261
|
if(!findAny.isPresent()){
|
|
262
|
result.addException(new IllegalArgumentException("Could not create wrapper for "+ wrapper.getSpecimenDto().getLabel()));
|
|
263
|
continue;
|
|
264
|
}
|
|
265
|
Taxon taxon = (Taxon) findAny.get();
|
|
266
|
|
|
267
|
SpecimenOrObservationBase<?> specimen = occurrenceService.load(wrapper.getSpecimenDto().getUuid());
|
|
268
|
|
|
269
|
TaxonDescription taxonDescription = taxon.getDescriptions().stream()
|
|
270
|
.filter(desc->desc.getTypes().contains(DescriptionType.INDIVIDUALS_ASSOCIATION))
|
|
271
|
.findFirst().orElseGet(()->{
|
|
272
|
TaxonDescription td = TaxonDescription.NewInstance(taxon);
|
|
273
|
td.addType(DescriptionType.INDIVIDUALS_ASSOCIATION);
|
|
274
|
td.setTitleCache("Specimens used by " + dataSet.getTitleCache() + " for " + getTaxonLabel(taxon), true);
|
|
275
|
return td;});
|
|
276
|
IndividualsAssociation association = null;
|
|
277
|
for (DescriptionElementBase el:taxonDescription.getElements()){
|
|
278
|
if (el instanceof IndividualsAssociation){
|
|
279
|
IndividualsAssociation indAss = (IndividualsAssociation)el;
|
|
280
|
if (indAss.getAssociatedSpecimenOrObservation().getUuid().equals(specimen.getUuid())){
|
|
281
|
association = indAss;
|
|
282
|
}
|
|
283
|
}
|
|
284
|
}
|
|
285
|
|
|
286
|
if (association == null){
|
|
287
|
association = IndividualsAssociation.NewInstance(specimen);
|
|
288
|
taxonDescription.addElement(association);
|
|
289
|
taxonService.saveOrUpdate(taxon);
|
|
290
|
result.addUpdatedObject(taxon);
|
|
291
|
}
|
|
292
|
|
|
293
|
|
|
294
|
|
|
295
|
UUID specimenDescriptionUuid = wrapper.getDescription().getDescriptionUuid();
|
|
296
|
DescriptionBaseDto descriptionDto = wrapper.getDescription();
|
|
297
|
DescriptionBase<?> specimenDescription = descriptionService.load(specimenDescriptionUuid);
|
|
298
|
//if description already exist use the loaded one and add changed data otherwise create a new one and add to specimen
|
|
299
|
if (specimenDescription == null){
|
|
300
|
specimenDescription = SpecimenDescription.NewInstance(specimen);
|
|
301
|
specimenDescription.setUuid(specimenDescriptionUuid);
|
|
302
|
List<DescriptionElementDto> elementDtos = descriptionDto.getElements();
|
|
303
|
|
|
304
|
for (DescriptionElementDto elementDto: elementDtos){
|
|
305
|
if (elementDto instanceof CategoricalDataDto){
|
|
306
|
eu.etaxonomy.cdm.model.description.Character feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, elementDto.getFeatureUuid());
|
|
307
|
CategoricalData data = CategoricalData.NewInstance(feature);
|
|
308
|
for (StateDataDto stateDto:((CategoricalDataDto) elementDto).getStates()){
|
|
309
|
State state = DefinedTermBase.getTermByClassAndUUID(State.class, stateDto.getState().getUuid());
|
|
310
|
data.addStateData(state);
|
|
311
|
specimenDescription.addElement(data);
|
|
312
|
}
|
|
313
|
}
|
|
314
|
if (elementDto instanceof QuantitativeDataDto){
|
|
315
|
eu.etaxonomy.cdm.model.description.Character feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, elementDto.getFeatureUuid());
|
|
316
|
QuantitativeData data = QuantitativeData.NewInstance(feature);
|
|
317
|
if (((QuantitativeDataDto) elementDto).getMeasurementUnit() != null){
|
|
318
|
MeasurementUnit unit = DefinedTermBase.getTermByClassAndUUID(MeasurementUnit.class, ((QuantitativeDataDto) elementDto).getMeasurementUnit().getUuid());
|
|
319
|
data.setUnit(unit);
|
|
320
|
}
|
|
321
|
|
|
322
|
for (StatisticalMeasurementValueDto stateDto:((QuantitativeDataDto) elementDto).getValues()){
|
|
323
|
StatisticalMeasure statMeasure = DefinedTermBase.getTermByClassAndUUID(StatisticalMeasure.class, stateDto.getType().getUuid());
|
|
324
|
StatisticalMeasurementValue value = StatisticalMeasurementValue.NewInstance(statMeasure, stateDto.getValue());
|
|
325
|
data.addStatisticalValue(value);
|
|
326
|
specimenDescription.addElement(data);
|
|
327
|
}
|
|
328
|
}
|
|
329
|
}
|
|
330
|
|
|
331
|
}else {
|
|
332
|
List<DescriptionElementDto> elementDtos = descriptionDto.getElements();
|
|
333
|
for (DescriptionElementDto elementDto: elementDtos){
|
|
334
|
if (elementDto instanceof CategoricalDataDto){
|
|
335
|
eu.etaxonomy.cdm.model.description.Character feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, elementDto.getFeatureUuid());
|
|
336
|
List<DescriptionElementBase> uniqueElementList = specimenDescription.getElements().stream().filter(element -> element.getUuid().equals(elementDto.getElementUuid())).collect(Collectors.toList());
