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package eu.etaxonomy.cdm.api.service;
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import java.math.BigDecimal;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Optional;
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import java.util.Set;
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import java.util.UUID;
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import java.util.stream.Collectors;
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import org.apache.log4j.Logger;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Service;
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import org.springframework.transaction.annotation.Transactional;
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import eu.etaxonomy.cdm.api.service.UpdateResult.Status;
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import eu.etaxonomy.cdm.api.service.config.DeleteDescriptiveDataSetConfigurator;
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import eu.etaxonomy.cdm.api.service.config.IdentifiableServiceConfiguratorImpl;
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import eu.etaxonomy.cdm.api.service.config.RemoveDescriptionsFromDescriptiveDataSetConfigurator;
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import eu.etaxonomy.cdm.api.service.dto.DescriptionBaseDto;
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import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO;
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import eu.etaxonomy.cdm.api.service.dto.SpecimenRowWrapperDTO;
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import eu.etaxonomy.cdm.api.service.dto.TaxonRowWrapperDTO;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
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import eu.etaxonomy.cdm.format.description.DefaultCategoricalDescriptionBuilder;
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import eu.etaxonomy.cdm.format.description.DefaultQuantitativeDescriptionBuilder;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.DescriptionType;
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import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
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import eu.etaxonomy.cdm.model.description.DescriptiveSystemRole;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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import eu.etaxonomy.cdm.model.description.PolytomousKey;
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import eu.etaxonomy.cdm.model.description.QuantitativeData;
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import eu.etaxonomy.cdm.model.description.SpecimenDescription;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.reference.CdmLinkSource;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.persistence.dao.description.IDescriptiveDataSetDao;
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import eu.etaxonomy.cdm.persistence.dao.term.IDefinedTermDao;
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import eu.etaxonomy.cdm.persistence.dto.MergeResult;
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import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
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import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
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import eu.etaxonomy.cdm.persistence.dto.TermDto;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
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import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGenerator;
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import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGeneratorConfigurator;
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@Service
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@Transactional(readOnly=true)
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public class DescriptiveDataSetService
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extends IdentifiableServiceBase<DescriptiveDataSet, IDescriptiveDataSetDao>
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implements IDescriptiveDataSetService {
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private static Logger logger = Logger.getLogger(DescriptiveDataSetService.class);
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@Autowired
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private IOccurrenceService occurrenceService;
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@Autowired
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private ITaxonService taxonService;
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@Autowired
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private IPolytomousKeyService polytomousKeyService;
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@Autowired
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private IDefinedTermDao termDao;
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@Autowired
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private IDescriptionService descriptionService;
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@Autowired
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private ITaxonNodeService taxonNodeService;
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@Override
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@Autowired
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protected void setDao(IDescriptiveDataSetDao dao) {
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this.dao = dao;
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}
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@Override
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public Map<DescriptionBase, Set<DescriptionElementBase>> getDescriptionElements(DescriptiveDataSet descriptiveDataSet, Set<Feature> features, Integer pageSize, Integer pageNumber,
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List<String> propertyPaths) {
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return dao.getDescriptionElements(descriptiveDataSet, features, pageSize, pageNumber, propertyPaths);
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}
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@Override
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public <T extends DescriptionElementBase> Map<UuidAndTitleCache, Map<UUID, Set<T>>> getTaxonFeatureDescriptionElementMap(
