import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
-import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
+import eu.etaxonomy.cdm.api.service.dto.TaxonDistributionDTO;
import eu.etaxonomy.cdm.api.service.pager.Pager;
import eu.etaxonomy.cdm.api.service.pager.impl.AbstractPagerImpl;
import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
import eu.etaxonomy.cdm.api.utility.DescriptionUtility;
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
-import eu.etaxonomy.cdm.common.monitor.IRemotingProgressMonitor;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.model.common.Annotation;
import eu.etaxonomy.cdm.model.common.AnnotationType;
import eu.etaxonomy.cdm.model.common.CdmBase;
import eu.etaxonomy.cdm.model.common.DefinedTerm;
-import eu.etaxonomy.cdm.model.common.IdentifiableSource;
import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.common.Marker;
import eu.etaxonomy.cdm.model.common.MarkerType;
-import eu.etaxonomy.cdm.model.common.OriginalSourceType;
import eu.etaxonomy.cdm.model.common.TermVocabulary;
-import eu.etaxonomy.cdm.model.description.CategoricalData;
-import eu.etaxonomy.cdm.model.description.Character;
import eu.etaxonomy.cdm.model.description.DescriptionBase;
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
import eu.etaxonomy.cdm.model.description.Feature;
import eu.etaxonomy.cdm.model.description.FeatureTree;
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
-import eu.etaxonomy.cdm.model.description.QuantitativeData;
import eu.etaxonomy.cdm.model.description.SpecimenDescription;
-import eu.etaxonomy.cdm.model.description.StateData;
-import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
import eu.etaxonomy.cdm.model.description.TaxonDescription;
import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
import eu.etaxonomy.cdm.model.description.TextData;
import eu.etaxonomy.cdm.model.name.TaxonName;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
import eu.etaxonomy.cdm.model.taxon.Taxon;
-import eu.etaxonomy.cdm.model.taxon.TaxonBase;
-import eu.etaxonomy.cdm.model.taxon.TaxonNode;
import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
import eu.etaxonomy.cdm.persistence.dao.common.ITermVocabularyDao;
import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;
import eu.etaxonomy.cdm.persistence.dao.description.IStatisticalMeasurementValueDao;
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
+import eu.etaxonomy.cdm.persistence.dto.MergeResult;
import eu.etaxonomy.cdm.persistence.dto.TermDto;
import eu.etaxonomy.cdm.persistence.query.OrderHint;
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
return descriptionElementDao.saveAll(descriptionElements);
}
+ @Override
+ @Transactional(readOnly = false)
+ public List<MergeResult<DescriptionBase>> mergeDescriptionElements(Collection<TaxonDistributionDTO> descriptionElements, boolean returnTransientEntity) {
+ List<MergeResult<DescriptionBase>> mergedObjects = new ArrayList();
+ List<Distribution> toDelete = new ArrayList<>();
+ for(TaxonDistributionDTO obj : descriptionElements) {
+ Iterator<TaxonDescription> iterator = obj.getDescriptionsWrapper().getDescriptions().iterator();
+ while (iterator.hasNext()){
+ TaxonDescription desc = iterator.next();
+ mergedObjects.add(dao.merge(desc, returnTransientEntity));
+ }
+
+
+ }
+
+ return mergedObjects;
+ }
+
/**
* FIXME Candidate for harmonization
* descriptionElementService.delete
}
- @Override
- @Transactional(readOnly=false)
- public UpdateResult aggregateTaxonDescription(UUID taxonNodeUuid, UUID descriptiveDataSetUuid,
- IRemotingProgressMonitor monitor){
- UpdateResult result = new UpdateResult();
-
- TaxonNode node = taxonNodeDao.load(taxonNodeUuid);
- Taxon taxon = HibernateProxyHelper.deproxy(taxonDao.load(node.getTaxon().getUuid()), Taxon.class);
- result.setCdmEntity(taxon);
-
- //get all "computed" descriptions from all sub nodes
- List<TaxonNode> childNodes = taxonNodeDao.listChildrenOf(node, null, null, true, false, null);
- List<TaxonDescription> computedDescriptions = new ArrayList<>();
-
- childNodes.stream().map(childNode -> childNode.getTaxon())
- .forEach(childTaxon -> childTaxon.getDescriptions().stream()
- // filter out non-computed descriptions
