Revision 71559ffe
Added by Katja Luther over 2 years ago
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/DescriptiveDataSetService.java | ||
|---|---|---|
| 23 | 23 |
import eu.etaxonomy.cdm.api.service.config.DeleteDescriptiveDataSetConfigurator; |
| 24 | 24 |
import eu.etaxonomy.cdm.api.service.config.IdentifiableServiceConfiguratorImpl; |
| 25 | 25 |
import eu.etaxonomy.cdm.api.service.config.RemoveDescriptionsFromDescriptiveDataSetConfigurator; |
| 26 |
import eu.etaxonomy.cdm.api.service.dto.CategoricalDataDto; |
|
| 26 | 27 |
import eu.etaxonomy.cdm.api.service.dto.DescriptionBaseDto; |
| 28 |
import eu.etaxonomy.cdm.api.service.dto.DescriptionElementDto; |
|
| 29 |
import eu.etaxonomy.cdm.api.service.dto.QuantitativeDataDto; |
|
| 27 | 30 |
import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO; |
| 31 |
import eu.etaxonomy.cdm.api.service.dto.SpecimenOrObservationDTOFactory; |
|
| 28 | 32 |
import eu.etaxonomy.cdm.api.service.dto.SpecimenRowWrapperDTO; |
| 33 |
import eu.etaxonomy.cdm.api.service.dto.StateDataDto; |
|
| 34 |
import eu.etaxonomy.cdm.api.service.dto.StatisticalMeasurementValueDto; |
|
| 29 | 35 |
import eu.etaxonomy.cdm.api.service.dto.TaxonRowWrapperDTO; |
| 30 | 36 |
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor; |
| 31 | 37 |
import eu.etaxonomy.cdm.filter.TaxonNodeFilter; |
| ... | ... | |
| 45 | 51 |
import eu.etaxonomy.cdm.model.description.PolytomousKey; |
| 46 | 52 |
import eu.etaxonomy.cdm.model.description.QuantitativeData; |
| 47 | 53 |
import eu.etaxonomy.cdm.model.description.SpecimenDescription; |
| 54 |
import eu.etaxonomy.cdm.model.description.State; |
|
| 48 | 55 |
import eu.etaxonomy.cdm.model.description.StatisticalMeasure; |
| 56 |
import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue; |
|
| 49 | 57 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 50 | 58 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 51 | 59 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| ... | ... | |
| 57 | 65 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 58 | 66 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 59 | 67 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| 68 |
import eu.etaxonomy.cdm.model.term.DefinedTermBase; |
|
| 60 | 69 |
import eu.etaxonomy.cdm.persistence.dao.description.IDescriptiveDataSetDao; |
| 61 | 70 |
import eu.etaxonomy.cdm.persistence.dao.term.IDefinedTermDao; |
| 71 |
import eu.etaxonomy.cdm.persistence.dto.DescriptiveDataSetBaseDto; |
|
| 62 | 72 |
import eu.etaxonomy.cdm.persistence.dto.MergeResult; |
| 63 | 73 |
import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper; |
| 64 | 74 |
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto; |
| ... | ... | |
| 117 | 127 |
return dao.getDescriptiveDataSetUuidAndTitleCache( limitOfInitialElements, pattern); |
| 118 | 128 |
} |
| 119 | 129 |
|
| 130 |
@Override |
|
| 131 |
public DescriptiveDataSetBaseDto getDescriptiveDataSetDtoByUuid(UUID uuid) {
|
|
| 132 |
return dao.getDescriptiveDataSetDtoByUuid(uuid); |
|
| 133 |
} |
|
| 134 |
|
|
| 135 |
|
|
| 120 | 136 |
@Override |
| 121 | 137 |
public ArrayList<RowWrapperDTO> getRowWrapper(UUID descriptiveDataSetUuid, IProgressMonitor monitor) {
|
| 122 | 138 |
DescriptiveDataSet descriptiveDataSet = load(descriptiveDataSetUuid); |
| ... | ... | |
| 223 | 239 |
public TaxonRowWrapperDTO createTaxonRowWrapper(UUID taxonDescriptionUuid, UUID descriptiveDataSetUuid) {
|
| 224 | 240 |
TaxonNode taxonNode = null; |
| 225 | 241 |
Classification classification = null; |
| 226 |
TaxonDescription description = (TaxonDescription) descriptionService.load(taxonDescriptionUuid, |
|
| 227 |
Arrays.asList("taxon", "descriptionElements", "descriptionElements.feature"));
|
|
| 242 |
// TaxonDescription description = (TaxonDescription) descriptionService.loadDto(taxonDescriptionUuid, |
|
| 243 |
// Arrays.asList("taxon", "descriptionElements", "descriptionElements.feature"));