|
|
337
|
List<State> allStates = new ArrayList<>();
|
|
338
|
CategoricalData element = null;
|
|
339
|
if (uniqueElementList.size() == 1){
|
|
340
|
element = HibernateProxyHelper.deproxy(uniqueElementList.get(0), CategoricalData.class);
|
|
341
|
}else{
|
|
342
|
element = CategoricalData.NewInstance(feature);
|
|
343
|
}
|
|
344
|
for (StateDataDto stateDto:((CategoricalDataDto) elementDto).getStates()){
|
|
345
|
State state = DefinedTermBase.getTermByClassAndUUID(State.class, stateDto.getState().getUuid());
|
|
346
|
allStates.add(state);
|
|
347
|
}
|
|
348
|
element.setStateDataOnly(allStates);
|
|
349
|
}
|
|
350
|
if (elementDto instanceof QuantitativeDataDto){
|
|
351
|
eu.etaxonomy.cdm.model.description.Character feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, elementDto.getFeatureUuid());
|
|
352
|
QuantitativeData data = QuantitativeData.NewInstance(feature);
|
|
353
|
if (((QuantitativeDataDto) elementDto).getMeasurementUnit() != null){
|
|
354
|
MeasurementUnit unit = DefinedTermBase.getTermByClassAndUUID(MeasurementUnit.class, ((QuantitativeDataDto) elementDto).getMeasurementUnit().getUuid());
|
|
355
|
data.setUnit(unit);
|
|
356
|
}
|
|
357
|
|
|
358
|
for (StatisticalMeasurementValueDto stateDto:((QuantitativeDataDto) elementDto).getValues()){
|
|
359
|
StatisticalMeasure statMeasure = DefinedTermBase.getTermByClassAndUUID(StatisticalMeasure.class, stateDto.getType().getUuid());
|
|
360
|
StatisticalMeasurementValue value = StatisticalMeasurementValue.NewInstance(statMeasure, stateDto.getValue());
|
|
361
|
data.addStatisticalValue(value);
|
|
362
|
specimenDescription.addElement(data);
|
|
363
|
}
|
|
364
|
}
|
|
365
|
}
|
|
366
|
}
|
|
367
|
if(addDatasetSource){
|
|
368
|
for (IdentifiableSource source: dataSet.getSources()) {
|
|
369
|
try {
|
|
370
|
specimenDescription.addSource(source.clone());
|
|
371
|
} catch (CloneNotSupportedException e) {
|
|
372
|
//nothing
|
|
373
|
}
|
|
374
|
}
|
|
375
|
|
|
376
|
}
|
|
377
|
|
|
378
|
//add specimen description to data set
|
|
379
|
specimenDescription.addDescriptiveDataSet(dataSet);
|
|
380
|
//add taxon description with IndividualsAssociation to the specimen to data set
|
|
381
|
taxonDescription.addDescriptiveDataSet(dataSet);
|
|
382
|
result.addUpdatedObject(specimen);
|
|
383
|
result.addUpdatedObject(specimenDescription);
|
|
384
|
result.addUpdatedObject(taxonDescription);
|
|
385
|
}
|
|
386
|
saveOrUpdate(dataSet);
|
|
387
|
return result;
|
|
388
|
}
|
|
389
|
|
|
390
|
private String getTaxonLabel(Taxon taxon) {
|
|
391
|
if (taxon.getName() != null){
|
|
392
|
return taxon.getName().getTitleCache();
|
|
393
|
}else{
|
|
394
|
return taxon.getTitleCache();
|
|
395
|
}
|
|
396
|
}
|
|
397
|
|
|
398
|
private SpecimenRowWrapperDTO createSpecimenRowWrapper(DescriptionBaseDto description, UUID taxonNodeUuid,
|
|
399
|
UUID datasetUuid) {
|
|
400
|
TaxonNodeDto taxonNode = taxonNodeService.dto(taxonNodeUuid);
|
|
401
|
DescriptiveDataSetBaseDto descriptiveDataSet = getDescriptiveDataSetDtoByUuid(datasetUuid);
|
|
402
|
// UuidAndTitleCache<SpecimenOrObservationBase> specimen = description.getSpecimenDto();
|
|
403
|
SpecimenOrObservationBase specimen = occurrenceService.find(description.getSpecimenDto().getUuid());
|
|
404
|
|
|
405
|
//supplemental information
|
|
406
|
if(taxonNode==null){
|
|
407
|
taxonNode = findTaxonNodeForDescription(description, descriptiveDataSet);
|
|
408
|
}
|
|
409
|
FieldUnit fieldUnit = null;
|
|
410
|
String identifier = null;
|
|
411
|
NamedArea country = null;
|
|
412
|
if(taxonNode==null){
|
|
413
|
return null;
|
|
414
|
}
|
|
415
|
//taxon node was found
|
|
416
|
|
|
417
|
//get field unit
|
|
418
|
Collection<FieldUnit> fieldUnits = occurrenceService.findFieldUnits(specimen.getUuid(),
|
|
419
|
Arrays.asList(new String[]{
|
|
420
|
"gatheringEvent",
|
|
421
|
"gatheringEvent.country"
|
|
422
|
}));
|
|
423
|
if(fieldUnits.size()>1){
|
|
424
|
logger.error("More than one or no field unit found for specimen"); //$NON-NLS-1$
|
|
425
|
return null;
|
|
426
|
}
|
|
427
|
else{
|
|
428
|
if (fieldUnits.size()>0){
|
|
429
|
fieldUnit = fieldUnits.iterator().next();
|
|
430
|
}
|
|
431
|
}
|
|
432
|
//get identifier
|
|
433
|
|
|
434
|
identifier = occurrenceService.getMostSignificantIdentifier(specimen.getUuid());
|
|
435
|
//get country
|
|
436
|
if(fieldUnit != null && fieldUnit.getGatheringEvent() != null){
|
|
437
|