- .filter(description -> description.getMarkers().stream()
- .anyMatch(marker -> marker.getMarkerType().equals(MarkerType.COMPUTED())))
- // add them to the list
- .forEach(computedDescription -> computedDescriptions.add(computedDescription)));
-
- UpdateResult aggregateDescription = aggregateDescription(taxon, computedDescriptions,
- "[Taxon Descriptions]"+taxon.getTitleCache(), descriptiveDataSetUuid);
- result.includeResult(aggregateDescription);
- result.setCdmEntity(aggregateDescription.getCdmEntity());
- aggregateDescription.setCdmEntity(null);
- return result;
- }
-
- @Override
- public UpdateResult aggregateDescription(UUID taxonUuid, List<UUID> descriptionUuids, String descriptionTitle
- , UUID descriptiveDataSetUuid) {
- UpdateResult result = new UpdateResult();
-
- TaxonBase taxonBase = taxonDao.load(taxonUuid);
- if(!(taxonBase instanceof Taxon)){
- result.addException(new ClassCastException("The given taxonUUID does not belong to a taxon"));
- result.setError();
- return result;
- }
- Taxon taxon = (Taxon)taxonBase;
-
- List<DescriptionBase> descriptions = load(descriptionUuids, null);
-
- UpdateResult aggregateDescriptionResult = aggregateDescription(taxon, descriptions, descriptionTitle, descriptiveDataSetUuid);
- result.setCdmEntity(aggregateDescriptionResult.getCdmEntity());
- aggregateDescriptionResult.setCdmEntity(null);
- result.includeResult(aggregateDescriptionResult);
- return result;
- }
-
- @SuppressWarnings("unchecked")
- private UpdateResult aggregateDescription(Taxon taxon, List<? extends DescriptionBase> descriptions, String descriptionTitle
- , UUID descriptiveDataSetUuid) {
- UpdateResult result = new UpdateResult();
- Map<Character, List<DescriptionElementBase>> featureToElementMap = new HashMap<>();
-
- DescriptiveDataSet dataSet = descriptiveDataSetDao.load(descriptiveDataSetUuid);
- if(dataSet==null){
- result.addException(new IllegalArgumentException("Could not find data set for uuid "+descriptiveDataSetUuid));
- result.setAbort();
- return result;
- }
-
- //extract all character description elements
- descriptions.forEach(description->{
- description.getElements()
- .stream()
- //filter out elements that do not have a Characters as Feature
- .filter(element->HibernateProxyHelper.isInstanceOf(((DescriptionElementBase)element).getFeature(), Character.class))
- .forEach(ele->{
- DescriptionElementBase descriptionElement = (DescriptionElementBase)ele;
- List<DescriptionElementBase> list = featureToElementMap.get(descriptionElement.getFeature());
- if(list==null){
- list = new ArrayList<>();
- }
- list.add(descriptionElement);
- featureToElementMap.put(HibernateProxyHelper.deproxy(descriptionElement.getFeature(), Character.class), list);
- });
- });
-
- TaxonDescription description = TaxonDescription.NewInstance(taxon);
- description.setTitleCache("[Aggregation] "+descriptionTitle, true);
- description.addMarker(Marker.NewInstance(MarkerType.COMPUTED(), true));
- IdentifiableSource source = IdentifiableSource.NewInstance(OriginalSourceType.Aggregation);
- description.addSource(source);
- description.addDescriptiveDataSet(dataSet);
-
- featureToElementMap.forEach((feature, elements)->{
- //aggregate categorical data
- if(feature.isSupportsCategoricalData()){
- CategoricalData aggregate = CategoricalData.NewInstance(feature);
- elements.stream()
- .filter(element->element instanceof CategoricalData)
- .forEach(categoricalData->((CategoricalData)categoricalData).getStateData()
- .forEach(stateData->aggregate.addStateData((StateData) stateData.clone())));
- description.addElement(aggregate);
- }
- //aggregate quantitative data
- else if(feature.isSupportsQuantitativeData()){
- QuantitativeData aggregate = QuantitativeData.NewInstance(feature);
- elements.stream()
- .filter(element->element instanceof QuantitativeData)
- .forEach(categoricalData->((QuantitativeData)categoricalData).getStatisticalValues()
- .forEach(statisticalValue->aggregate.addStatisticalValue((StatisticalMeasurementValue) statisticalValue.clone())));
- description.addElement(aggregate);
- }
- });
- result.addUpdatedObject(taxon);
- result.setCdmEntity(description);
- return result;
- }
}
BGBM BDI Projects / cdmlib.git / blobdiff