|
|
| 244 |
DescriptionBaseDto description = descriptionService.loadDto(taxonDescriptionUuid); |
|
| 245 |
|
|
| 228 | 246 |
DescriptiveDataSet descriptiveDataSet = dao.load(descriptiveDataSetUuid, null); |
| 229 | 247 |
Optional<TaxonNode> first = descriptiveDataSet.getTaxonSubtreeFilter().stream() |
| 230 | 248 |
.filter(node->node.getClassification()!=null).findFirst(); |
| 231 | 249 |
Optional<Classification> classificationOptional = first.map(node->node.getClassification()); |
| 232 | 250 |
Set<DescriptionBaseDto> descriptions = new HashSet<>(); |
| 251 |
TaxonNodeDto nodeDto = null; |
|
| 233 | 252 |
if(classificationOptional.isPresent()){
|
| 234 | 253 |
classification = classificationOptional.get(); |
| 235 |
Taxon taxon = (Taxon) taxonService.load(description.getTaxon().getId(), Arrays.asList("taxonNodes", "taxonNodes.classification"));
|
|
| 236 |
taxonNode = taxon.getTaxonNode(classification); |
|
| 237 |
for (DescriptionBase desc: taxon.getDescriptions()){
|
|
| 238 |
descriptions.add(new DescriptionBaseDto(desc)); |
|
| 239 |
} |
|
| 240 |
} |
|
| 254 |
// Taxon taxon = (Taxon) taxonService.load(description.getTaxonDto().getId(), Arrays.asList("taxonNodes", "taxonNodes.classification"));
|
|
| 255 |
nodeDto = taxonNodeService.dto(description.getTaxonDto().getUuid(), classification.getUuid()); |
|
| 256 |
// taxonNode = taxon.getTaxonNode(classification); |
|
| 241 | 257 |
|
| 258 |
// for (DescriptionBase desc: taxon.getDescriptions()){
|
|
| 259 |
// descriptions.add(DescriptionBaseDto.fromDescription(desc)); |
|
| 260 |
// } |
|
| 261 |
} |
|
| 262 |
descriptions = new HashSet<>(descriptionService.loadDtosForTaxon(description.getTaxonDto().getUuid())); |
|
| 242 | 263 |
|
| 243 |
return new TaxonRowWrapperDTO(new DescriptionBaseDto(description), new TaxonNodeDto(taxonNode), descriptions);
|
|
| 264 |
return new TaxonRowWrapperDTO(description, nodeDto, descriptions);
|
|
| 244 | 265 |
} |
| 245 | 266 |
|
| 246 | 267 |
@Override |
| ... | ... | |
| 283 | 304 |
taxonService.saveOrUpdate(taxon); |
| 284 | 305 |
result.addUpdatedObject(taxon); |
| 285 | 306 |
} |
| 286 |
DescriptionBase<?> specimenDescription = wrapper.getDescription().getDescription(); |
|
| 287 |
if (specimenDescription.isPersited()){
|
|
| 288 |
specimenDescription = descriptionService.load(specimenDescription.getUuid()); |
|
| 307 |
UUID specimenDescriptionUuid = wrapper.getDescription().getDescriptionUuid(); |
|
| 308 |
DescriptionBaseDto descriptionDto = wrapper.getDescription(); |
|
| 309 |
DescriptionBase<?> specimenDescription = descriptionService.load(specimenDescriptionUuid); |
|
| 310 |
//if description already exist use the loaded one and add changed data otherwise create a new one and add to specimen |
|
| 311 |
if (specimenDescription == null){
|
|
| 312 |
specimenDescription = SpecimenDescription.NewInstance(specimen); |
|
| 313 |
List<DescriptionElementDto> elementDtos = descriptionDto.getElements(); |
|
| 314 |
List<DescriptionElementBase> elements = new ArrayList<>(); |
|
| 315 |
for (DescriptionElementDto elementDto: elementDtos){
|
|
| 316 |
if (elementDto instanceof CategoricalDataDto){
|
|
| 317 |
eu.etaxonomy.cdm.model.description.Character feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, elementDto.getFeatureUuid()); |
|
| 318 |
CategoricalData data = CategoricalData.NewInstance(feature); |
|
| 319 |
for (StateDataDto stateDto:((CategoricalDataDto) elementDto).getStates()){
|
|
| 320 |
State state = DefinedTermBase.getTermByClassAndUUID(State.class, stateDto.getState().getUuid()); |
|
| 321 |
data.addStateData(state); |
|
| 322 |
specimenDescription.addElement(data); |
|
| 323 |
} |
|
| 324 |
} |
|
| 325 |
if (elementDto instanceof QuantitativeDataDto){
|
|
| 326 |
eu.etaxonomy.cdm.model.description.Character feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, elementDto.getFeatureUuid()); |
|
| 327 |
