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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.api.service;
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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.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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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.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.hibernate.Query;
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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.description.MissingMaximumMode;
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import eu.etaxonomy.cdm.api.service.description.MissingMinimumMode;
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import eu.etaxonomy.cdm.api.service.description.StructuredDescriptionAggregation;
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import eu.etaxonomy.cdm.api.service.dto.CategoricalDataDto;
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import eu.etaxonomy.cdm.api.service.dto.DescriptionBaseDto;
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import eu.etaxonomy.cdm.api.service.dto.DescriptionElementDto;
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import eu.etaxonomy.cdm.api.service.dto.QuantitativeDataDto;
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import eu.etaxonomy.cdm.api.service.dto.StateDataDto;
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import eu.etaxonomy.cdm.api.service.dto.StatisticalMeasurementValueDto;
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import eu.etaxonomy.cdm.api.service.dto.TaxonDistributionDTO;
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import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.api.service.pager.PagerUtils;
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import eu.etaxonomy.cdm.api.service.pager.impl.AbstractPagerImpl;
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import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.format.description.MicroFormatQuantitativeDescriptionBuilder;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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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.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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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.DescriptionElementSource;
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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.Feature;
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import eu.etaxonomy.cdm.model.description.MeasurementUnit;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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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.State;
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import eu.etaxonomy.cdm.model.description.StateData;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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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.media.Media;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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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.reference.ICdmTarget;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.TermTree;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;
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import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionElementDao;
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import eu.etaxonomy.cdm.persistence.dao.description.IDescriptiveDataSetDao;
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import eu.etaxonomy.cdm.persistence.dao.description.IStatisticalMeasurementValueDao;
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import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;
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import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
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import eu.etaxonomy.cdm.persistence.dao.term.IDefinedTermDao;
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import eu.etaxonomy.cdm.persistence.dao.term.ITermNodeDao;
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import eu.etaxonomy.cdm.persistence.dao.term.ITermTreeDao;
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import eu.etaxonomy.cdm.persistence.dao.term.ITermVocabularyDao;
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import eu.etaxonomy.cdm.persistence.dto.FeatureDto;
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import eu.etaxonomy.cdm.persistence.dto.MergeResult;
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import eu.etaxonomy.cdm.persistence.dto.SortableTaxonNodeQueryResult;
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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.query.OrderHint;
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import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
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/**
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* @author a.mueller
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* @author a.kohlbecker
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*
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* @since 24.06.2008
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*/
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@Service
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@Transactional(readOnly = true)
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public class DescriptionServiceImpl
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extends IdentifiableServiceBase<DescriptionBase,IDescriptionDao>
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implements IDescriptionService {
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private static final Logger logger = Logger.getLogger(DescriptionServiceImpl.class);
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protected IDescriptionElementDao descriptionElementDao;
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protected ITermTreeDao featureTreeDao;
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protected IDescriptiveDataSetDao descriptiveDataSetDao;
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protected ITermNodeDao termNodeDao;
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protected ITermVocabularyDao vocabularyDao;
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protected IDefinedTermDao definedTermDao;
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protected IStatisticalMeasurementValueDao statisticalMeasurementValueDao;
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protected ITaxonDao taxonDao;
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protected ITaxonNameDao nameDao;
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protected IOccurrenceDao occurrenceDao;
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protected ITaxonNodeDao taxonNodeDao;
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protected IDescriptiveDataSetDao dataSetDao;
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protected ITermService termService;
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//TODO change to Interface
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private NaturalLanguageGenerator naturalLanguageGenerator;
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@Autowired
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protected void setFeatureTreeDao(ITermTreeDao featureTreeDao) {
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this.featureTreeDao = featureTreeDao;
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}
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@Autowired
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protected void setDescriptiveDataSetDao(IDescriptiveDataSetDao descriptiveDataSetDao) {
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this.descriptiveDataSetDao = descriptiveDataSetDao;
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}
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@Autowired
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protected void setTermNodeDao(ITermNodeDao featureNodeDao) {
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this.termNodeDao = featureNodeDao;
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}
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@Autowired
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protected void setVocabularyDao(ITermVocabularyDao vocabularyDao) {
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this.vocabularyDao = vocabularyDao;
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}
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@Autowired
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protected void setDefinedTermDao(IDefinedTermDao definedTermDao) {
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this.definedTermDao = definedTermDao;
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}
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@Autowired