country = fieldUnit.getGatheringEvent().getCountry();
|
|
438
|
}
|
|
439
|
//get default taxon description
|
|
440
|
// TaxonDescription defaultTaxonDescription = findDefaultDescription(description.getUuid(), descriptiveDataSet.getUuid());
|
|
441
|
DescriptionBaseDto defaultTaxonDescription = recurseDefaultDescription(taxonNode, descriptiveDataSet);
|
|
442
|
TaxonRowWrapperDTO taxonRowWrapper = defaultTaxonDescription != null
|
|
443
|
? createTaxonRowWrapper(defaultTaxonDescription.getDescriptionUuid(), descriptiveDataSet.getUuid()) : null;
|
|
444
|
// use description not specimen for specimenRow
|
|
445
|
SpecimenRowWrapperDTO specimenRowWrapperDTO = new SpecimenRowWrapperDTO(description, SpecimenOrObservationDTOFactory.fromEntity(specimen), specimen.getRecordBasis(), taxonNode, fieldUnit, identifier, country);
|
|
446
|
specimenRowWrapperDTO.setDefaultDescription(taxonRowWrapper);
|
|
447
|
return specimenRowWrapperDTO;
|
|
448
|
}
|
|
449
|
|
|
450
|
@Override
|
|
451
|
public SpecimenRowWrapperDTO createSpecimenRowWrapper(DescriptionBaseDto description, UUID descriptiveDataSetUuid){
|
|
452
|
return createSpecimenRowWrapper(description, null, descriptiveDataSetUuid);
|
|
453
|
}
|
|
454
|
|
|
455
|
@Override
|
|
456
|
public SpecimenRowWrapperDTO createSpecimenRowWrapper(UUID specimenUuid, UUID taxonNodeUuid, UUID descriptiveDataSetUuid){
|
|
457
|
|
|
458
|
SpecimenOrObservationBase<?> specimen = occurrenceService.load(specimenUuid);
|
|
459
|
DescriptionBaseDto specimenDescription = findSpecimenDescription(descriptiveDataSetUuid, specimen);
|
|
460
|
return createSpecimenRowWrapper(specimenDescription, taxonNodeUuid, descriptiveDataSetUuid);
|
|
461
|
}
|
|
462
|
|
|
463
|
@Override
|
|
464
|
@Transactional(readOnly = false)
|
|
465
|
public UpdateResult updateCaches(Class<? extends DescriptiveDataSet> clazz, Integer stepSize,
|
|
466
|
IIdentifiableEntityCacheStrategy<DescriptiveDataSet> cacheStrategy, IProgressMonitor monitor) {
|
|
467
|
if (clazz == null) {
|
|
468
|
clazz = DescriptiveDataSet.class;
|
|
469
|
}
|
|
470
|
return super.updateCachesImpl(clazz, stepSize, cacheStrategy, monitor);
|
|
471
|
}
|
|
472
|
|
|
473
|
// private TaxonDescription findTaxonDescriptionByDescriptionType(DescriptiveDataSetBaseDto dataSet, UUID taxonUuid, DescriptionType descriptionType){
|
|
474
|
// descriptionService.find
|
|
475
|
// Optional<TaxonDescription> first = taxon.getDescriptions().stream()
|
|
476
|
// .filter(desc -> desc.getTypes().stream().anyMatch(type -> type.equals(descriptionType)))
|
|
477
|
// .filter(desc -> dataSet.getDescriptions().contains(desc))
|
|
478
|
// .findFirst();
|
|
479
|
// if(first.isPresent()){
|
|
480
|
// return HibernateProxyHelper.deproxy(descriptionService.load(first.get().getUuid(),
|
|
481
|
// Arrays.asList("taxon", "descriptionElements", "descriptionElements.feature")), TaxonDescription.class);
|
|
482
|
// }
|
|
483
|
// return null;
|
|
484
|
// }
|
|
485
|
//
|
|
486
|
// @Override
|
|
487
|
// public TaxonDescription findTaxonDescriptionByDescriptionType(UUID dataSetUuid, UUID taxonNodeUuid, DescriptionType descriptionType){
|
|
488
|
// DescriptiveDataSet dataSet = load(dataSetUuid);
|
|
489
|
// TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);
|
|
490
|
// return findTaxonDescriptionByDescriptionType(dataSet, taxonNode.getTaxon(), descriptionType);
|
|
491
|
// }
|
|
492
|
@Override
|
|
493
|
public DescriptionBaseDto getTaxonDescriptionForDescriptiveDataSetAndType(DescriptiveDataSetBaseDto dataSet, UUID taxonUuid, DescriptionType descriptionType){
|
|
494
|
Session session = getSession();
|
|
495
|
String queryString = "SELECT d.uuid FROM DescriptiveDataSet a JOIN a.descriptions as d JOIN d.taxon t WHERE t.uuid = :taxonuuid AND a.uuid = :dataSetUuid and :descriptionType IN d.types";
|
|
496
|
|
|
497
|
Query query;
|
|
498
|
query = session.createQuery(queryString);
|
|
499
|
query.setParameter("taxonuuid", taxonUuid);
|
|
500
|
query.setParameter("dataSetUuid", dataSet.getUuid());
|
|
501
|
query.setParameter("descriptionType", descriptionType.getKey());
|
|
502
|
|
|
503
|
@SuppressWarnings("unchecked")
|
|
504
|
List<UUID> result = query.list();
|
|
505
|
List<DescriptionBaseDto> list = new ArrayList<>();
|
|
506
|
list.addAll(descriptionService.loadDtos(new HashSet(result)));
|
|
507
|
|
|
508
|
if (list.isEmpty()){
|
|
509
|
return null;
|
|
510
|
}else {
|
|
511
|
List<DescriptionBaseDto> correctTypeOnly = new ArrayList<>();
|
|
512
|