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Class<T> clazz, UUID descriptiveDataSetUuid, DescriptiveSystemRole role) {
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return dao.getTaxonFeatureDescriptionElementMap(clazz, descriptiveDataSetUuid, role);
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}
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@Override
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public List<UuidAndTitleCache<DescriptiveDataSet>> getDescriptiveDataSetUuidAndTitleCache(Integer limitOfInitialElements, String pattern) {
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return dao.getDescriptiveDataSetUuidAndTitleCache( limitOfInitialElements, pattern);
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}
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@Override
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public ArrayList<RowWrapperDTO> getRowWrapper(UUID descriptiveDataSetUuid, IProgressMonitor monitor) {
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DescriptiveDataSet descriptiveDataSet = load(descriptiveDataSetUuid);
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monitor.beginTask("Load row wrapper", descriptiveDataSet.getDescriptions().size());
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ArrayList<RowWrapperDTO> wrappers = new ArrayList<>();
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Set<DescriptionBase> descriptions = descriptiveDataSet.getDescriptions();
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for (DescriptionBase description : descriptions) {
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if(monitor.isCanceled()){
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return new ArrayList<>();
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}
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RowWrapperDTO rowWrapper = null;
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// only viable descriptions are aggregated, literature or default descriptions
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if(HibernateProxyHelper.isInstanceOf(description, TaxonDescription.class) &&
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(description.isAggregatedStructuredDescription()
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|| description.getTypes().contains(DescriptionType.DEFAULT_VALUES_FOR_AGGREGATION)
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|| description.getTypes().contains(DescriptionType.SECONDARY_DATA)
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)){
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rowWrapper = createTaxonRowWrapper(description.getUuid(), descriptiveDataSet.getUuid());
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}
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else if (HibernateProxyHelper.isInstanceOf(description, SpecimenDescription.class)&&
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!description.getTypes().contains(DescriptionType.CLONE_FOR_SOURCE)){
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rowWrapper = createSpecimenRowWrapper(HibernateProxyHelper.deproxy(description, SpecimenDescription.class), descriptiveDataSetUuid);
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}
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if(rowWrapper!=null){
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wrappers.add(rowWrapper);
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}
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monitor.worked(1);
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}
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return wrappers;
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}
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@Override
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public Collection<SpecimenNodeWrapper> loadSpecimens(DescriptiveDataSet descriptiveDataSet){
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List<UUID> filteredNodes = findFilteredTaxonNodes(descriptiveDataSet);
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if(filteredNodes.isEmpty()){
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return Collections.EMPTY_SET;
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}
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Collection<SpecimenNodeWrapper> result = occurrenceService.listUuidAndTitleCacheByAssociatedTaxon(filteredNodes, null, null);
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return result;
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}
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@Override
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public Collection<SpecimenNodeWrapper> loadSpecimens(UUID descriptiveDataSetUuid){
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DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);
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return loadSpecimens(dataSet);
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}
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@Override
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public List<UUID> findFilteredTaxonNodes(DescriptiveDataSet descriptiveDataSet){
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TaxonNodeFilter filter = TaxonNodeFilter.NewRankInstance(descriptiveDataSet.getMinRank(), descriptiveDataSet.getMaxRank());
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descriptiveDataSet.getGeoFilter().forEach(area -> filter.orArea(area.getUuid()));
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descriptiveDataSet.getTaxonSubtreeFilter().forEach(node -> filter.orSubtree(node));
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filter.setIncludeUnpublished(true);
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return taxonNodeService.uuidList(filter);
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}
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@Override
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public List<TaxonNode> loadFilteredTaxonNodes(DescriptiveDataSet descriptiveDataSet, List<String> propertyPaths){
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return taxonNodeService.load(findFilteredTaxonNodes(descriptiveDataSet), propertyPaths);
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}
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@Override