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protected void setTermService(ITermService definedTermService) {
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this.termService = definedTermService;
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}
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@Autowired
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protected void statisticalMeasurementValueDao(IStatisticalMeasurementValueDao statisticalMeasurementValueDao) {
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this.statisticalMeasurementValueDao = statisticalMeasurementValueDao;
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}
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@Autowired
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protected void setDescriptionElementDao(IDescriptionElementDao descriptionElementDao) {
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this.descriptionElementDao = descriptionElementDao;
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}
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@Autowired
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protected void setNaturalLanguageGenerator(NaturalLanguageGenerator naturalLanguageGenerator) {
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this.naturalLanguageGenerator = naturalLanguageGenerator;
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}
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@Autowired
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protected void setTaxonDao(ITaxonDao taxonDao) {
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this.taxonDao = taxonDao;
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}
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@Autowired
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protected void setTaxonNodeDao(ITaxonNodeDao taxonNodeDao) {
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this.taxonNodeDao = taxonNodeDao;
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}
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@Autowired
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protected void setDataSetDao(IDescriptiveDataSetDao dataSetDao) {
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this.dataSetDao = dataSetDao;
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}
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public DescriptionServiceImpl() {
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logger.debug("Load DescriptionService Bean");
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}
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@Override
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@Transactional(readOnly = false)
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public UpdateResult updateCaches(Class<? extends DescriptionBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<DescriptionBase> cacheStrategy, IProgressMonitor monitor) {
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if (clazz == null){
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clazz = DescriptionBase.class;
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}
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return super.updateCachesImpl(clazz, stepSize, cacheStrategy, monitor);
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}
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@Override
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public TermVocabulary<Feature> getDefaultFeatureVocabulary(){
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String uuidFeature = "b187d555-f06f-4d65-9e53-da7c93f8eaa8";
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UUID featureUuid = UUID.fromString(uuidFeature);
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return vocabularyDao.findByUuid(featureUuid);
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}
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@Override
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@Autowired
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protected void setDao(IDescriptionDao dao) {
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this.dao = dao;
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}
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@Override
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public long count(Class<? extends DescriptionBase> type, Boolean hasImages, Boolean hasText,Set<Feature> feature) {
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return dao.countDescriptions(type, hasImages, hasText, feature);
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}
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@Override
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public <T extends DescriptionElementBase> Pager<T> pageDescriptionElements(DescriptionBase description, Class<? extends DescriptionBase> descriptionType,
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Set<Feature> features, Class<T> type, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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List<T> results = listDescriptionElements(description, descriptionType, features, type, pageSize, pageNumber, propertyPaths);
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return new DefaultPagerImpl<>(pageNumber, Integer.valueOf(results.size()).longValue(), pageSize, results);
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}
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@Override
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@Deprecated
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public <T extends DescriptionElementBase> Pager<T> getDescriptionElements(DescriptionBase description,
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Set<Feature> features, Class<T> type, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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return pageDescriptionElements(description, null, features, type, pageSize, pageNumber, propertyPaths);
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}
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@Override
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public <T extends DescriptionElementBase> List<T> listDescriptionElements(DescriptionBase description,
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Class<? extends DescriptionBase> descriptionType, Set<Feature> features, Class<T> type, Integer pageSize, Integer pageNumber,
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List<String> propertyPaths) {
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long numberOfResults = dao.countDescriptionElements(description, descriptionType, features, type);
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List<T> results = new ArrayList<T>();
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if(AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)) {
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results = dao.getDescriptionElements(description, descriptionType, features, type, pageSize, pageNumber, propertyPaths);
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}
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return results;
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}
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@Override
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@Deprecated
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public <T extends DescriptionElementBase> List<T> listDescriptionElements(DescriptionBase description,
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Set<Feature> features, Class<T> type, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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return listDescriptionElements(description, null, features, type, pageSize, pageNumber, propertyPaths);
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}
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@Override
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public Pager<Media> getMedia(DescriptionElementBase descriptionElement, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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Long numberOfResults = descriptionElementDao.countMedia(descriptionElement);
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List<Media> results = new ArrayList<Media>();
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = descriptionElementDao.getMedia(descriptionElement, pageSize, pageNumber, propertyPaths);
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}
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return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
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}
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@Override
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public Pager<TaxonDescription> pageTaxonDescriptions(Taxon taxon, Set<DefinedTerm> scopes, Set<NamedArea> geographicalScope, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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Set<MarkerType> markerTypes = null;