for (DescriptionBaseDto dto: list) {
|
|
513
|
if (dto.getTypes().contains(descriptionType)) {
|
|
514
|
correctTypeOnly.add(dto);
|
|
515
|
}
|
|
516
|
}
|
|
517
|
if (correctTypeOnly.isEmpty()) {
|
|
518
|
return null;
|
|
519
|
}else {
|
|
520
|
return correctTypeOnly.get(0);
|
|
521
|
}
|
|
522
|
}
|
|
523
|
|
|
524
|
// return list.get(0);
|
|
525
|
}
|
|
526
|
|
|
527
|
@Override
|
|
528
|
@Transactional(readOnly=false)
|
|
529
|
public UpdateResult generatePolytomousKey(UUID descriptiveDataSetUuid, UUID taxonUuid) {
|
|
530
|
UpdateResult result = new UpdateResult();
|
|
531
|
|
|
532
|
PolytomousKeyGeneratorConfigurator keyConfig = new PolytomousKeyGeneratorConfigurator();
|
|
533
|
DescriptiveDataSet descriptiveDataSet = load(descriptiveDataSetUuid);
|
|
534
|
keyConfig.setDataSet(descriptiveDataSet);
|
|
535
|
PolytomousKey key = new PolytomousKeyGenerator().invoke(keyConfig);
|
|
536
|
IdentifiableServiceConfiguratorImpl<PolytomousKey> serviceConfig= new IdentifiableServiceConfiguratorImpl<>();
|
|
537
|
serviceConfig.setTitleSearchString(descriptiveDataSet.getTitleCache());
|
|
538
|
List<PolytomousKey> list = polytomousKeyService.findByTitle(serviceConfig).getRecords();
|
|
539
|
if(list!=null){
|
|
540
|
list.forEach(polytomousKey->polytomousKeyService.delete(polytomousKey));
|
|
541
|
}
|
|
542
|
key.setTitleCache(descriptiveDataSet.getTitleCache(), true);
|
|
543
|
|
|
544
|
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
|
|
545
|
key.addTaxonomicScope(taxon);
|
|
546
|
|
|
547
|
polytomousKeyService.saveOrUpdate(key);
|
|
548
|
|
|
549
|
result.setCdmEntity(key);
|
|
550
|
result.addUpdatedObject(taxon);
|
|
551
|
return result;
|
|
552
|
}
|
|
553
|
|
|
554
|
@Override
|
|
555
|
@Transactional(readOnly=false)
|
|
556
|
public DeleteResult removeDescription(UUID descriptionUuid, UUID descriptiveDataSetUuid, RemoveDescriptionsFromDescriptiveDataSetConfigurator config) {
|
|
557
|
DeleteResult result = new DeleteResult();
|
|
558
|
DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);
|
|
559
|
DescriptionBase<?> descriptionBase = descriptionService.load(descriptionUuid);
|
|
560
|
if(dataSet==null || descriptionBase==null){
|
|
561
|
result.setError();
|
|
562
|
}
|
|
563
|
else{
|
|
564
|
removeDescriptionFromDataSet(result, dataSet, descriptionBase, config);
|
|
565
|
}
|
|
566
|
return result;
|
|
567
|
}
|
|
568
|
|
|
569
|
|
|
570
|
@Override
|
|
571
|
@Transactional(readOnly=false)
|
|
572
|
public DeleteResult removeDescriptions(List<UUID> descriptionUuids, UUID descriptiveDataSetUuid, RemoveDescriptionsFromDescriptiveDataSetConfigurator config) {
|
|
573
|
DeleteResult result = new DeleteResult();
|
|
574
|
DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);
|
|
575
|
List<DescriptionBase> descriptions = descriptionService.load(descriptionUuids, null);
|
|
576
|
if(dataSet==null || descriptions==null){
|
|
577
|
result.setError();
|
|
578
|
}
|
|
579
|
else{
|
|
580
|
for (DescriptionBase<?> description: descriptions){
|
|
581
|
removeDescriptionFromDataSet(result, dataSet, description, config);
|
|
582
|
}
|
|
583
|
}
|
|
584
|
return result;
|
|
585
|
}
|
|
586
|
|
|
587
|
private void removeDescriptionFromDataSet(DeleteResult result, DescriptiveDataSet dataSet,
|
|
588
|
DescriptionBase<?> description, RemoveDescriptionsFromDescriptiveDataSetConfigurator config) {
|
|
589
|
if (description == null){
|
|
590
|
return;
|
|
591
|
}
|
|
592
|
boolean success = dataSet.removeDescription(description);
|
|
593
|
result.addDeletedObject(description);// remove taxon description with IndividualsAssociation from data set
|
|
594
|
if(description instanceof SpecimenDescription){
|
|
595
|
@SuppressWarnings({ "unchecked", "cast" })
|
|
596
|
//NOTE: don't remove cast as it does not compile on some systems
|
|
597
|
Set<IndividualsAssociation> associations = (Set<IndividualsAssociation>)dataSet.getDescriptions()
|
|
598
|
.stream()
|
|
599
|
.flatMap(desc->desc.getElements().stream())// put all description element in one stream
|
|
600
|
.filter(element->element instanceof IndividualsAssociation)
|
|
601
|
.map(ia->(IndividualsAssociation)ia)
|
|
602
|
.collect(Collectors.toSet());
|
|
603
|
|
|
604
|
for (IndividualsAssociation individualsAssociation : associations) {
|
|
605
|
if(individualsAssociation.getAssociatedSpecimenOrObservation().equals(description.getDescribedSpecimenOrObservation())){
|
|
606
|
dataSet.removeDescription(individualsAssociation.getInDescription());