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public TaxonDescription findDefaultDescription(UUID specimenDescriptionUuid, UUID dataSetUuid){
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SpecimenDescription specimenDescription = (SpecimenDescription) descriptionService.load(specimenDescriptionUuid);
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DescriptiveDataSet dataSet = load(dataSetUuid);
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TaxonNode node = findTaxonNodeForDescription(specimenDescription, dataSet);
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return recurseDefaultDescription(node, dataSet);
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}
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private TaxonDescription recurseDefaultDescription(TaxonNode node, DescriptiveDataSet dataSet){
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TaxonDescription defaultDescription = null;
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if(node!=null && node.getTaxon()!=null){
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defaultDescription = findTaxonDescriptionByDescriptionType(dataSet, node.getTaxon(), DescriptionType.DEFAULT_VALUES_FOR_AGGREGATION);
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if(defaultDescription==null && node.getParent()!=null){
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defaultDescription = recurseDefaultDescription(node.getParent(), dataSet);
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}
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}
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return defaultDescription;
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}
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private TaxonNode findTaxonNodeForDescription(SpecimenDescription description, DescriptiveDataSet descriptiveDataSet){
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SpecimenOrObservationBase specimen = description.getDescribedSpecimenOrObservation();
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//get taxon node
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Set<IndividualsAssociation> associations = (Set<IndividualsAssociation>)descriptiveDataSet.getDescriptions()
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.stream()
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.flatMap(desc->desc.getElements().stream())// put all description element in one stream
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.filter(element->element instanceof IndividualsAssociation)
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.map(ia->(IndividualsAssociation)ia)
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.collect(Collectors.toSet());
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Classification classification = descriptiveDataSet.getTaxonSubtreeFilter().iterator().next().getClassification();
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for (IndividualsAssociation individualsAssociation : associations) {
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if(individualsAssociation.getAssociatedSpecimenOrObservation().equals(specimen)){
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return ((TaxonDescription) individualsAssociation.getInDescription()).getTaxon().getTaxonNode(classification);
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}
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}
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return null;
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}
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@Override
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public TaxonRowWrapperDTO createTaxonRowWrapper(UUID taxonDescriptionUuid, UUID descriptiveDataSetUuid) {
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TaxonNode taxonNode = null;
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Classification classification = null;
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TaxonDescription description = (TaxonDescription) descriptionService.load(taxonDescriptionUuid,
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Arrays.asList("taxon", "descriptionElements", "descriptionElements.feature"));
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DescriptiveDataSet descriptiveDataSet = dao.load(descriptiveDataSetUuid, null);
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Optional<TaxonNode> first = descriptiveDataSet.getTaxonSubtreeFilter().stream()
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.filter(node->node.getClassification()!=null).findFirst();
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Optional<Classification> classificationOptional = first.map(node->node.getClassification());
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Set<DescriptionBaseDto> descriptions = new HashSet<>();
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if(classificationOptional.isPresent()){
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classification = classificationOptional.get();
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Taxon taxon = (Taxon) taxonService.load(description.getTaxon().getId(), Arrays.asList("taxonNodes", "taxonNodes.classification"));
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taxonNode = taxon.getTaxonNode(classification);
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for (DescriptionBase desc: taxon.getDescriptions()){
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descriptions.add(new DescriptionBaseDto(desc));
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}
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}
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return new TaxonRowWrapperDTO(new DescriptionBaseDto(description), new TaxonNodeDto(taxonNode), descriptions);
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}
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@Override
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@Transactional(readOnly=false)
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public UpdateResult addRowWrapperToDataset(Collection<SpecimenRowWrapperDTO> wrappers, UUID datasetUuid){
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UpdateResult result = new UpdateResult();
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DescriptiveDataSet dataSet = load(datasetUuid);
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result.setCdmEntity(dataSet);