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Set<DescriptionType> descriptionTypes = null;
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return pageTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, descriptionTypes, pageSize, pageNumber, propertyPaths);
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}
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@Override
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public List<TaxonDescription> listTaxonDescriptions(Taxon taxon, Set<DefinedTerm> scopes, Set<NamedArea> geographicalScope, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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Set<MarkerType> markerTypes = null;
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Set<DescriptionType> descriptionTypes = null;
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return listTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, descriptionTypes, pageSize, pageNumber, propertyPaths);
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}
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@Override
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public Pager<TaxonDescription> pageTaxonDescriptions(Taxon taxon, Set<DefinedTerm> scopes, Set<NamedArea> geographicalScope, Set<MarkerType> markerTypes, Set<DescriptionType> descriptionTypes, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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long numberOfResults = dao.countTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, descriptionTypes);
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List<TaxonDescription> results = new ArrayList<>();
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.listTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, descriptionTypes, pageSize, pageNumber, propertyPaths);
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}
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return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
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}
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@Override
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public List<TaxonDescription> listTaxonDescriptions(Taxon taxon, Set<DefinedTerm> scopes, Set<NamedArea> geographicalScope, Set<MarkerType> markerTypes, Set<DescriptionType> descriptionTypes, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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List<TaxonDescription> results = dao.listTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, descriptionTypes, pageSize, pageNumber, propertyPaths);
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return results;
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}
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@Override
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public List<Media> listTaxonDescriptionMedia(UUID taxonUuid, boolean limitToGalleries, Set<MarkerType> markerTypes, Integer pageSize, Integer pageNumber, List<String> propertyPaths){
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return this.dao.listTaxonDescriptionMedia(taxonUuid, limitToGalleries, markerTypes, pageSize, pageNumber, propertyPaths);
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}
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@Override
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public int countTaxonDescriptionMedia(UUID taxonUuid, boolean limitToGalleries, Set<MarkerType> markerTypes){
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return this.dao.countTaxonDescriptionMedia(taxonUuid, limitToGalleries, markerTypes);
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}
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@Override
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public Pager<TaxonNameDescription> getTaxonNameDescriptions(TaxonName name, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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long numberOfResults = dao.countTaxonNameDescriptions(name);
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List<TaxonNameDescription> results = new ArrayList<>();
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.getTaxonNameDescriptions(name, pageSize, pageNumber,propertyPaths);
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}
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return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
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}
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@Override
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public Pager<DescriptionBase> page(Class<? extends DescriptionBase> type, Boolean hasImages, Boolean hasText, Set<Feature> feature, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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long numberOfResults = dao.countDescriptions(type, hasImages, hasText, feature);
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@SuppressWarnings("rawtypes")
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List<DescriptionBase> results = new ArrayList<>();
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.listDescriptions(type, hasImages, hasText, feature, pageSize, pageNumber,orderHints,propertyPaths);
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}
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return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
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}
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/**
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* FIXME Candidate for harmonization
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* Rename: searchByDistribution
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*/
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@Override
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public Pager<TaxonDescription> searchDescriptionByDistribution(Set<NamedArea> namedAreas, PresenceAbsenceTerm presence, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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long numberOfResults = dao.countDescriptionByDistribution(namedAreas, presence);
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List<TaxonDescription> results = new ArrayList<>();
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.searchDescriptionByDistribution(namedAreas, presence, pageSize, pageNumber,orderHints,propertyPaths);
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}
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return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
|
357
|
}
|
358
|
|
359
|
/**
|
360
|
* FIXME Candidate for harmonization
|
361
|
* move: descriptionElementService.search
|
362
|
*/
|
363
|
@Override
|
364
|
// public Pager<T> searchElements(Class<? extends T> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
365
|
public <S extends DescriptionElementBase> Pager<S> searchElements(Class<S> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
366
|
long numberOfResults = descriptionElementDao.count(clazz, queryString);
|
367
|
|
368
|
List<S> results = new ArrayList<>();
|
369
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
370
|
results = (List<S>)descriptionElementDao.search(clazz, queryString, pageSize, pageNumber, orderHints, propertyPaths);
|
371
|
}
|
372
|
|
373
|
return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
|
374
|
}
|
375
|
|
376
|
@Override
|
377
|
@Transactional(readOnly = false)
|
378
|
public List<MergeResult<DescriptionBase>> mergeDescriptionElements(Collection<TaxonDistributionDTO> descriptionElements, boolean returnTransientEntity) {
|
379
|
List<MergeResult<DescriptionBase>> mergedObjects = new ArrayList<>();
|
380
|
|
381
|
for(TaxonDistributionDTO obj : descriptionElements) {
|
382
|
Iterator<TaxonDescription> iterator = obj.getDescriptionsWrapper().getDescriptions().iterator();
|
383
|
List<DescriptionBase> list = new ArrayList(obj.getDescriptionsWrapper().getDescriptions());
|
384
|
// Map<UUID, DescriptionBase> map = dao.saveOrUpdateAll(list);
|
385
|
// MergeResult<DescriptionBase> mergeResult = new MergeResult<DescriptionBase>(mergedEntity, newEntities)
|
386
|
// mergedObjects.add(map.values());
|
387
|
while (iterator.hasNext()){
|
388
|
TaxonDescription desc = iterator.next();
|
389
|
mergedObjects.add(dao.merge(desc, returnTransientEntity));
|
390
|
}
|
391
|
}
|
392
|
|
393
|
return mergedObjects;
|
394
|
}
|
395
|
|
396
|
@Override
|
397
|
@Transactional(readOnly = false)
|
398
|
public UpdateResult mergeDescriptions(Collection<DescriptionBaseDto> descriptions, UUID descriptiveDataSetUuid) {
|
399
|
|
400
|
UpdateResult result = new UpdateResult();
|
401
|
DescriptiveDataSet dataSet = descriptiveDataSetDao.load(descriptiveDataSetUuid);
|
402
|
Set<DescriptionBase> descriptionsOfDataSet = dataSet.getDescriptions();
|
403
|
HashMap<UUID, Set<DescriptionBase>> descriptionSpecimenMap = new HashMap<>();
|
404
|
Set<DescriptionBase> specimenDescriptions;
|
405
|
for (DescriptionBase<?> descriptionBase: descriptionsOfDataSet){
|
406
|
if (descriptionBase.getDescribedSpecimenOrObservation() != null){
|
407
|