|
|
607
|
result.addUpdatedObject(individualsAssociation.getInDescription());
|
|
608
|
}
|
|
609
|
}
|
|
610
|
}
|
|
611
|
if (description instanceof TaxonDescription){
|
|
612
|
DeleteResult isDeletable = descriptionService.isDeletable(description.getUuid());
|
|
613
|
for (CdmBase relatedCdmBase: isDeletable.getRelatedObjects()){
|
|
614
|
if (relatedCdmBase instanceof CdmLinkSource){
|
|
615
|
CdmLinkSource linkSource = (CdmLinkSource)relatedCdmBase;
|
|
616
|
if (linkSource.getTarget().equals(this)){
|
|
617
|
|
|
618
|
}
|
|
619
|
}
|
|
620
|
}
|
|
621
|
|
|
622
|
|
|
623
|
}
|
|
624
|
if (!config.isOnlyRemoveDescriptionsFromDataSet()){
|
|
625
|
DeleteResult deleteResult = descriptionService.deleteDescription(description);
|
|
626
|
result.includeResult(deleteResult);
|
|
627
|
result.addUpdatedObject(dataSet);
|
|
628
|
}else{
|
|
629
|
MergeResult<DescriptiveDataSet> mergeResult = dao.merge(dataSet, true);
|
|
630
|
result.addUpdatedObject(mergeResult.getMergedEntity());
|
|
631
|
}
|
|
632
|
|
|
633
|
result.setStatus(success?Status.OK:Status.ERROR);
|
|
634
|
}
|
|
635
|
|
|
636
|
@Override
|
|
637
|
@Transactional(readOnly = false)
|
|
638
|
public DeleteResult delete(UUID datasetUuid, DeleteDescriptiveDataSetConfigurator config, IProgressMonitor monitor){
|
|
639
|
DescriptiveDataSet dataSet = dao.load(datasetUuid);
|
|
640
|
monitor.beginTask("Delete Descriptive Dataset", dataSet.getDescriptions().size() +1);
|
|
641
|
|
|
642
|
DeleteResult result = new DeleteResult();
|
|
643
|
DeleteResult descriptionResult = new DeleteResult();
|
|
644
|
if (!dataSet.getDescriptions().isEmpty()){
|
|
645
|
Set<DescriptionBase> descriptions = new HashSet<>();;
|
|
646
|
for (DescriptionBase<?> desc: dataSet.getDescriptions()){
|
|
647
|
descriptions.add(desc);
|
|
648
|
}
|
|
649
|
monitor.subTask("Delete descriptions");
|
|
650
|
for (DescriptionBase<?> desc: descriptions){
|
|
651
|
dataSet.removeDescription(desc);
|
|
652
|
if (desc instanceof SpecimenDescription && config.isDeleteAllSpecimenDescriptions()){
|
|
653
|
descriptionResult.includeResult(descriptionService.deleteDescription(desc));
|
|
654
|
}else if (desc instanceof TaxonDescription){
|
|
655
|
if( desc.getTypes().contains(DescriptionType.DEFAULT_VALUES_FOR_AGGREGATION) && config.isDeleteAllDefaultDescriptions()){
|
|
656
|
descriptionResult.includeResult(descriptionService.deleteDescription(desc));
|
|
657
|
}else if (desc.getTypes().contains(DescriptionType.SECONDARY_DATA) && config.isDeleteAllLiteratureDescriptions()){
|
|
658
|
descriptionResult.includeResult(descriptionService.deleteDescription(desc));
|
|
659
|
}else if (desc.getTypes().contains(DescriptionType.AGGREGATED_STRUC_DESC) && config.isDeleteAllAggregatedDescriptions()){
|
|
660
|
descriptionResult.includeResult(descriptionService.deleteDescription(desc));
|
|
661
|
}
|
|
662
|
}
|
|
663
|
}
|
|
664
|
}
|
|
665
|
dao.delete(dataSet);
|
|
666
|
monitor.worked(1);
|
|
667
|
monitor.done();
|
|
668
|
result.includeResult(descriptionResult);
|
|
669
|
result.setStatus(Status.OK);
|
|
670
|
result.addDeletedObject(dataSet);
|
|
671
|
return result;
|
|
672
|
}
|
|
673
|
|
|
674
|
@Override
|
|
675
|
@Transactional(readOnly=false)
|
|
676
|
public TaxonRowWrapperDTO createTaxonDescription(UUID dataSetUuid, UUID taxonNodeUuid, DescriptionType descriptionType){
|
|
677
|
DescriptiveDataSet dataSet = load(dataSetUuid);
|
|
678
|
TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid, Arrays.asList("taxon"));
|
|
679
|
TaxonDescription newTaxonDescription = TaxonDescription.NewInstance(taxonNode.getTaxon());
|
|
680
|
newTaxonDescription.setTitleCache(dataSet.getLabel()+": "+newTaxonDescription.generateTitle(), true); //$NON-NLS-2$
|
|
681
|
newTaxonDescription.getTypes().add(descriptionType);
|
|
682
|
dataSet.addDescription(newTaxonDescription);
|
|
683
|
saveOrUpdate(dataSet);
|
|
684
|
return createTaxonRowWrapper(newTaxonDescription.getUuid(), dataSet.getUuid());
|
|
685
|
}
|
|
686
|
|
|
687
|
@Override
|
|
688
|
public Map<UUID, List<TermDto>> getSupportedStatesForFeature(Set<UUID> featureUuids){
|
|
689
|
return termDao.getSupportedStatesForFeature(featureUuids);
|
|
690
|
}
|
|
691
|
|
|
692
|
@Override
|
|
693
|
@Transactional(readOnly=false)
|
|
694
|
public DescriptionBaseDto findSpecimenDescription(UUID descriptiveDataSetUuid, SpecimenOrObservationBase specimen){
|
|
695
|
DescriptiveDataSetBaseDto dataSet = this.getDescriptiveDataSetDtoByUuid(descriptiveDataSetUuid);