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List<UUID> taxonUuids = wrappers.stream().map(wrapper->wrapper.getTaxonNode().getTaxonUuid()).collect(Collectors.toList());
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List<TaxonBase> taxa = taxonService.load(taxonUuids, Arrays.asList(new String[]{"descriptions"}));
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for (SpecimenRowWrapperDTO wrapper : wrappers) {
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Optional<TaxonBase> findAny = taxa.stream().filter(taxon->taxon.getUuid().equals(wrapper.getTaxonNode().getTaxonUuid())).findAny();
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if(!findAny.isPresent()){
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result.addException(new IllegalArgumentException("Could not create wrapper for "+wrapper.getSpecimen().getTitleCache()));
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continue;
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}
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Taxon taxon = (Taxon) findAny.get();
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// UUID taxonDescriptionUuid = wrapper..getTaxonDescriptionUuid();
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TaxonDescription taxonDescription = null;
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// if(taxonDescriptionUuid!=null){
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// taxonDescription = (TaxonDescription) descriptionService.load(taxonDescriptionUuid);
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// }
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SpecimenOrObservationBase specimen = occurrenceService.load(wrapper.getSpecimen().getUuid());
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if(taxonDescription==null){
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Optional<TaxonDescription> associationDescriptionOptional = taxon.getDescriptions().stream()
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.filter(desc->desc.getTypes().contains(DescriptionType.INDIVIDUALS_ASSOCIATION))
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.findFirst();
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if(!associationDescriptionOptional.isPresent()){
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taxonDescription = TaxonDescription.NewInstance(taxon);
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}
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else{
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taxonDescription = associationDescriptionOptional.get();
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}
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IndividualsAssociation association = IndividualsAssociation.NewInstance(specimen);
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taxonDescription.addElement(association);
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taxonService.saveOrUpdate(taxon);
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result.addUpdatedObject(taxon);
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}
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DescriptionBase specimenDescription = wrapper.getDescription().getDescription();
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if (specimenDescription.isPersited()){
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specimenDescription = descriptionService.load(specimenDescription.getUuid());
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}else {
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specimen.addDescription(specimenDescription);
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}
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// SpecimenRowWrapperDTO rowWrapper = createSpecimenRowWrapper(specimenDescription, wrapper.getTaxonNode().getUuid(), datasetUuid);
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if(wrapper==null){
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result.addException(new IllegalArgumentException("Could not create wrapper for "+wrapper.getDescription().getDescription()));
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continue;
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}
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//add specimen description to data set
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// specimenDescription = (SpecimenDescription) descriptionService.load(rowWrapper.getDescription().getDescription().getUuid());
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specimenDescription.addDescriptiveDataSet(dataSet);
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//add taxon description with IndividualsAssociation to the specimen to data set
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taxonDescription.addDescriptiveDataSet(dataSet);
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result.addUpdatedObject(specimen);
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result.addUpdatedObject(specimenDescription);
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result.addUpdatedObject(taxonDescription);
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}
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saveOrUpdate(dataSet);
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return result;
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}
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private SpecimenRowWrapperDTO createSpecimenRowWrapper(SpecimenDescription description, UUID taxonNodeUuid,
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UUID datasetUuid) {
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TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);
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DescriptiveDataSet descriptiveDataSet = load(datasetUuid);
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SpecimenOrObservationBase specimen = HibernateProxyHelper.deproxy(description.getDescribedSpecimenOrObservation(), SpecimenOrObservationBase.class);
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//supplemental information
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if(taxonNode==null){
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taxonNode = findTaxonNodeForDescription(description, descriptiveDataSet);
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}
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FieldUnit fieldUnit = null;
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String identifier = null;