specimenDescriptions = descriptionSpecimenMap.get(descriptionBase.getDescribedSpecimenOrObservation().getUuid());
|
408
|
if (specimenDescriptions == null){
|
409
|
specimenDescriptions = new HashSet<>();
|
410
|
}
|
411
|
specimenDescriptions.add(descriptionBase);
|
412
|
descriptionSpecimenMap.put(descriptionBase.getDescribedSpecimenOrObservation().getUuid(), specimenDescriptions);
|
413
|
}
|
414
|
if (descriptionBase instanceof TaxonDescription){
|
415
|
specimenDescriptions = descriptionSpecimenMap.get(((TaxonDescription)descriptionBase).getTaxon().getUuid());
|
416
|
if (specimenDescriptions == null){
|
417
|
specimenDescriptions = new HashSet<>();
|
418
|
}
|
419
|
specimenDescriptions.add(descriptionBase);
|
420
|
descriptionSpecimenMap.put(((TaxonDescription)descriptionBase).getTaxon().getUuid(), specimenDescriptions);
|
421
|
}
|
422
|
if (descriptionBase instanceof TaxonNameDescription){
|
423
|
specimenDescriptions = descriptionSpecimenMap.get(((TaxonNameDescription)descriptionBase).getTaxonName().getUuid());
|
424
|
if (specimenDescriptions == null){
|
425
|
specimenDescriptions = new HashSet<>();
|
426
|
}
|
427
|
specimenDescriptions.add(descriptionBase);
|
428
|
descriptionSpecimenMap.put(((TaxonNameDescription)descriptionBase).getTaxonName().getUuid(), specimenDescriptions);
|
429
|
}
|
430
|
}
|
431
|
MergeResult<DescriptionBase> mergeResult = null;
|
432
|
for(DescriptionBaseDto descDto : descriptions) {
|
433
|
|
434
|
UUID descriptionUUID = descDto.getDescriptionUuid();
|
435
|
DescriptionBase<?> description = load(descriptionUUID);
|
436
|
|
437
|
UUID describedObjectUuid = null;
|
438
|
if (description instanceof SpecimenDescription){
|
439
|
describedObjectUuid = descDto.getSpecimenDto().getUuid();
|
440
|
}else if (description instanceof TaxonDescription){
|
441
|
describedObjectUuid = descDto.getTaxonDto().getUuid();
|
442
|
}else if (description instanceof TaxonNameDescription){
|
443
|
describedObjectUuid = descDto.getNameDto().getUuid();
|
444
|
}
|
445
|
|
446
|
Set<DescriptionBase> descSpecimen = descriptionSpecimenMap.get(describedObjectUuid);
|
447
|
|
448
|
if (descSpecimen != null ){
|
449
|
|
450
|
// TODO: elements are Dtos now, no cdm entities, needs to get the value and replace or create new description element
|
451
|
Set<DescriptionElementDto> elements = new HashSet<>();
|
452
|
for (Object element: descDto.getElements()){
|
453
|
elements.add((DescriptionElementDto)element);
|
454
|
}
|
455
|
|
456
|
DescriptionBase<?> desc = null;
|
457
|
for (DescriptionBase<?> tempDesc: descSpecimen){
|
458
|
if (tempDesc.getUuid().equals(descDto.getDescriptionUuid())){
|
459
|
desc = tempDesc;
|
460
|
break;
|
461
|
}
|
462
|
}
|
463
|
|
464
|
Set<DescriptionElementBase> removeElements = new HashSet<>();
|
465
|
Set<DescriptionElementBase> descriptionElements = desc.getElements();
|
466
|
for (DescriptionElementBase elementBase: descriptionElements){
|
467
|
UUID descElementUuid = elementBase.getUuid();
|
468
|
if (descElementUuid != null){
|
469
|
List<DescriptionElementDto> equalUuidsElements = elements.stream().filter( e -> e != null && e.getElementUuid() != null && e.getElementUuid().equals(descElementUuid)).collect(Collectors.toList());
|
470
|
if (equalUuidsElements.size() == 0 || (equalUuidsElements.size() == 1 && equalUuidsElements.get(0)instanceof QuantitativeDataDto && ((QuantitativeDataDto)equalUuidsElements.get(0)).getValues().isEmpty())){
|
471
|
removeElements.add(elementBase);
|
472
|
}
|
473
|
}
|
474
|
}
|
475
|
if (!removeElements.isEmpty()){
|
476
|
for (DescriptionElementBase el: removeElements){
|
477
|
desc.removeElement(el);
|
478
|
}
|
479
|
}
|
480
|
|
481
|
// description.setDescribedSpecimenOrObservation(null);
|
482
|
|
483
|
for (DescriptionElementDto descElement: elements){
|
484
|
if (descElement == null){
|
485
|
continue;
|
486
|
}
|
487
|
UUID descElementUuid = descElement.getElementUuid();
|
488
|
if (descElement instanceof CategoricalDataDto && ((CategoricalDataDto)descElement).getStates().isEmpty() || descElement instanceof QuantitativeDataDto && ((QuantitativeDataDto)descElement).getValues().isEmpty()){
|
489
|
continue;
|
490
|
}
|
491
|
List<DescriptionElementBase> equalUuidsElements = descriptionElements.stream().filter( e -> e.getUuid().equals(descElementUuid)).collect(Collectors.toList());
|
492
|
eu.etaxonomy.cdm.model.description.Feature feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Feature.class, descElement.getFeatureUuid());
|
493
|
if (feature == null){
|
494
|
feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, descElement.getFeatureUuid());
|
495
|
}
|
496
|
if (equalUuidsElements.size() == 0){
|
497
|
if (descElement instanceof CategoricalDataDto){
|
498
|
|
499
|
CategoricalData elementBase = CategoricalData.NewInstance(feature);
|
500
|
List<StateDataDto> stateDtos = ((CategoricalDataDto)descElement).getStates();
|
501
|
for (StateDataDto dataDto: stateDtos){
|
502
|
//create new statedata
|
503
|
State newState = DefinedTermBase.getTermByClassAndUUID(State.class, dataDto.getState().getUuid());
|
504
|
StateData newStateData = StateData.NewInstance(newState);
|
505
|
elementBase.addStateData(newStateData);
|
506
|
}
|
507
|
desc.addElement(elementBase);
|
508
|
}
|
509
|
if (descElement instanceof QuantitativeDataDto){
|
510
|
|
511
|
QuantitativeData data = QuantitativeData.NewInstance(feature);
|
512
|
if (((QuantitativeDataDto) descElement).getMeasurementUnit() != null){
|
513
|
MeasurementUnit unit = DefinedTermBase.getTermByClassAndUUID(MeasurementUnit.class, ((QuantitativeDataDto) descElement).getMeasurementUnit().getUuid());
|
514
|
data.setUnit(unit);
|
515
|
}
|
516
|
Set<StatisticalMeasurementValue> statisticalValues = new HashSet<>();
|
517
|
Set<StatisticalMeasurementValueDto> valueDtos = ((QuantitativeDataDto)descElement).getValues();
|
518
|
data.getStatisticalValues().clear();
|
519
|
for (StatisticalMeasurementValueDto dataDto: valueDtos){
|
520
|
//create new statedata
|
521
|
StatisticalMeasurementValue newStatisticalMeasurement = StatisticalMeasurementValue.NewInstance(DefinedTermBase.getTermByClassAndUUID(StatisticalMeasure.class, dataDto.getType().getUuid()), dataDto.getValue());
|
522
|
statisticalValues.add(newStatisticalMeasurement);
|
523
|
data.addStatisticalValue(newStatisticalMeasurement);
|
524
|
}
|
525
|
|
526
|
// data.getStatisticalValues().addAll(statisticalValues);
|
527
|
data = StructuredDescriptionAggregation.handleMissingMinOrMax(data,
|
528
|
MissingMinimumMode.MinToZero, MissingMaximumMode.MaxToMin);
|
529
|
desc.addElement(data);
|
530
|
}
|
531
|
|
532
|
//create new element
|
533
|
}else{
|
534
|
DescriptionElementBase elementBase = equalUuidsElements.get(0);
|
535
|
if (elementBase.isInstanceOf(CategoricalData.class)){
|
536
|
CategoricalData data = HibernateProxyHelper.deproxy(elementBase, CategoricalData.class);
|
537
|
List<StateData> states = new ArrayList<>(data.getStateData());
|
538
|
List<StateDataDto> stateDtos = ((CategoricalDataDto)descElement).getStates();
|
539
|
|
540
|
data.getStateData().clear();
|
541
|
if (stateDtos.isEmpty()){
|
542
|
desc.removeElement(data);
|
543
|
}else{
|
544
|
for (StateDataDto dataDto: stateDtos){
|
545
|
State newState = DefinedTermBase.getTermByClassAndUUID(State.class, dataDto.getState().getUuid());
|
546
|
StateData newStateData = StateData.NewInstance(newState);
|
547
|
data.addStateData(newStateData);
|
548
|
}
|
549
|
}
|
550
|
|
551
|
}else if (elementBase.isInstanceOf(QuantitativeData.class)){
|
552
|
QuantitativeData data = HibernateProxyHelper.deproxy(elementBase, QuantitativeData.class);
|
553
|
|
554
|
Set<StatisticalMeasurementValue> statisticalValues = new HashSet<>();
|
555
|
if (((QuantitativeDataDto) descElement).getMeasurementUnit() != null){
|
556
|
MeasurementUnit unit = DefinedTermBase.getTermByClassAndUUID(MeasurementUnit.class, ((QuantitativeDataDto) descElement).getMeasurementUnit().getUuid());
|
557
|
if (data.getUnit() == null || (data.getUnit() != null && !data.getUnit().equals(unit))){
|
558
|
data.setUnit(unit);
|
559
|
}
|
560
|
}
|
561
|
Set<StatisticalMeasurementValueDto> valueDtos = ((QuantitativeDataDto)descElement).getValues();
|
562
|
data.getStatisticalValues().clear();
|
563
|
if (valueDtos.isEmpty()){
|
564
|
desc.removeElement(data);
|
565
|
}else{
|
566
|
for (StatisticalMeasurementValueDto dataDto: valueDtos){
|
567
|
//create new statedata
|
568
|
StatisticalMeasure statMeasure = DefinedTermBase.getTermByClassAndUUID(StatisticalMeasure.class, dataDto.getType().getUuid());
|
569
|
|
570
|
StatisticalMeasurementValue newStatisticalMeasurement = StatisticalMeasurementValue.NewInstance(statMeasure, dataDto.getValue());
|
571
|
statisticalValues.add(newStatisticalMeasurement);
|
572
|
data.addStatisticalValue(newStatisticalMeasurement);
|
573
|
}
|
574
|
|
575
|
// data.getStatisticalValues().addAll(statisticalValues);
|
576
|
data = StructuredDescriptionAggregation.handleMissingMinOrMax(data,
|
577
|
MissingMinimumMode.MinToZero, MissingMaximumMode.MaxToMin);
|
578
|
}
|
579
|
|
580
|
}
|
581
|
}
|
582
|
//remove deleted elements
|
583
|
|
584
|
}
|
585
|
|
586
|
descriptionSpecimenMap.get(describedObjectUuid).add(desc);
|
587
|
|
588
|
description = desc;
|
589
|