|
|
696
|
// SpecimenOrObservationBase specimen = occurrenceService.load(specimenUuid);
|
|
697
|
|
|
698
|
TermTreeDto datasetFeatures = dataSet.getDescriptiveSystem();
|
|
699
|
List<DescriptionElementBase> matchingDescriptionElements = new ArrayList<>();
|
|
700
|
|
|
701
|
for (SpecimenDescription specimenDescription : (Set<SpecimenDescription>) specimen.getDescriptions()) {
|
|
702
|
specimenDescription = (SpecimenDescription) descriptionService.load(specimenDescription.getUuid());
|
|
703
|
|
|
704
|
//check if description is already added to data set
|
|
705
|
if(dataSet.getDescriptionUuids().contains(specimenDescription.getUuid()) ){
|
|
706
|
return DescriptionBaseDto.fromDescription(specimenDescription);
|
|
707
|
}
|
|
708
|
|
|
709
|
//gather specimen description features and check for match with dataset features
|
|
710
|
Set<Feature> specimenDescriptionFeatures = new HashSet<>();
|
|
711
|
for (DescriptionElementBase specimenDescriptionElement : specimenDescription.getElements()) {
|
|
712
|
Feature feature = specimenDescriptionElement.getFeature();
|
|
713
|
specimenDescriptionFeatures.add(feature);
|
|
714
|
boolean contains = false;
|
|
715
|
for (TermDto featureDto:datasetFeatures.getTerms()){
|
|
716
|
if (featureDto.getUuid().equals(feature.getUuid())){
|
|
717
|
contains = true;
|
|
718
|
break;
|
|
719
|
}
|
|
720
|
}
|
|
721
|
if(contains && RowWrapperDTO.hasData(specimenDescriptionElement)){
|
|
722
|
matchingDescriptionElements.add(specimenDescriptionElement);
|
|
723
|
}
|
|
724
|
}
|
|
725
|
}
|
|
726
|
//Create new specimen description if description has not already been added to the dataset
|
|
727
|
SpecimenDescription newDesription = SpecimenDescription.NewInstance(specimen);
|
|
728
|
newDesription.setTitleCache("Dataset "+dataSet.getTitleCache()+": "+newDesription.generateTitle(), true); //$NON-NLS-2$
|
|
729
|
|
|
730
|
//check for equals description element (same feature and same values)
|
|
731
|
Map<Feature, List<DescriptionElementBase>> featureToElementMap = new HashMap<>();
|
|
732
|
for(DescriptionElementBase element:matchingDescriptionElements){
|
|
733
|
List<DescriptionElementBase> list = featureToElementMap.get(element.getFeature());
|
|
734
|
if(list==null){
|
|
735
|
list = new ArrayList<>();
|
|
736
|
}
|
|
737
|
list.add(element);
|
|
738
|
featureToElementMap.put(element.getFeature(), list);
|
|
739
|
}
|
|
740
|
Set<DescriptionElementBase> descriptionElementsToClone = new HashSet<>();
|
|
741
|
for(Feature feature:featureToElementMap.keySet()){
|
|
742
|
List<DescriptionElementBase> elements = featureToElementMap.get(feature);
|
|
743
|
//no duplicate description elements found for this feature
|
|
744
|
if(elements.size()==1){
|
|
745
|
descriptionElementsToClone.add(elements.get(0));
|
|
746
|
}
|
|
747
|
//duplicates found -> check if all are equal
|
|
748
|
else{
|
|
749
|
DescriptionElementBase match = null;
|
|
750
|
for (DescriptionElementBase descriptionElementBase : elements) {
|
|
751
|
if(match==null){
|
|
752
|
match = descriptionElementBase;
|
|
753
|
}
|
|
754
|
else if(!new DescriptionElementCompareWrapper(match).equals(new DescriptionElementCompareWrapper(descriptionElementBase))){
|
|
755
|
match = null;
|
|
756
|
//TODO: propagate message
|
|
757
|
// MessagingUtils.informationDialog(Messages.CharacterMatrix_MULTIPLE_DATA,
|
|
758
|
// String.format(Messages.CharacterMatrix_MULTIPLE_DATA_MESSAGE, feature.getLabel()));
|
|
759
|
break;
|
|
760
|
}
|
|
761
|
}
|
|
762
|
if(match!=null){
|
|
763
|
descriptionElementsToClone.add(match);
|
|
764
|
}
|
|
765
|
}
|
|
766
|
}
|
|
767
|
//clone matching descriptionElements
|
|
768
|
for (DescriptionElementBase descriptionElementBase : descriptionElementsToClone) {
|
|
769
|
DescriptionElementBase clone;
|
|
770
|
clone = descriptionElementBase.clone(newDesription);
|
|
771
|
clone.getSources().forEach(source -> {
|
|
772
|
if(descriptionElementBase instanceof CategoricalData){
|
|
773
|
TextData label = new DefaultCategoricalDescriptionBuilder().build((CategoricalData) descriptionElementBase, Arrays.asList(new Language[]{Language.DEFAULT()}));
|
|
774
|
source.setOriginalInfo(label.getText(Language.DEFAULT()));
|
|
775
|
}
|
|
776
|
else if(descriptionElementBase instanceof QuantitativeData){
|
|
777
|
TextData label = new DefaultQuantitativeDescriptionBuilder().build((QuantitativeData) descriptionElementBase, Arrays.asList(new Language[]{Language.DEFAULT()}));