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NamedArea country = null;
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if(taxonNode==null){
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return null;
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}
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//taxon node was found
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//get field unit
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Collection<FieldUnit> fieldUnits = occurrenceService.findFieldUnits(specimen.getUuid(),
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Arrays.asList(new String[]{
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"gatheringEvent",
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"gatheringEvent.country"
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}));
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if(fieldUnits.size()>1){
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logger.error("More than one or no field unit found for specimen"); //$NON-NLS-1$
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return null;
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}
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else{
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if (fieldUnits != null && fieldUnits.size()>0){
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fieldUnit = fieldUnits.iterator().next();
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}
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}
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//get identifier
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if(HibernateProxyHelper.isInstanceOf(specimen, DerivedUnit.class)){
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identifier = occurrenceService.getMostSignificantIdentifier(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class));
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}
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//get country
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if(fieldUnit!=null && fieldUnit.getGatheringEvent()!=null){
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country = fieldUnit.getGatheringEvent().getCountry();
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}
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//get default taxon description
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// TaxonDescription defaultTaxonDescription = findDefaultDescription(description.getUuid(), descriptiveDataSet.getUuid());
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TaxonDescription defaultTaxonDescription = recurseDefaultDescription(taxonNode, descriptiveDataSet);
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TaxonRowWrapperDTO taxonRowWrapper = defaultTaxonDescription != null
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? createTaxonRowWrapper(defaultTaxonDescription.getUuid(), descriptiveDataSet.getUuid()) : null;
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// use description not specimen for specimenRow
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SpecimenRowWrapperDTO specimenRowWrapperDTO = new SpecimenRowWrapperDTO(new DescriptionBaseDto(description), specimen.getRecordBasis(), new TaxonNodeDto(taxonNode), fieldUnit, identifier, country);
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specimenRowWrapperDTO.setDefaultDescription(taxonRowWrapper);
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return specimenRowWrapperDTO;
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}
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@Override
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public SpecimenRowWrapperDTO createSpecimenRowWrapper(SpecimenDescription description, UUID descriptiveDataSetUuid){
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return createSpecimenRowWrapper(description, null, descriptiveDataSetUuid);
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}
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368
|
|
369
|
@Override
|
370
|
public SpecimenRowWrapperDTO createSpecimenRowWrapper(UUID specimenUuid, UUID taxonNodeUuid, UUID descriptiveDataSetUuid){
|
371
|
|
372
|
SpecimenOrObservationBase<?> specimen = occurrenceService.load(specimenUuid);
|
373
|
SpecimenDescription specimenDescription = findSpecimenDescription(descriptiveDataSetUuid, specimen, true);
|
374
|
return createSpecimenRowWrapper(specimenDescription, taxonNodeUuid, descriptiveDataSetUuid);
|
375
|
}
|
376
|
|
377
|
@Override
|
378
|
@Transactional(readOnly = false)
|
379
|
public UpdateResult updateCaches(Class<? extends DescriptiveDataSet> clazz, Integer stepSize,
|
380
|
IIdentifiableEntityCacheStrategy<DescriptiveDataSet> cacheStrategy, IProgressMonitor monitor) {
|
381
|
if (clazz == null) {
|
382
|
clazz = DescriptiveDataSet.class;
|
383
|
}
|
384
|
return super.updateCachesImpl(clazz, stepSize, cacheStrategy, monitor);
|
385
|
}
|
386
|
|
387
|
private TaxonDescription findTaxonDescriptionByDescriptionType(DescriptiveDataSet dataSet, Taxon taxon, DescriptionType descriptionType){
|
388
|
Optional<TaxonDescription> first = taxon.getDescriptions().stream()
|
389
|
.filter(desc -> desc.getTypes().stream().anyMatch(type -> type.equals(descriptionType)))
|
390
|
.filter(desc -> dataSet.getDescriptions().contains(desc))
|
391
|
.findFirst();
|
392
|
if(first.isPresent()){
|
393
|
return HibernateProxyHelper.deproxy(descriptionService.load(first.get().getUuid(),
|
394
|
Arrays.asList("taxon", "descriptionElements", "descriptionElements.feature")), TaxonDescription.class);
|
395
|
}
|
396
|
return null;
|
397
|
}
|
398
|
|
399
|
@Override
|
400
|
public TaxonDescription findTaxonDescriptionByDescriptionType(UUID dataSetUuid, UUID taxonNodeUuid, DescriptionType descriptionType){
|
401
|
DescriptiveDataSet dataSet = load(dataSetUuid);
|
402
|
TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);
|
403
|
return findTaxonDescriptionByDescriptionType(dataSet, taxonNode.getTaxon(), descriptionType);
|
404
|
}
|
405
|
|
406
|
@Override
|
407
|
@Transactional(readOnly=false)
|
408
|
public UpdateResult generatePolytomousKey(UUID descriptiveDataSetUuid, UUID taxonUuid) {
|
409
|
UpdateResult result = new UpdateResult();
|
410
|
|
411
|
PolytomousKeyGeneratorConfigurator keyConfig = new PolytomousKeyGeneratorConfigurator();
|
412
|
DescriptiveDataSet descriptiveDataSet = load(descriptiveDataSetUuid);
|
413
|
keyConfig.setDataSet(descriptiveDataSet);