}
|
590
|
try{
|
591
|
if (description != null){
|
592
|
mergeResult = dao.merge(description, true);
|
593
|
result.addUpdatedObject( mergeResult.getMergedEntity());
|
594
|
}
|
595
|
|
596
|
// if (description instanceof SpecimenDescription){
|
597
|
// result.addUpdatedObject(mergeResult.getMergedEntity().getDescribedSpecimenOrObservation());
|
598
|
// }else if (description instanceof TaxonDescription){
|
599
|
// result.addUpdatedObject(((TaxonDescription)mergeResult.getMergedEntity()).getTaxon());
|
600
|
// }else if (description instanceof TaxonNameDescription){
|
601
|
// result.addUpdatedObject(((TaxonNameDescription)mergeResult.getMergedEntity()).getTaxonName());
|
602
|
// }
|
603
|
}catch(Exception e){
|
604
|
e.printStackTrace();
|
605
|
}
|
606
|
|
607
|
}
|
608
|
|
609
|
return result;
|
610
|
}
|
611
|
|
612
|
@Override
|
613
|
@Transactional(readOnly = false)
|
614
|
public DeleteResult deleteDescription(DescriptionBase<?> description) {
|
615
|
|
616
|
DeleteResult deleteResult = new DeleteResult();
|
617
|
if (description == null){
|
618
|
return deleteResult;
|
619
|
}
|
620
|
//avoid lazy init exception
|
621
|
description = load(description.getId(), Arrays.asList("descriptiveDataSets"));
|
622
|
|
623
|
deleteResult = isDeletable(description.getUuid());
|
624
|
if (deleteResult.getRelatedObjects() != null && deleteResult.getRelatedObjects().size() == 1){
|
625
|
Iterator<CdmBase> relObjects = deleteResult.getRelatedObjects().iterator();
|
626
|
CdmBase next = relObjects.next();
|
627
|
if (next instanceof CdmLinkSource){
|
628
|
CdmLinkSource source = (CdmLinkSource)next;
|
629
|
ICdmTarget target = source.getTarget();
|
630
|
|
631
|
|
632
|
}
|
633
|
}
|
634
|
if (deleteResult.isOk() ){
|
635
|
CdmBase.deproxy(description);
|
636
|
if (description instanceof TaxonDescription){
|
637
|
TaxonDescription taxDescription = (TaxonDescription)description;
|
638
|
Taxon tax = taxDescription.getTaxon();
|
639
|
if (tax != null){
|
640
|
tax.removeDescription(taxDescription, true);
|
641
|
deleteResult.addUpdatedObject(tax);
|
642
|
}
|
643
|
}
|
644
|
else if (description instanceof SpecimenDescription){
|
645
|
SpecimenDescription specimenDescription = (SpecimenDescription)description;
|
646
|
SpecimenOrObservationBase<?> specimen = specimenDescription.getDescribedSpecimenOrObservation();
|
647
|
if (specimen != null){
|
648
|
specimen.removeDescription(specimenDescription);
|
649
|
deleteResult.addUpdatedObject(specimen);
|
650
|
}
|
651
|
}
|
652
|
|
653
|
for (DescriptiveDataSet dataset : description.getDescriptiveDataSets()) {
|
654
|
dataset.removeDescription(description);
|
655
|
}
|
656
|
|
657
|
dao.delete(description);
|
658
|
deleteResult.addDeletedObject(description);
|
659
|
deleteResult.setCdmEntity(description);
|
660
|
}else{
|
661
|
logger.info(deleteResult.getExceptions().toString());
|
662
|
}
|
663
|
|
664
|
return deleteResult;
|
665
|
}
|
666
|
|
667
|
@Override
|
668
|
@Transactional(readOnly = false)
|
669
|
public DeleteResult deleteDescription(UUID descriptionUuid) {
|
670
|
return deleteDescription(dao.load(descriptionUuid));
|
671
|
}
|
672
|
|
673
|
|
674
|
|
675
|
@Override
|
676
|
public DeleteResult isDeletable(UUID descriptionUuid){
|
677
|
DeleteResult result = new DeleteResult();
|
678
|
DescriptionBase<?> description = this.load(descriptionUuid);
|
679
|
Set<CdmBase> references = commonService.getReferencingObjectsForDeletion(description);
|
680
|
|
681
|
if (references == null || references.isEmpty()){
|
682
|
return result;
|
683
|
}
|
684
|
for (CdmBase ref: references){
|
685
|
if (description instanceof TaxonDescription && ref instanceof Taxon && ref.equals(((TaxonDescription)description).getTaxon())){
|
686
|
continue;
|
687
|
} else if (description instanceof TaxonNameDescription && ref instanceof TaxonName && ref.equals(((TaxonNameDescription)description).getTaxonName())){
|
688
|
continue;
|
689
|
} else if (description instanceof SpecimenDescription && ref instanceof SpecimenOrObservationBase && ref.equals(((SpecimenDescription)description).getDescribedSpecimenOrObservation())){
|
690
|
continue;
|
691
|
} else if (ref instanceof DescriptionElementBase){
|
692
|
continue;
|
693
|
} else if (ref instanceof CdmLinkSource && ((CdmLinkSource)ref).hasNoTarget()) {
|
694
|
continue; //maybe only workaround #9801
|
695
|
}else {
|
696
|
String message = "The description can't be completely deleted because it is referenced by " + ref.getUserFriendlyTypeName() ;
|
697
|
result.setAbort();
|
698
|
result.addException(new ReferencedObjectUndeletableException(message));
|
699
|
result.addRelatedObject(ref);
|
700
|
}
|
701
|
}
|
702
|
|
703
|
return result;
|
704
|
}
|
705
|
|
706
|
@Override
|
707
|
@Deprecated
|
708
|
public <T extends DescriptionElementBase> List<T> getDescriptionElementsForTaxon(
|
709
|
Taxon taxon, Set<Feature> features,
|
710
|
Class<T> type, Integer pageSize,
|
711
|
Integer pageNumber, List<String> propertyPaths) {
|
712
|
return listDescriptionElementsForTaxon(taxon, features, type, pageSize, pageNumber, propertyPaths);
|
713
|
}
|
714
|
|
715
|
@Override
|
716
|
public <T extends DescriptionElementBase> List<T> listDescriptionElementsForTaxon(
|
717
|
Taxon taxon, Set<Feature> features,
|
718
|
Class<T> type, Integer pageSize,
|
719
|
Integer pageNumber, List<String> propertyPaths) {
|
720
|
return dao.getDescriptionElementForTaxon(taxon.getUuid(), features, type, pageSize, pageNumber, propertyPaths);
|
721
|
}
|
722
|
|
723
|
@Override
|
724
|
public <T extends DescriptionElementBase> Pager<T> pageDescriptionElementsForTaxon(
|
725
|
Taxon taxon, Set<Feature> features,
|
726
|
Class<T> type, Integer pageSize,
|
727
|
Integer pageNumber, List<String> propertyPaths) {
|
728
|
if (logger.isDebugEnabled()){logger.debug(" get count ...");}
|
729
|
Long count = dao.countDescriptionElementForTaxon(taxon.getUuid(), features, type);
|
730
|
List<T> descriptionElements;
|
731
|
if(AbstractPagerImpl.hasResultsInRange(count, pageNumber, pageSize)){ // no point checking again
|
732
|
if (logger.isDebugEnabled()){logger.debug(" get list ...");}
|
733
|
descriptionElements = listDescriptionElementsForTaxon(taxon, features, type, pageSize, pageNumber, propertyPaths);
|
734
|
} else {
|
735
|
descriptionElements = new ArrayList<T>(0);
|
736
|
}
|
737
|
if (logger.isDebugEnabled()){logger.debug(" service - DONE ...");}
|
738
|
return new DefaultPagerImpl<T>(pageNumber, count, pageSize, descriptionElements);
|
739
|
}
|
740
|
|
741
|
@Override
|
742
|
public String generateNaturalLanguageDescription(TermTree featureTree,
|
743
|
TaxonDescription description, List<Language> preferredLanguages, String separator) {
|
744
|
|
745
|
Language lang = preferredLanguages.size() > 0 ? preferredLanguages.get(0) : Language.DEFAULT();
|
746
|
|
747
|
description = (TaxonDescription)load(description.getUuid());
|
748
|
featureTree = featureTreeDao.load(featureTree.getUuid());
|
749
|
|
750
|
StringBuilder naturalLanguageDescription = new StringBuilder();
|
751
|
|
752
|
MarkerType useMarkerType = (MarkerType) definedTermDao.load(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
753
|
boolean isUseDescription = false;
|
754
|
if(!description.getMarkers().isEmpty()) {
|
755
|
for (Marker marker: description.getMarkers()) {
|
756
|
MarkerType markerType = marker.getMarkerType();
|
757
|
if (markerType.equals(useMarkerType)) {
|
758
|
isUseDescription = true;
|
759
|
}
|
760
|
|
761
|
}
|
762
|
}
|
763
|
|
764
|
if(description.hasStructuredData() && !isUseDescription){
|
765
|
|
766
|
|
767
|
String lastCategory = null;
|
768
|
String categorySeparator = ". ";
|
769
|
|
770
|
List<TextData> textDataList;
|
771
|
TextData naturalLanguageDescriptionText = null;
|
772
|
|
773
|
boolean useMicroFormatQuantitativeDescriptionBuilder = false;
|
774
|
|
775
|
if(useMicroFormatQuantitativeDescriptionBuilder){
|
776
|
|
777
|
MicroFormatQuantitativeDescriptionBuilder micro = new MicroFormatQuantitativeDescriptionBuilder();
|
778
|
naturalLanguageGenerator.setQuantitativeDescriptionBuilder(micro);
|
779
|
naturalLanguageDescriptionText = naturalLanguageGenerator.generateSingleTextData(featureTree, (description), lang);
|
780
|
|
781
|
} else {
|
782
|
|
783
|
naturalLanguageDescriptionText = naturalLanguageGenerator.generateSingleTextData(
|
784
|
featureTree,
|
785
|
(description),
|
786
|
lang);
|
787
|
}
|
788
|
|
789
|
return naturalLanguageDescriptionText.getText(lang);
|
790
|
|
791
|
//
|
792
|
// boolean doItBetter = false;
|
793
|
//
|
794
|
// for (TextData textData : textDataList.toArray(new TextData[textDataList.size()])){
|
795
|
// if(textData.getMultilanguageText().size() > 0){
|
796
|
//
|
797
|
// if (!textData.getFeature().equals(Feature.UNKNOWN())) {
|
798
|
// String featureLabel = textData.getFeature().getLabel(lang);
|
799
|
//
|
800
|
// if(doItBetter){
|
801
|
// /*
|
802
|
// * WARNING
|
803
|
// * The code lines below are desinged to handle
|
804
|
// * a special case where as the feature label contains
|
805
|
// * hierarchical information on the features. This code
|
806
|
// * exist only as a base for discussion, and is not
|
807
|
// * intendet to be used in production.