|
|
778
|
source.setOriginalInfo(label.getText(Language.DEFAULT()));
|
|
779
|
}
|
|
780
|
});
|
|
781
|
}
|
|
782
|
|
|
783
|
//add sources of data set
|
|
784
|
// if(addDatasetSource){
|
|
785
|
// dataSet.getSources().forEach(source->{
|
|
786
|
// try {
|
|
787
|
// newDesription.addSource(source.clone());
|
|
788
|
// } catch (CloneNotSupportedException e) {
|
|
789
|
// //nothing
|
|
790
|
// }
|
|
791
|
// });
|
|
792
|
// }
|
|
793
|
return DescriptionBaseDto.fromDescription(newDesription);
|
|
794
|
|
|
795
|
}
|
|
796
|
|
|
797
|
//TODO: this should either be solved in the model class itself
|
|
798
|
//OR this should cover all possibilities including modifiers for example
|
|
799
|
private class DescriptionElementCompareWrapper {
|
|
800
|
|
|
801
|
private DescriptionElementBase element;
|
|
802
|
private Set<UUID> stateUuids = new HashSet<>();
|
|
803
|
private Set<BigDecimal> avgs = new HashSet<>();
|
|
804
|
private Set<BigDecimal> exacts = new HashSet<>();
|
|
805
|
private Set<BigDecimal> maxs = new HashSet<>();
|
|
806
|
private Set<BigDecimal> mins = new HashSet<>();
|
|
807
|
private Set<BigDecimal> sampleSizes = new HashSet<>();
|
|
808
|
private Set<BigDecimal> standardDevs = new HashSet<>();
|
|
809
|
private Set<BigDecimal> lowerBounds = new HashSet<>();
|
|
810
|
private Set<BigDecimal> upperBounds = new HashSet<>();
|
|
811
|
private Set<BigDecimal> variances = new HashSet<>();
|
|
812
|
|
|
813
|
public DescriptionElementCompareWrapper(DescriptionElementBase element) {
|
|
814
|
this.element = element;
|
|
815
|
if(element.isInstanceOf(CategoricalData.class)){
|
|
816
|
CategoricalData elementData = (CategoricalData)element;
|
|
817
|
elementData.getStatesOnly().forEach(state->stateUuids.add(state.getUuid()));
|
|
818
|
}
|
|
819
|
else if(element.isInstanceOf(QuantitativeData.class)){
|
|
820
|
QuantitativeData elementData = (QuantitativeData)element;
|
|
821
|
elementData.getStatisticalValues().forEach(value->{
|
|
822
|
if(value.getType().equals(StatisticalMeasure.AVERAGE())){
|
|
823
|
avgs.add(value.getValue());
|
|
824
|
}
|
|
825
|
else if(value.getType().equals(StatisticalMeasure.EXACT_VALUE())){
|
|
826
|
exacts.add(value.getValue());
|
|
827
|
|
|
828
|
}
|
|
829
|
else if(value.getType().equals(StatisticalMeasure.MAX())){
|
|
830
|
maxs.add(value.getValue());
|
|
831
|
}
|
|
832
|
else if(value.getType().equals(StatisticalMeasure.MIN())){
|
|
833
|
mins.add(value.getValue());
|
|
834
|
}
|
|
835
|
else if(value.getType().equals(StatisticalMeasure.SAMPLE_SIZE())){
|
|
836
|
sampleSizes.add(value.getValue());
|
|
837
|
|
|
838
|
}
|
|
839
|
else if(value.getType().equals(StatisticalMeasure.STANDARD_DEVIATION())){
|
|
840
|
standardDevs.add(value.getValue());
|
|
841
|
}
|
|
842
|
else if(value.getType().equals(StatisticalMeasure.TYPICAL_LOWER_BOUNDARY())){
|
|
843
|
lowerBounds.add(value.getValue());
|
|
844
|
|
|
845
|
}
|
|
846
|
else if(value.getType().equals(StatisticalMeasure.TYPICAL_UPPER_BOUNDARY())){
|
|
847
|
upperBounds.add(value.getValue());
|
|
848
|
}
|
|
849
|
else if(value.getType().equals(StatisticalMeasure.VARIANCE())){
|
|
850
|
variances.add(value.getValue());
|
|
851
|
}
|
|
852
|
});
|
|
853
|
}
|
|
854
|
}
|
|
855
|
|
|
856
|
@Override
|
|
857
|
public int hashCode() {
|
|
858
|
final int prime = 31;
|
|
859
|
int result = 1;
|
|
860
|
result = prime * result + getOuterType().hashCode();
|
|
861
|
result = prime * result + ((avgs == null) ? 0 : avgs.hashCode());
|
|
862
|
result = prime * result + ((element == null) ? 0 : element.hashCode());
|
|
863
|
result = prime * result + ((exacts == null) ? 0 : exacts.hashCode());
|
|
864
|
result = prime * result + ((lowerBounds == null) ? 0 : lowerBounds.hashCode());
|
|
865
|
result = prime * result + ((maxs == null) ? 0 : maxs.hashCode());
|
|
866
|
result = prime * result + ((mins == null) ? 0 : mins.hashCode());
|
|
867
|
result = prime * result + ((sampleSizes == null) ? 0 : sampleSizes.hashCode());
|
|
868
|
result = prime * result + ((standardDevs == null) ? 0 : standardDevs.hashCode());
|
|
869
|
result = prime * result + ((stateUuids == null) ? 0 : stateUuids.hashCode());
|
|
870
|
result = prime * result + ((upperBounds == null) ? 0 : upperBounds.hashCode());
|
|
871
|
result = prime * result + ((variances == null) ? 0 : variances.hashCode());
|
|
872
|
return result;
|
|
873
|
}
|
|
874
|
|
|
875
|
@Override
|
|
876
|
public boolean equals(Object obj) {
|
|
877
|