|
414
|
PolytomousKey key = new PolytomousKeyGenerator().invoke(keyConfig);
|
415
|
IdentifiableServiceConfiguratorImpl<PolytomousKey> serviceConfig= new IdentifiableServiceConfiguratorImpl<>();
|
416
|
serviceConfig.setTitleSearchString(descriptiveDataSet.getTitleCache());
|
417
|
List<PolytomousKey> list = polytomousKeyService.findByTitle(serviceConfig).getRecords();
|
418
|
if(list!=null){
|
419
|
list.forEach(polytomousKey->polytomousKeyService.delete(polytomousKey));
|
420
|
}
|
421
|
key.setTitleCache(descriptiveDataSet.getTitleCache(), true);
|
422
|
|
423
|
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
|
424
|
key.addTaxonomicScope(taxon);
|
425
|
|
426
|
polytomousKeyService.saveOrUpdate(key);
|
427
|
|
428
|
result.setCdmEntity(key);
|
429
|
result.addUpdatedObject(taxon);
|
430
|
return result;
|
431
|
}
|
432
|
|
433
|
@Override
|
434
|
@Transactional(readOnly=false)
|
435
|
public DeleteResult removeDescription(UUID descriptionUuid, UUID descriptiveDataSetUuid, RemoveDescriptionsFromDescriptiveDataSetConfigurator config) {
|
436
|
DeleteResult result = new DeleteResult();
|
437
|
DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);
|
438
|
DescriptionBase descriptionBase = descriptionService.load(descriptionUuid);
|
439
|
if(dataSet==null || descriptionBase==null){
|
440
|
result.setError();
|
441
|
}
|
442
|
else{
|
443
|
removeDescriptionFromDataSet(result, dataSet, descriptionBase, config);
|
444
|
}
|
445
|
return result;
|
446
|
}
|
447
|
|
448
|
|
449
|
@Override
|
450
|
@Transactional(readOnly=false)
|
451
|
public DeleteResult removeDescriptions(List<UUID> descriptionUuids, UUID descriptiveDataSetUuid, RemoveDescriptionsFromDescriptiveDataSetConfigurator config) {
|
452
|
DeleteResult result = new DeleteResult();
|
453
|
DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);
|
454
|
List<DescriptionBase> descriptions = descriptionService.load(descriptionUuids, null);
|
455
|
if(dataSet==null || descriptions==null){
|
456
|
result.setError();
|
457
|
}
|
458
|
else{
|
459
|
for (DescriptionBase description: descriptions){
|
460
|
removeDescriptionFromDataSet(result, dataSet, description, config);
|
461
|
}
|
462
|
|
463
|
|
464
|
}
|
465
|
return result;
|
466
|
}
|
467
|
|
468
|
/**
|
469
|
* @param result
|
470
|
* @param dataSet
|
471
|
* @param description
|
472
|
*/
|
473
|
private void removeDescriptionFromDataSet(DeleteResult result, DescriptiveDataSet dataSet,
|
474
|
DescriptionBase description, RemoveDescriptionsFromDescriptiveDataSetConfigurator config) {
|
475
|
if (description == null){
|
476
|
return;
|
477
|
}
|
478
|
boolean success = dataSet.removeDescription(description);
|
479
|
result.addDeletedObject(description);// remove taxon description with IndividualsAssociation from data set
|
480
|
if(description instanceof SpecimenDescription){
|
481
|
@SuppressWarnings("cast")
|
482
|
Set<IndividualsAssociation> associations = (Set<IndividualsAssociation>)dataSet.getDescriptions()
|
483
|
.stream()
|
484
|
.flatMap(desc->desc.getElements().stream())// put all description element in one stream
|
485
|
.filter(element->element instanceof IndividualsAssociation)
|
486
|
.map(ia->(IndividualsAssociation)ia)
|
487
|
.collect(Collectors.toSet());
|
488
|
Classification classification = dataSet.getTaxonSubtreeFilter().iterator().next().getClassification();
|
489
|
for (IndividualsAssociation individualsAssociation : associations) {
|
490
|
if(individualsAssociation.getAssociatedSpecimenOrObservation().equals(description.getDescribedSpecimenOrObservation())){
|
491
|
dataSet.removeDescription(individualsAssociation.getInDescription());
|
492
|
result.addUpdatedObject(individualsAssociation.getInDescription());
|
493
|
}
|
494
|
}
|
495
|
}
|
496
|
if (description instanceof TaxonDescription){
|
497
|
UUID taxonUuid = ((TaxonDescription)description).getTaxon().getUuid();
|
498
|
DeleteResult isDeletable = descriptionService.isDeletable(description.getUuid());
|
499
|
for (CdmBase relatedCdmBase: isDeletable.getRelatedObjects()){
|
500
|
if (relatedCdmBase instanceof CdmLinkSource){
|
501
|
CdmLinkSource linkSource = (CdmLinkSource)relatedCdmBase;
|
502
|
if (linkSource.getTarget().equals(this)){
|
503
|
|
504
|
}
|
505
|
}
|
506
|
}
|
507
|
|
508
|
|
509
|
}
|
510
|
if (!config.isOnlyRemoveDescriptionsFromDataSet()){
|
511
|
DeleteResult deleteResult = descriptionService.deleteDescription(description);
|
512
|
result.includeResult(deleteResult);
|
513
|
result.addUpdatedObject(dataSet);
|
514
|
}else{
|
515
|
MergeResult<DescriptiveDataSet> mergeResult = dao.merge(dataSet, true);
|
516
|
result.addUpdatedObject(mergeResult.getMergedEntity());
|
517
|
}
|
518
|
|
519
|
result.setStatus(success?Status.OK:Status.ERROR);
|
520
|
}
|
521
|
|
522
|
@Override
|
523
|
@Transactional(readOnly = false)
|
524
|
public DeleteResult delete(UUID datasetUuid, DeleteDescriptiveDataSetConfigurator config, IProgressMonitor monitor){
|
525
|
DescriptiveDataSet dataSet = dao.load(datasetUuid);
|
526
|
monitor.beginTask("Delete Descriptive Dataset", dataSet.getDescriptions().size() +1);
|
527
|
|
528
|
DeleteResult result = new DeleteResult();
|
529
|
DeleteResult descriptionResult = new DeleteResult();
|
530
|
if (!dataSet.getDescriptions().isEmpty()){
|
531
|
Set<DescriptionBase> descriptions = new HashSet();;
|
532
|
for (DescriptionBase desc: dataSet.getDescriptions()){
|
533
|
descriptions.add(desc);
|
534
|
}
|
535
|
monitor.subTask("Delete descriptions");
|
536
|
for (DescriptionBase desc: descriptions){
|
537
|
dataSet.removeDescription(desc);
|
538
|
if (desc instanceof SpecimenDescription && config.isDeleteAllSpecimenDescriptions()){
|
539
|
descriptionResult.includeResult(descriptionService.deleteDescription(desc));
|
540
|
}else if (desc instanceof TaxonDescription){
|
541
|
if( desc.getTypes().contains(DescriptionType.DEFAULT_VALUES_FOR_AGGREGATION) && config.isDeleteAllDefaultDescriptions()){
|
542
|
descriptionResult.includeResult(descriptionService.deleteDescription(desc));
|
543
|
}else if (desc.getTypes().contains(DescriptionType.SECONDARY_DATA) && config.isDeleteAllLiteratureDescriptions()){
|
544
|
descriptionResult.includeResult(descriptionService.deleteDescription(desc));
|
545
|
}else if (desc.getTypes().contains(DescriptionType.AGGREGATED_STRUC_DESC) && config.isDeleteAllAggregatedDescriptions()){
|
546
|
descriptionResult.includeResult(descriptionService.deleteDescription(desc));
|
547
|
}
|
548
|
|
549
|
}
|