|
808
|
// */
|
809
|
// featureLabel = StringUtils.remove(featureLabel, '>');
|
810
|
//
|
811
|
// String[] labelTokens = StringUtils.split(featureLabel, '<');
|
812
|
// if(labelTokens[0].equals(lastCategory) && labelTokens.length > 1){
|
813
|
// if(naturalLanguageDescription.length() > 0){
|
814
|
// naturalLanguageDescription.append(separator);
|
815
|
// }
|
816
|
// naturalLanguageDescription.append(labelTokens[1]);
|
817
|
// } else {
|
818
|
// if(naturalLanguageDescription.length() > 0){
|
819
|
// naturalLanguageDescription.append(categorySeparator);
|
820
|
// }
|
821
|
// naturalLanguageDescription.append(StringUtils.join(labelTokens));
|
822
|
// }
|
823
|
// lastCategory = labelTokens[0];
|
824
|
// // end of demo code
|
825
|
// } else {
|
826
|
// if(naturalLanguageDescription.length() > 0){
|
827
|
// naturalLanguageDescription.append(separator);
|
828
|
// }
|
829
|
// naturalLanguageDescription.append(textData.getFeature().getLabel(lang));
|
830
|
// }
|
831
|
// } else {
|
832
|
// if(naturalLanguageDescription.length() > 0){
|
833
|
// naturalLanguageDescription.append(separator);
|
834
|
// }
|
835
|
// }
|
836
|
// String text = textData.getMultilanguageText().values().iterator().next().getText();
|
837
|
// naturalLanguageDescription.append(text);
|
838
|
//
|
839
|
// }
|
840
|
// }
|
841
|
|
842
|
}
|
843
|
else if (isUseDescription) {
|
844
|
//AT: Left Blank in case we need to generate a Natural language text string.
|
845
|
}
|
846
|
return naturalLanguageDescription.toString();
|
847
|
}
|
848
|
|
849
|
|
850
|
@Override
|
851
|
public boolean hasStructuredData(DescriptionBase<?> description) {
|
852
|
return load(description.getUuid()).hasStructuredData();
|
853
|
}
|
854
|
|
855
|
|
856
|
@Override
|
857
|
// @Transactional(readOnly = false)
|
858
|
public UpdateResult moveDescriptionElementsToDescription(
|
859
|
Collection<DescriptionElementBase> descriptionElements,
|
860
|
DescriptionBase targetDescription,
|
861
|
boolean isCopy,
|
862
|
boolean setNameInSource) {
|
863
|
|
864
|
UpdateResult result = new UpdateResult();
|
865
|
if (descriptionElements.isEmpty() || descriptionElements.iterator().next() == null){
|
866
|
result.setAbort();
|
867
|
return result;
|
868
|
}
|
869
|
|
870
|
|
871
|
if (! isCopy && descriptionElements == descriptionElements.iterator().next().getInDescription().getElements()){
|
872
|
//if the descriptionElements collection is the elements set of a description, put it in a separate set before to avoid concurrent modification exceptions
|
873
|
descriptionElements = new HashSet<DescriptionElementBase>(descriptionElements);
|
874
|
// descriptionElementsTmp.addAll(descriptionElements);
|
875
|
// descriptionElements = descriptionElementsTmp;
|
876
|
}
|
877
|
for (DescriptionElementBase element : descriptionElements){
|
878
|
DescriptionBase<?> description = element.getInDescription();
|
879
|
description = HibernateProxyHelper.deproxy(dao.load(description.getUuid()));
|
880
|
Taxon taxon;
|
881
|
TaxonName name = null;
|
882
|
if (description instanceof TaxonDescription){
|
883
|
TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(description, TaxonDescription.class);
|
884
|
if (taxonDescription.getTaxon() != null){
|
885
|
taxon = (Taxon) taxonDao.load(taxonDescription.getTaxon().getUuid());
|
886
|
name = taxon.getName();
|
887
|
}
|
888
|
|
889
|
|
890
|
}
|
891
|
DescriptionElementBase newElement = element.clone();
|
892
|
if (setNameInSource) {
|
893
|
for (DescriptionElementSource source: newElement.getSources()){
|
894
|
if (source.getNameUsedInSource() == null){
|
895
|
source.setNameUsedInSource(name);
|
896
|
}
|
897
|
}
|
898
|
|
899
|
}
|
900
|
targetDescription.addElement(newElement);
|
901
|
if (! isCopy){
|
902
|
description.removeElement(element);
|
903
|
dao.saveOrUpdate(description);
|
904
|
result.addUpdatedObject(description);
|
905
|
// if (description.getElements().isEmpty()){
|
906
|
// if (description instanceof TaxonDescription){
|
907
|
// TaxonDescription taxDescription = HibernateProxyHelper.deproxy(description, TaxonDescription.class);
|
908
|
// if (taxDescription.getTaxon() != null){
|
909
|
// taxDescription.getTaxon().removeDescription((TaxonDescription)description);
|
910
|
// }
|
911
|
// }
|
912
|
// dao.delete(description);
|
913
|
//
|
914
|
// }//else{
|
915
|
// dao.saveOrUpdate(description);
|
916
|
// result.addUpdatedObject(description);
|
917
|
// }
|
918
|
}
|
919
|
|
920
|
|
921
|
}
|
922
|
dao.saveOrUpdate(targetDescription);
|
923
|
result.addUpdatedObject(targetDescription);
|
924
|
if (targetDescription instanceof TaxonDescription){
|
925
|
result.addUpdatedObject(((TaxonDescription)targetDescription).getTaxon());
|
926
|
}
|
927
|
return result;
|
928
|
}
|
929
|
|
930
|
@Override
|
931
|
@Transactional(readOnly = false)
|
932
|
public UpdateResult moveDescriptionElementsToDescription(
|
933
|
Set<UUID> descriptionElementUUIDs,
|
934
|
UUID targetDescriptionUuid,
|
935
|
boolean isCopy, boolean setNameInSource) {
|
936
|
Set<DescriptionElementBase> descriptionElements = new HashSet<DescriptionElementBase>();
|
937
|
for(UUID deUuid : descriptionElementUUIDs) {
|
938
|
DescriptionElementBase element = descriptionElementDao.load(deUuid);
|
939
|
if (element != null){
|
940
|
descriptionElements.add(element);
|
941
|
}
|
942
|
}
|
943
|
DescriptionBase targetDescription = dao.load(targetDescriptionUuid);
|
944
|
|
945
|
return moveDescriptionElementsToDescription(descriptionElements, targetDescription, isCopy, setNameInSource);
|
946
|
}
|
947
|
|
948
|
@Override
|
949
|
@Transactional(readOnly = false)
|
950
|
public UpdateResult moveDescriptionElementsToDescription(
|
951
|
Set<UUID> descriptionElementUUIDs,
|
952
|
DescriptionBase targetDescription,
|
953
|
boolean isCopy, boolean setNameInSource) {
|
954
|
Set<DescriptionElementBase> descriptionElements = new HashSet<DescriptionElementBase>();
|
955
|
for(UUID deUuid : descriptionElementUUIDs) {