QuantitativeData data = QuantitativeData.NewInstance(feature); |
|
| 328 |
for (StatisticalMeasurementValueDto stateDto:((QuantitativeDataDto) elementDto).getValues()){
|
|
| 329 |
StatisticalMeasure statMeasure = DefinedTermBase.getTermByClassAndUUID(StatisticalMeasure.class, stateDto.getType().getUuid()); |
|
| 330 |
StatisticalMeasurementValue value = StatisticalMeasurementValue.NewInstance(statMeasure, stateDto.getValue()); |
|
| 331 |
data.addStatisticalValue(value); |
|
| 332 |
specimenDescription.addElement(data); |
|
| 333 |
} |
|
| 334 |
} |
|
| 335 |
} |
|
| 336 |
|
|
| 289 | 337 |
}else {
|
| 290 |
specimen.addDescription(specimenDescription); |
|
| 338 |
List<DescriptionElementDto> elementDtos = descriptionDto.getElements(); |
|
| 339 |
for (DescriptionElementDto elementDto: elementDtos){
|
|
| 340 |
if (elementDto instanceof CategoricalDataDto){
|
|
| 341 |
eu.etaxonomy.cdm.model.description.Character feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, elementDto.getFeatureUuid()); |
|
| 342 |
List<DescriptionElementBase> uniqueElementList = specimenDescription.getElements().stream().filter(element -> element.getUuid().equals(elementDto.getElementUuid())).collect(Collectors.toList()); |
|
| 343 |
List<State> allStates = new ArrayList<>(); |
|
| 344 |
CategoricalData element = null; |
|
| 345 |
if (uniqueElementList.size() == 1){
|
|
| 346 |
element = HibernateProxyHelper.deproxy(uniqueElementList.get(0), CategoricalData.class); |
|
| 347 |
}else{
|
|
| 348 |
element = CategoricalData.NewInstance(feature); |
|
| 349 |
} |
|
| 350 |
for (StateDataDto stateDto:((CategoricalDataDto) elementDto).getStates()){
|
|
| 351 |
State state = DefinedTermBase.getTermByClassAndUUID(State.class, stateDto.getState().getUuid()); |
|
| 352 |
allStates.add(state); |
|
| 353 |
} |
|
| 354 |
element.setStateDataOnly(allStates); |
|
| 355 |
} |
|
| 356 |
} |
|
| 291 | 357 |
} |
| 292 | 358 |
// SpecimenRowWrapperDTO rowWrapper = createSpecimenRowWrapper(specimenDescription, wrapper.getTaxonNode().getUuid(), datasetUuid); |
| 293 | 359 |
if(wrapper==null){
|
| 294 |
result.addException(new IllegalArgumentException("Could not create wrapper for "+wrapper.getDescription().getDescription()));
|
|
| 360 |
result.addException(new IllegalArgumentException("Could not create wrapper for "+wrapper.getDescription()));
|
|
| 295 | 361 |
continue; |
| 296 | 362 |
} |
| 297 | 363 |
//add specimen description to data set |
| ... | ... | |
| 356 | 422 |
TaxonRowWrapperDTO taxonRowWrapper = defaultTaxonDescription != null |
| 357 | 423 |
? createTaxonRowWrapper(defaultTaxonDescription.getUuid(), descriptiveDataSet.getUuid()) : null; |
| 358 | 424 |
// use description not specimen for specimenRow |
| 359 |
SpecimenRowWrapperDTO specimenRowWrapperDTO = new SpecimenRowWrapperDTO(new DescriptionBaseDto(description), specimen.getRecordBasis(), new TaxonNodeDto(taxonNode), fieldUnit, identifier, country);
|
|
| 425 |
SpecimenRowWrapperDTO specimenRowWrapperDTO = new SpecimenRowWrapperDTO(DescriptionBaseDto.fromDescription(description), SpecimenOrObservationDTOFactory.fromEntity(specimen), specimen.getRecordBasis(), new TaxonNodeDto(taxonNode), fieldUnit, identifier, country);
|
|
| 360 | 426 |
specimenRowWrapperDTO.setDefaultDescription(taxonRowWrapper); |
| 361 | 427 |
return specimenRowWrapperDTO; |
| 362 | 428 |
} |
| ... | ... | |
| 584 | 650 |
} |
| 585 | 651 |
|
| 586 | 652 |
@Override |
| 587 |
public List<TermDto> getSupportedStatesForFeature(UUID featureUuid){
|
|
| 588 |
return termDao.getSupportedStatesForFeature(featureUuid); |
|
| 653 |
public Map<UUID, List<TermDto>> getSupportedStatesForFeature(Set<UUID> featureUuids){
|
|
| 654 |
return termDao.getSupportedStatesForFeature(featureUuids);
|
|
| 589 | 655 |
} |
| 590 | 656 |
|
| 591 | 657 |
@Override |
Also available in: Unified diff
ref #9710: switch to dtos for descriptive data set and descriptions for character matrix