550
|
|
551
|
}
|
552
|
|
553
|
|
554
|
}
|
555
|
UUID uuid = dao.delete(dataSet);
|
556
|
monitor.worked(1);
|
557
|
monitor.done();
|
558
|
result.includeResult(descriptionResult);
|
559
|
result.setStatus(Status.OK);
|
560
|
result.addDeletedObject(dataSet);
|
561
|
return result;
|
562
|
}
|
563
|
|
564
|
@Override
|
565
|
@Transactional(readOnly=false)
|
566
|
public TaxonRowWrapperDTO createTaxonDescription(UUID dataSetUuid, UUID taxonNodeUuid, DescriptionType descriptionType){
|
567
|
DescriptiveDataSet dataSet = load(dataSetUuid);
|
568
|
TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid, Arrays.asList("taxon"));
|
569
|
TaxonDescription newTaxonDescription = TaxonDescription.NewInstance(taxonNode.getTaxon());
|
570
|
newTaxonDescription.setTitleCache(dataSet.getLabel()+": "+newTaxonDescription.generateTitle(), true); //$NON-NLS-2$
|
571
|
newTaxonDescription.getTypes().add(descriptionType);
|
572
|
|
573
|
dataSet.getDescriptiveSystem().getDistinctTerms().forEach(wsFeature->{
|
574
|
if(wsFeature.isSupportsCategoricalData()){
|
575
|
newTaxonDescription.addElement(CategoricalData.NewInstance(wsFeature));
|
576
|
}
|
577
|
else if(wsFeature.isSupportsQuantitativeData()){
|
578
|
newTaxonDescription.addElement(QuantitativeData.NewInstance(wsFeature));
|
579
|
}
|
580
|
});
|
581
|
dataSet.addDescription(newTaxonDescription);
|
582
|
saveOrUpdate(dataSet);
|
583
|
return createTaxonRowWrapper(newTaxonDescription.getUuid(), dataSet.getUuid());
|
584
|
}
|
585
|
|
586
|
@Override
|
587
|
public List<TermDto> getSupportedStatesForFeature(UUID featureUuid){
|
588
|
return termDao.getSupportedStatesForFeature(featureUuid);
|
589
|
}
|
590
|
|
591
|
@Override
|
592
|
@Transactional(readOnly=false)
|
593
|
public SpecimenDescription findSpecimenDescription(UUID descriptiveDataSetUuid, SpecimenOrObservationBase specimen, boolean addDatasetSource){
|
594
|
DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);
|
595
|
// SpecimenOrObservationBase specimen = occurrenceService.load(specimenUuid);
|
596
|
|
597
|
Set<? extends Feature> datasetFeatures = dataSet.getDescriptiveSystem().getDistinctTerms();
|
598
|
List<DescriptionElementBase> matchingDescriptionElements = new ArrayList<>();
|
599
|
|
600
|
for (SpecimenDescription specimenDescription : (Set<SpecimenDescription>) specimen.getDescriptions()) {
|
601
|
specimenDescription = (SpecimenDescription) descriptionService.load(specimenDescription.getUuid());
|
602
|
|
603
|
//check if description is already added to data set
|
604
|
if(dataSet.getDescriptions().contains(specimenDescription) ){
|
605
|
return specimenDescription;
|
606
|
}
|
607
|
|
608
|
//gather specimen description features and check for match with dataset features
|
609
|
Set<Feature> specimenDescriptionFeatures = new HashSet<>();
|
610
|
for (DescriptionElementBase specimenDescriptionElement : specimenDescription.getElements()) {
|
611
|
Feature feature = specimenDescriptionElement.getFeature();
|
612
|
specimenDescriptionFeatures.add(feature);
|
613
|
if(datasetFeatures.contains(feature) && RowWrapperDTO.hasData(specimenDescriptionElement)){
|
614
|
matchingDescriptionElements.add(specimenDescriptionElement);
|
615
|
}
|
616
|
}
|
617
|
}
|
618
|
//Create new specimen description if description has not already been added to the dataset
|
619
|
SpecimenDescription newDesription = SpecimenDescription.NewInstance(specimen);
|
620
|
newDesription.setTitleCache("Dataset "+dataSet.getLabel()+": "+newDesription.generateTitle(), true); //$NON-NLS-2$
|
621
|
|
622
|
//check for equals description element (same feature and same values)
|
623
|
Map<Feature, List<DescriptionElementBase>> featureToElementMap = new HashMap<>();
|
624
|
for(DescriptionElementBase element:matchingDescriptionElements){
|
625
|
List<DescriptionElementBase> list = featureToElementMap.get(element.getFeature());
|
626
|
if(list==null){
|
627
|
list = new ArrayList<>();
|
628
|
}
|
629
|
list.add(element);
|
630
|
featureToElementMap.put(element.getFeature(), list);
|
631
|
}
|
632
|
Set<DescriptionElementBase> descriptionElementsToClone = new HashSet<>();
|
633
|
for(Feature feature:featureToElementMap.keySet()){
|
634
|
List<DescriptionElementBase> elements = featureToElementMap.get(feature);
|
635
|
//no duplicate description elements found for this feature
|
636
|
if(elements.size()==1){
|
637
|
descriptionElementsToClone.add(elements.get(0));
|
638
|
}
|
639
|
//duplicates found -> check if all are equal
|
640
|
else{
|
641
|
DescriptionElementBase match = null;
|
642
|
for (DescriptionElementBase descriptionElementBase : elements) {
|
643
|
if(match==null){
|
644
|
match = descriptionElementBase;
|
645
|
}
|
646
|
else if(!new DescriptionElementCompareWrapper(match).equals(new DescriptionElementCompareWrapper(descriptionElementBase))){
|
647
|
match = null;
|
648
|
//TODO: propagate message
|
649
|
// MessagingUtils.informationDialog(Messages.CharacterMatrix_MULTIPLE_DATA,
|
650
|
// String.format(Messages.CharacterMatrix_MULTIPLE_DATA_MESSAGE, feature.getLabel()));
|
651
|
break;
|
652
|
}
|
653
|
}
|
654
|
if(match!=null){
|
655
|
descriptionElementsToClone.add(match);
|
656
|
}
|
657
|
}
|
658
|
}
|
659
|
//clone matching descriptionElements
|
660
|
for (DescriptionElementBase descriptionElementBase : descriptionElementsToClone) {
|
661
|
DescriptionElementBase clone;
|
662
|
try {
|
663
|
clone = descriptionElementBase.clone(newDesription);
|
664
|
clone.getSources().forEach(source -> {
|
665
|
if(descriptionElementBase instanceof CategoricalData){
|
666
|
TextData label = new DefaultCategoricalDescriptionBuilder().build((CategoricalData) descriptionElementBase, Arrays.asList(new Language[]{Language.DEFAULT()}));
|
667
|
source.setOriginalNameString(label.getText(Language.DEFAULT()));
|
668
|
}
|
669
|
else if(descriptionElementBase instanceof QuantitativeData){
|
670
|
TextData label = new DefaultQuantitativeDescriptionBuilder().build((QuantitativeData) descriptionElementBase, Arrays.asList(new Language[]{Language.DEFAULT()}));
|
671
|
source.setOriginalNameString(label.getText(Language.DEFAULT()));
|
672
|
}
|
673
|
});
|
674
|
} catch (CloneNotSupportedException e) {
|
675
|
//nothing
|
676
|
}
|
677
|
}
|
678
|
|
679
|
//add sources of data set
|
680
|
if(addDatasetSource){
|
681
|
dataSet.getSources().forEach(source->{
|
682
|
try {
|
683
|
newDesription.addSource(source.clone());
|
684
|
} catch (CloneNotSupportedException e) {
|
685
|
//nothing
|
686
|
}
|
687