|
956
|
DescriptionElementBase element = descriptionElementDao.load(deUuid);
|
957
|
if (element != null){
|
958
|
descriptionElements.add(element);
|
959
|
}
|
960
|
}
|
961
|
DescriptionBase newTargetDescription;
|
962
|
if (targetDescription.isPersited()){
|
963
|
newTargetDescription = dao.load(targetDescription.getUuid());
|
964
|
}else{
|
965
|
if (targetDescription instanceof TaxonDescription){
|
966
|
Taxon taxon = (Taxon)taxonDao.load(((TaxonDescription)targetDescription).getTaxon().getUuid());
|
967
|
|
968
|
newTargetDescription = TaxonDescription.NewInstance(taxon, targetDescription.isImageGallery());
|
969
|
|
970
|
}else if (targetDescription instanceof TaxonNameDescription){
|
971
|
TaxonName name = nameDao.load(((TaxonNameDescription)targetDescription).getTaxonName().getUuid());
|
972
|
newTargetDescription = TaxonNameDescription.NewInstance(name);
|
973
|
}else {
|
974
|
SpecimenOrObservationBase specimen = occurrenceDao.load(((SpecimenDescription)targetDescription).getDescribedSpecimenOrObservation().getUuid());
|
975
|
newTargetDescription = SpecimenDescription.NewInstance(specimen);
|
976
|
}
|
977
|
|
978
|
newTargetDescription.addSources(targetDescription.getSources());
|
979
|
newTargetDescription.setTitleCache(targetDescription.getTitleCache(), targetDescription.isProtectedTitleCache());
|
980
|
|
981
|
}
|
982
|
return moveDescriptionElementsToDescription(descriptionElements, newTargetDescription, isCopy, setNameInSource);
|
983
|
}
|
984
|
|
985
|
|
986
|
@Override
|
987
|
@Transactional(readOnly = false)
|
988
|
public UpdateResult moveDescriptionElementsToDescription(
|
989
|
Set<UUID> descriptionElementUUIDs,
|
990
|
UUID targetTaxonUuid,
|
991
|
String moveMessage,
|
992
|
boolean isCopy, boolean setNameInSource) {
|
993
|
Taxon targetTaxon = CdmBase.deproxy(taxonDao.load(targetTaxonUuid), Taxon.class);
|
994
|
DescriptionBase targetDescription = TaxonDescription.NewInstance(targetTaxon);
|
995
|
targetDescription.setTitleCache(moveMessage, true);
|
996
|
Annotation annotation = Annotation.NewInstance(moveMessage, Language.getDefaultLanguage());
|
997
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
998
|
targetDescription.addAnnotation(annotation);
|
999
|
|
1000
|
targetDescription = dao.save(targetDescription);
|
1001
|
Set<DescriptionElementBase> descriptionElements = new HashSet<DescriptionElementBase>();
|
1002
|
for(UUID deUuid : descriptionElementUUIDs) {
|
1003
|
descriptionElements.add(descriptionElementDao.load(deUuid));
|
1004
|
}
|
1005
|
|
1006
|
return moveDescriptionElementsToDescription(descriptionElements, targetDescription, isCopy, setNameInSource);
|
1007
|
}
|
1008
|
|
1009
|
@Override
|
1010
|
public Pager<TermDto> pageNamedAreasInUse(boolean includeAllParents, Integer pageSize,
|
1011
|
Integer pageIndex){
|
1012
|
List<TermDto> results = dao.listNamedAreasInUse(includeAllParents, null, null);
|
1013
|
List<TermDto> subList = PagerUtils.pageList(results, pageIndex, pageSize);
|
1014
|
return new DefaultPagerImpl<TermDto>(pageIndex, results.size(), pageSize, subList);
|
1015
|
}
|
1016
|
|
1017
|
|
1018
|
@Override
|
1019
|
@Transactional(readOnly = false)
|
1020
|
public UpdateResult moveTaxonDescriptions(Taxon sourceTaxon, Taxon targetTaxon, boolean setNameInSource) {
|
1021
|
List<TaxonDescription> descriptions = new ArrayList<>(sourceTaxon.getDescriptions());
|
1022
|
UpdateResult result = new UpdateResult();
|
1023
|
result.addUpdatedObject(sourceTaxon);
|
1024
|
result.addUpdatedObject(targetTaxon);
|
1025
|
for(TaxonDescription description : descriptions){
|
1026
|
targetTaxon.addDescription(prepareDescriptionForMove(description, sourceTaxon, setNameInSource));
|
1027
|
}
|
1028
|
return result;
|
1029
|
}
|
1030
|
|
1031
|
private TaxonDescription prepareDescriptionForMove(TaxonDescription description, Taxon sourceTaxon, boolean setNameInSource){
|
1032
|
String moveMessage = String.format("Description moved from %s", sourceTaxon);
|
1033
|
if(description.isProtectedTitleCache()){
|
1034
|
String separator = "";
|
1035
|
if(!StringUtils.isBlank(description.getTitleCache())){
|
1036
|
separator = " - ";
|
1037
|
}
|
1038
|
description.setTitleCache(description.getTitleCache() + separator + moveMessage, true);
|
1039
|
}
|
1040
|
else{
|
1041
|
description.setTitleCache(moveMessage, true);
|
1042
|
}
|
1043
|
Annotation annotation = Annotation.NewInstance(moveMessage, Language.getDefaultLanguage());
|
1044
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
1045
|
description.addAnnotation(annotation);
|
1046
|
if(setNameInSource){
|
1047
|
for (DescriptionElementBase element: description.getElements()){
|
1048
|
for (DescriptionElementSource source: element.getSources()){
|
1049
|
if (source.getNameUsedInSource() == null){
|
1050
|
source.setNameUsedInSource(sourceTaxon.getName());
|
1051
|
}
|
1052
|
}
|
1053
|
}
|
1054
|
}
|
1055
|
return description;
|
1056
|
}
|
1057
|
|
1058
|
@Override
|
1059
|
@Transactional(readOnly = false)
|
1060
|
public UpdateResult moveTaxonDescriptions(UUID sourceTaxonUuid, UUID targetTaxonUuid, boolean setNameInSource) {
|
1061
|
Taxon sourceTaxon = HibernateProxyHelper.deproxy(taxonDao.load(sourceTaxonUuid), Taxon.class);
|
1062
|
Taxon targetTaxon = HibernateProxyHelper.deproxy(taxonDao.load(targetTaxonUuid), Taxon.class);
|
1063
|
return moveTaxonDescriptions(sourceTaxon, targetTaxon, setNameInSource);
|
1064
|
|
1065
|
}
|
1066
|
|
1067
|
@Override
|
1068
|
@Transactional(readOnly = false)
|
1069
|
public UpdateResult moveTaxonDescription(UUID descriptionUuid, UUID targetTaxonUuid, boolean setNameInSource){
|
1070
|
TaxonDescription description = HibernateProxyHelper.deproxy(dao.load(descriptionUuid), TaxonDescription.class);
|
1071
|
Taxon targetTaxon = HibernateProxyHelper.deproxy(taxonDao.load(targetTaxonUuid), Taxon.class);
|
1072
|
Taxon sourceTaxon = description.getTaxon();
|
1073
|
UpdateResult result = new UpdateResult();