if (this == obj) {
|
|
878
|
return true;
|
|
879
|
}
|
|
880
|
if (obj == null) {
|
|
881
|
return false;
|
|
882
|
}
|
|
883
|
if (getClass() != obj.getClass()) {
|
|
884
|
return false;
|
|
885
|
}
|
|
886
|
DescriptionElementCompareWrapper other = (DescriptionElementCompareWrapper) obj;
|
|
887
|
if (!getOuterType().equals(other.getOuterType())) {
|
|
888
|
return false;
|
|
889
|
}
|
|
890
|
if (avgs == null) {
|
|
891
|
if (other.avgs != null) {
|
|
892
|
return false;
|
|
893
|
}
|
|
894
|
} else if (!avgs.equals(other.avgs)) {
|
|
895
|
return false;
|
|
896
|
}
|
|
897
|
if (element == null) {
|
|
898
|
if (other.element != null) {
|
|
899
|
return false;
|
|
900
|
}
|
|
901
|
} else if (!element.equals(other.element)) {
|
|
902
|
return false;
|
|
903
|
}
|
|
904
|
if (exacts == null) {
|
|
905
|
if (other.exacts != null) {
|
|
906
|
return false;
|
|
907
|
}
|
|
908
|
} else if (!exacts.equals(other.exacts)) {
|
|
909
|
return false;
|
|
910
|
}
|
|
911
|
if (lowerBounds == null) {
|
|
912
|
if (other.lowerBounds != null) {
|
|
913
|
return false;
|
|
914
|
}
|
|
915
|
} else if (!lowerBounds.equals(other.lowerBounds)) {
|
|
916
|
return false;
|
|
917
|
}
|
|
918
|
if (maxs == null) {
|
|
919
|
if (other.maxs != null) {
|
|
920
|
return false;
|
|
921
|
}
|
|
922
|
} else if (!maxs.equals(other.maxs)) {
|
|
923
|
return false;
|
|
924
|
}
|
|
925
|
if (mins == null) {
|
|
926
|
if (other.mins != null) {
|
|
927
|
return false;
|
|
928
|
}
|
|
929
|
} else if (!mins.equals(other.mins)) {
|
|
930
|
return false;
|
|
931
|
}
|
|
932
|
if (sampleSizes == null) {
|
|
933
|
if (other.sampleSizes != null) {
|
|
934
|
return false;
|
|
935
|
}
|
|
936
|
} else if (!sampleSizes.equals(other.sampleSizes)) {
|
|
937
|
return false;
|
|
938
|
}
|
|
939
|
if (standardDevs == null) {
|
|
940
|
if (other.standardDevs != null) {
|
|
941
|
return false;
|
|
942
|
}
|
|
943
|
} else if (!standardDevs.equals(other.standardDevs)) {
|
|
944
|
return false;
|
|
945
|
}
|
|
946
|
if (stateUuids == null) {
|
|
947
|
if (other.stateUuids != null) {
|
|
948
|
return false;
|
|
949
|
}
|
|
950
|
} else if (!stateUuids.equals(other.stateUuids)) {
|
|
951
|
return false;
|
|
952
|
}
|
|
953
|
if (upperBounds == null) {
|
|
954
|
if (other.upperBounds != null) {
|
|
955
|
return false;
|
|
956
|
}
|
|
957
|
} else if (!upperBounds.equals(other.upperBounds)) {
|
|
958
|
return false;
|
|
959
|
}
|
|
960
|
if (variances == null) {
|
|
961
|
if (other.variances != null) {
|
|
962
|
return false;
|
|
963
|
}
|
|
964
|
} else if (!variances.equals(other.variances)) {
|
|
965
|
return false;
|
|
966
|
}
|
|
967
|
return true;
|
|
968
|
}
|
|
969
|
|
|
970
|
private DescriptiveDataSetService getOuterType() {
|
|
971
|
return DescriptiveDataSetService.this;
|
|
972
|
}
|
|
973
|
}
|
|
974
|
|
|
975
|
@Override
|
|
976
|
public DescriptiveDataSetBaseDto getDescriptiveDataSetDtoByUuid(UUID uuid) {
|
|
977
|
return dao.getDescriptiveDataSetDtoByUuid(uuid);
|
|
978
|
}
|
|
979
|
|
|
980
|
@Override
|
|
981
|
public TaxonRowWrapperDTO createTaxonRowWrapper(DescriptionBaseDto description, UUID descriptiveDataSetUuid) {
|
|
982
|
Classification classification = null;
|
|
983
|
DescriptiveDataSet descriptiveDataSet = dao.load(descriptiveDataSetUuid, null);
|
|
984
|
Optional<TaxonNode> first = descriptiveDataSet.getTaxonSubtreeFilter().stream()
|
|
985
|
.filter(node->node.getClassification()!=null).findFirst();
|
|
986
|
Optional<Classification> classificationOptional = first.map(node->node.getClassification());
|
|
987
|
Set<DescriptionBaseDto> descriptions = new HashSet<>();
|
|
988
|
TaxonNodeDto nodeDto = null;
|
|
989
|
if(classificationOptional.isPresent()){
|
|
990
|
classification = classificationOptional.get();
|
|
991
|
nodeDto = taxonNodeService.dto(description.getTaxonDto().getUuid(), classification.getUuid());
|
|
992
|
}
|
|
993
|
|
|
994
|
return new TaxonRowWrapperDTO(description, nodeDto, descriptions);
|
|
995
|
}
|
|
996
|
|
|
997
|
// @Override
|
|
998
|
// public DescriptionBaseDto findTaxonDescriptionByDescriptionType(UUID dataSetUuid, UUID taxonNodeUuid, DescriptionType descriptionType){
|
|
999
|
// DescriptiveDataSetBaseDto dataSet = getDescriptiveDataSetDtoByUuid(dataSetUuid);
|
|
1000
|
// TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);
|
|
1001
|
// return findTaxonDescriptionByDescriptionType(dataSet, taxonNode.getTaxon(), descriptionType);
|
|
1002
|
// }
|
|
1003
|
|
|
1004
|
}
|