|
});
|
688
|
}
|
689
|
return newDesription;
|
690
|
|
691
|
}
|
692
|
|
693
|
//TODO: this should either be solved in the model class itself
|
694
|
//OR this should cover all possibilities including modifiers for example
|
695
|
private class DescriptionElementCompareWrapper {
|
696
|
|
697
|
private DescriptionElementBase element;
|
698
|
private Set<UUID> stateUuids = new HashSet<>();
|
699
|
private Set<BigDecimal> avgs = new HashSet<>();
|
700
|
private Set<BigDecimal> exacts = new HashSet<>();
|
701
|
private Set<BigDecimal> maxs = new HashSet<>();
|
702
|
private Set<BigDecimal> mins = new HashSet<>();
|
703
|
private Set<BigDecimal> sampleSizes = new HashSet<>();
|
704
|
private Set<BigDecimal> standardDevs = new HashSet<>();
|
705
|
private Set<BigDecimal> lowerBounds = new HashSet<>();
|
706
|
private Set<BigDecimal> upperBounds = new HashSet<>();
|
707
|
private Set<BigDecimal> variances = new HashSet<>();
|
708
|
|
709
|
public DescriptionElementCompareWrapper(DescriptionElementBase element) {
|
710
|
this.element = element;
|
711
|
if(element.isInstanceOf(CategoricalData.class)){
|
712
|
CategoricalData elementData = (CategoricalData)element;
|
713
|
elementData.getStatesOnly().forEach(state->stateUuids.add(state.getUuid()));
|
714
|
}
|
715
|
else if(element.isInstanceOf(QuantitativeData.class)){
|
716
|
QuantitativeData elementData = (QuantitativeData)element;
|
717
|
elementData.getStatisticalValues().forEach(value->{
|
718
|
if(value.getType().equals(StatisticalMeasure.AVERAGE())){
|
719
|
avgs.add(value.getValue());
|
720
|
}
|
721
|
else if(value.getType().equals(StatisticalMeasure.EXACT_VALUE())){
|
722
|
exacts.add(value.getValue());
|
723
|
|
724
|
}
|
725
|
else if(value.getType().equals(StatisticalMeasure.MAX())){
|
726
|
maxs.add(value.getValue());
|
727
|
}
|
728
|
else if(value.getType().equals(StatisticalMeasure.MIN())){
|
729
|
mins.add(value.getValue());
|
730
|
}
|
731
|
else if(value.getType().equals(StatisticalMeasure.SAMPLE_SIZE())){
|
732
|
sampleSizes.add(value.getValue());
|
733
|
|
734
|
}
|
735
|
else if(value.getType().equals(StatisticalMeasure.STANDARD_DEVIATION())){
|
736
|
standardDevs.add(value.getValue());
|
737
|
}
|
738
|
else if(value.getType().equals(StatisticalMeasure.TYPICAL_LOWER_BOUNDARY())){
|
739
|
lowerBounds.add(value.getValue());
|
740
|
|
741
|
}
|
742
|
else if(value.getType().equals(StatisticalMeasure.TYPICAL_UPPER_BOUNDARY())){
|
743
|
upperBounds.add(value.getValue());
|
744
|
}
|
745
|
else if(value.getType().equals(StatisticalMeasure.VARIANCE())){
|
746
|
variances.add(value.getValue());
|
747
|
}
|
748
|
});
|
749
|
}
|
750
|
}
|
751
|
|
752
|
@Override
|
753
|
public int hashCode() {
|
754
|
final int prime = 31;
|
755
|
int result = 1;
|
756
|
result = prime * result + getOuterType().hashCode();
|
757
|
result = prime * result + ((avgs == null) ? 0 : avgs.hashCode());
|
758
|
result = prime * result + ((element == null) ? 0 : element.hashCode());
|
759
|
result = prime * result + ((exacts == null) ? 0 : exacts.hashCode());
|
760
|
result = prime * result + ((lowerBounds == null) ? 0 : lowerBounds.hashCode());
|
761
|
result = prime * result + ((maxs == null) ? 0 : maxs.hashCode());
|
762
|
result = prime * result + ((mins == null) ? 0 : mins.hashCode());
|
763
|
result = prime * result + ((sampleSizes == null) ? 0 : sampleSizes.hashCode());
|
764
|
result = prime * result + ((standardDevs == null) ? 0 : standardDevs.hashCode());
|
765
|
result = prime * result + ((stateUuids == null) ? 0 : stateUuids.hashCode());
|
766
|
result = prime * result + ((upperBounds == null) ? 0 : upperBounds.hashCode());
|
767
|
result = prime * result + ((variances == null) ? 0 : variances.hashCode());
|
768
|
return result;
|
769
|
}
|
770
|
|
771
|
@Override
|
772
|
public boolean equals(Object obj) {
|
773
|
if (this == obj) {
|
774
|
return true;
|
775
|
}
|
776
|
if (obj == null) {
|
777
|
return false;
|
778
|
}
|
779
|
if (getClass() != obj.getClass()) {
|
780
|
return false;
|
781
|
}
|
782
|
DescriptionElementCompareWrapper other = (DescriptionElementCompareWrapper) obj;
|
783
|
if (!getOuterType().equals(other.getOuterType())) {
|
784
|
return false;
|
785
|
}
|
786
|
if (avgs == null) {
|
787
|
if (other.avgs != null) {
|
788
|
return false;
|
789
|
}
|
790
|
} else if (!avgs.equals(other.avgs)) {
|
791
|
return false;
|
792
|
}
|
793
|
if (element == null) {
|
794
|
if (other.element != null) {
|
795
|
return false;
|
796
|
}
|
797
|
} else if (!element.equals(other.element)) {
|
798
|
return false;
|
799
|
}
|
800
|
if (exacts == null) {
|
801
|
if (other.exacts != null) {
|
802
|
return false;
|
803
|
}
|
804
|
} else if (!exacts.equals(other.exacts)) {
|
805
|
return false;
|
806
|
}
|
807
|
if (lowerBounds == null) {
|
808
|
if (other.lowerBounds != null) {
|
809
|
return false;
|
810
|
}
|
811
|
} else if (!lowerBounds.equals(other.lowerBounds)) {
|
812
|
return false;
|
813
|
}
|
814
|
if (maxs == null) {
|
815
|
if (other.maxs != null) {
|
816
|
return false;
|
817
|
}
|
818
|
} else if (!maxs.equals(other.maxs)) {
|
819
|
return false;
|
820
|
}
|
821
|
if (mins == null) {
|
822
|
if (other.mins != null) {
|
823
|
return false;
|
824
|
}
|
825
|
} else if (!mins.equals(other.mins)) {
|
826
|
return false;
|
827
|
}
|
828
|
if (sampleSizes == null) {
|
829
|
if (other.sampleSizes != null) {
|
830
|
return false;
|
831
|
}
|
832
|
} else if (!sampleSizes.equals(other.sampleSizes)) {
|
833
|
return false;
|
834
|
}
|
835
|
if (standardDevs == null) {
|
836
|
if (other.standardDevs != null) {
|
837
|
return false;
|
838
|
}
|
839
|
} else if (!standardDevs.equals(other.standardDevs)) {
|
840
|
return false;
|
841
|
}
|
842
|
if (stateUuids == null) {
|
843
|
if (other.stateUuids != null) {
|
844
|
return false;
|
845
|
}
|
846
|
} else if (!stateUuids.equals(other.stateUuids)) {
|
847
|
return false;
|
848
|
}
|
849
|
if (upperBounds == null) {
|
850
|
if (other.upperBounds != null) {
|
851
|
return false;
|
852
|
}
|
853
|
} else if (!upperBounds.equals(other.upperBounds)) {
|
854
|
return false;
|
855
|
}
|
856
|
if (variances == null) {
|
857
|
if (other.variances != null) {
|
858
|
return false;
|
859
|
}
|
860
|
} else if (!variances.equals(other.variances)) {
|
861
|
return false;
|
862
|
}
|
863
|
return true;
|
864
|
}
|
865
|
|
866
|
private DescriptiveDataSetService getOuterType() {
|
867
|
return DescriptiveDataSetService.this;
|
868
|
}
|
869
|
|
870
|
|
871
|
|
872
|
}
|
873
|
|
874
|
}
|