|
1074
|
result.addUpdatedObject(sourceTaxon);
|
1075
|
result.addUpdatedObject(targetTaxon);
|
1076
|
|
1077
|
targetTaxon.addDescription(prepareDescriptionForMove(description, sourceTaxon, setNameInSource));
|
1078
|
return result;
|
1079
|
|
1080
|
}
|
1081
|
|
1082
|
@Override
|
1083
|
public DescriptionBaseDto loadDto(UUID descriptionUuid) {
|
1084
|
String sqlSelect = DescriptionBaseDto.getDescriptionBaseDtoSelect();
|
1085
|
Query query = getSession().createQuery(sqlSelect);
|
1086
|
List<UUID> uuids = new ArrayList<UUID>();
|
1087
|
uuids.add(descriptionUuid);
|
1088
|
query.setParameterList("uuid", uuids);
|
1089
|
|
1090
|
@SuppressWarnings("unchecked")
|
1091
|
List<Object[]> result = query.list();
|
1092
|
|
1093
|
List<DescriptionBaseDto> list = DescriptionBaseDto.descriptionBaseDtoListFrom(result);
|
1094
|
|
1095
|
if (list.size()== 1){
|
1096
|
DescriptionBaseDto dto = list.get(0);
|
1097
|
//get categorical data
|
1098
|
sqlSelect = CategoricalDataDto.getCategoricalDtoSelect();
|
1099
|
query = getSession().createQuery(sqlSelect);
|
1100
|
query.setParameter("uuid", descriptionUuid);
|
1101
|
@SuppressWarnings("unchecked")
|
1102
|
List<Object[]> resultCat = query.list();
|
1103
|
List<CategoricalDataDto> listCategorical = CategoricalDataDto.categoricalDataDtoListFrom(resultCat);
|
1104
|
|
1105
|
List<UUID> featureUuids = new ArrayList<>();
|
1106
|
for (CategoricalDataDto catDto: listCategorical){
|
1107
|
featureUuids.add(catDto.getFeatureUuid());
|
1108
|
}
|
1109
|
Map<UUID, TermDto> featureDtos = termService.findFeatureByUUIDsAsDtos(featureUuids);
|
1110
|
for (CategoricalDataDto catDto: listCategorical){
|
1111
|
FeatureDto featuredto = (FeatureDto)featureDtos.get(catDto.getFeatureUuid());
|
1112
|
catDto.setFeatureDto(featuredto);
|
1113
|
}
|
1114
|
dto.getElements().addAll(listCategorical);
|
1115
|
//get quantitative data
|
1116
|
sqlSelect = QuantitativeDataDto.getQuantitativeDataDtoSelect();
|
1117
|
query = getSession().createQuery(sqlSelect);
|
1118
|
query.setParameter("uuid", descriptionUuid);
|
1119
|
@SuppressWarnings("unchecked")
|
1120
|
List<Object[]> resultQuant = query.list();
|
1121
|
List<QuantitativeDataDto> listQuant = QuantitativeDataDto.quantitativeDataDtoListFrom(resultQuant);
|
1122
|
dto.getElements().addAll(listQuant);
|
1123
|
return dto;
|
1124
|
}else{
|
1125
|
return null;
|
1126
|
}
|
1127
|
|
1128
|
}
|
1129
|
@Override
|
1130
|
public List<DescriptionBaseDto> loadDtos(Set<UUID> descriptionUuids) {
|
1131
|
String sqlSelect = DescriptionBaseDto.getDescriptionBaseDtoSelect();
|
1132
|
Query query = getSession().createQuery(sqlSelect);
|
1133
|
query.setParameterList("uuid", descriptionUuids);
|
1134
|
|
1135
|
@SuppressWarnings("unchecked")
|
1136
|
List<Object[]> result = query.list();
|
1137
|
|
1138
|
List<DescriptionBaseDto> list = DescriptionBaseDto.descriptionBaseDtoListFrom(result);
|
1139
|
|
1140
|
for (DescriptionBaseDto dto: list){
|
1141
|
|
1142
|
//get categorical data
|
1143
|
sqlSelect = CategoricalDataDto.getCategoricalDtoSelect();
|
1144
|
query = getSession().createQuery(sqlSelect);
|
1145
|
query.setParameter("uuid", dto.getDescriptionUuid());
|
1146
|
@SuppressWarnings("unchecked")
|
1147
|
List<Object[]> resultCat = query.list();
|
1148
|
List<CategoricalDataDto> listCategorical = CategoricalDataDto.categoricalDataDtoListFrom(resultCat);
|
1149
|
|
1150
|
List<UUID> featureUuids = new ArrayList<>();
|
1151
|
for (CategoricalDataDto catDto: listCategorical){
|
1152
|
featureUuids.add(catDto.getFeatureUuid());
|
1153
|
}
|
1154
|
Map<UUID, TermDto> featureDtos = termService.findFeatureByUUIDsAsDtos(featureUuids);
|
1155
|
for (CategoricalDataDto catDto: listCategorical){
|
1156
|
FeatureDto featuredto = (FeatureDto)featureDtos.get(catDto.getFeatureUuid());
|
1157
|
catDto.setFeatureDto(featuredto);
|
1158
|
}
|
1159
|
dto.getElements().addAll(listCategorical);
|
1160
|
//get quantitative data
|
1161
|
sqlSelect = QuantitativeDataDto.getQuantitativeDataDtoSelect();
|
1162
|
query = getSession().createQuery(sqlSelect);
|
1163
|
query.setParameter("uuid", dto.getDescriptionUuid());
|
1164
|
@SuppressWarnings("unchecked")
|
1165
|
List<Object[]> resultQuant = query.list();
|
1166
|
List<QuantitativeDataDto> listQuant = QuantitativeDataDto.quantitativeDataDtoListFrom(resultQuant);
|
1167
|
dto.getElements().addAll(listQuant);
|
1168
|
|
1169
|
}
|
1170
|
return list;
|
1171
|
|
1172
|
}
|
1173
|
|
1174
|
@Override
|
1175
|
public List<DescriptionBaseDto> loadDtosForTaxon(UUID taxonUuid) {
|
1176
|
String sqlSelect = DescriptionBaseDto.getDescriptionBaseDtoForTaxonSelect();
|
1177
|
Query query = getSession().createQuery(sqlSelect);
|
1178
|
query.setParameter("uuid", taxonUuid);
|
1179
|
|
1180
|
@SuppressWarnings("unchecked")
|
1181
|
List<Object[]> result = query.list();
|
1182
|
|
1183
|
List<DescriptionBaseDto> list = DescriptionBaseDto.descriptionBaseDtoListFrom(result);
|
1184
|
|
1185
|
return list;
|
1186
|
|
1187
|
}
|
1188
|
|
1189
|
@Override
|
1190
|
public TaxonNodeDto findTaxonNodeDtoForIndividualAssociation(UUID specimenUuid, UUID classificationUuid) {
|
1191
|
//get specimen used in description
|
1192
|
//get individial associations with this specimen
|
1193
|
//get taxon node for the classification
|
1194
|
@SuppressWarnings("unchecked")
|
1195
|
List<SortableTaxonNodeQueryResult> result = dao.getNodeOfIndividualAssociationForSpecimen(specimenUuid, classificationUuid);
|
1196
|
|
1197
|
if (!result.isEmpty()){
|
1198
|
List<TaxonNodeDto> dtos = taxonNodeDao.createNodeDtos(result);
|
1199
|
if (dtos.size() == 1){
|
1200
|
return dtos.get(0);
|
1201
|
}else{
|
1202
|
logger.debug("There is more than one taxon associated to the specimen with uuid: " + specimenUuid + " return the first in the list");
|
1203
|
return dtos.get(0);
|
1204
|
}
|
1205
|
}
|
1206
|
|
1207
|
|
1208
|
|
1209
|
return null;
|
1210
|
}
|
1211
|
|
1212
|
|
1213
|
|
1214
|
|
1215
|
}
|