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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 org.apache.commons.lang.StringUtils;
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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.dto.DescriptionBaseDto;
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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.impl.AbstractPagerImpl;
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import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
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import eu.etaxonomy.cdm.api.utility.DescriptionUtility;
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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.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.Distribution;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.SpecimenDescription;
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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.location.NamedAreaLevel;
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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.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.MergeResult;
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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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*/
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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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@Autowired
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private IProgressMonitorService progressMonitorService;
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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 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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/**
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*
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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, results.size(), 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<Annotation> getDescriptionElementAnnotations(DescriptionElementBase annotatedObj, MarkerType status, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
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long numberOfResults = descriptionElementDao.countAnnotations(annotatedObj, status);
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List<Annotation> 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 = descriptionElementDao.getAnnotations(annotatedObj, status, 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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@Override
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public Pager<Media> getMedia(DescriptionElementBase descriptionElement, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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Integer 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<Media>(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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@Deprecated
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public DistributionTree getOrderedDistributions(
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Set<TaxonDescription> taxonDescriptions,
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boolean subAreaPreference,
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boolean statusOrderPreference,
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Set<MarkerType> hiddenAreaMarkerTypes,
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Set<NamedAreaLevel> omitLevels, List<String> propertyPaths){
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List<Distribution> distList = new ArrayList<Distribution>();
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|
329
|
List<UUID> uuids = new ArrayList<UUID>();
|
|
330
|
for (TaxonDescription taxonDescription : taxonDescriptions) {
|
|
331
|
if (! taxonDescription.isImageGallery()){ //image galleries should not have descriptions, but better filter fully on DTYPE of description element
|
|
332
|
uuids.add(taxonDescription.getUuid());
|
|
333
|
}
|
|
334
|
}
|
|
335
|
|
|
336
|
List<DescriptionBase> desclist = dao.list(uuids, null, null, null, propertyPaths);
|
|
337
|
for (DescriptionBase desc : desclist) {
|
|
338
|
if (desc.isInstanceOf(TaxonDescription.class)){
|
|
339
|
Set<DescriptionElementBase> elements = desc.getElements();
|
|
340
|
for (DescriptionElementBase element : elements) {
|
|
341
|
if (element.isInstanceOf(Distribution.class)) {
|
|
342
|
Distribution distribution = (Distribution) element;
|
|
343
|
if(distribution.getArea() != null){
|
|
344
|
distList.add(distribution);
|
|
345
|
}
|
|
346
|
}
|
|
347
|
}
|
|
348
|
}
|
|
349
|
}
|
|
350
|
|
|
351
|
//old
|
|
352
|
// for (TaxonDescription taxonDescription : taxonDescriptions) {
|
|
353
|
// if (logger.isDebugEnabled()){ logger.debug("load taxon description " + taxonDescription.getUuid());}
|
|
354
|
// //TODO why not loading all description via .list ? This may improve performance
|
|
355
|
// taxonDescription = (TaxonDescription) dao.load(taxonDescription.getUuid(), propertyPaths);
|
|
356
|
// Set<DescriptionElementBase> elements = taxonDescription.getElements();
|
|
357
|
// for (DescriptionElementBase element : elements) {
|
|
358
|
// if (element.isInstanceOf(Distribution.class)) {
|
|
359
|
// Distribution distribution = (Distribution) element;
|
|
360
|
// if(distribution.getArea() != null){
|
|
361
|
// distList.add(distribution);
|
|
362
|
// }
|
|
363
|
// }
|
|
364
|
// }
|
|
365
|
// }
|
|
366
|
|
|
367
|
if (logger.isDebugEnabled()){logger.debug("filter tree for " + distList.size() + " distributions ...");}
|
|
368
|
|
|
369
|
// filter distributions
|
|
370
|
Collection<Distribution> filteredDistributions = DescriptionUtility.filterDistributions(distList, hiddenAreaMarkerTypes, true, statusOrderPreference, false);
|
|
371
|
distList.clear();
|
|
372
|
distList.addAll(filteredDistributions);
|
|
373
|
|
|
374
|
return DescriptionUtility.orderDistributions(definedTermDao, omitLevels, distList, hiddenAreaMarkerTypes, null);
|
|
375
|
}
|
|
376
|
|
|
377
|
|
|
378
|
@Override
|
|
379
|
public Pager<TaxonNameDescription> getTaxonNameDescriptions(TaxonName name, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
|
|
380
|
long numberOfResults = dao.countTaxonNameDescriptions(name);
|
|
381
|
|
|
382
|
List<TaxonNameDescription> results = new ArrayList<>();
|
|
383
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
|
384
|
results = dao.getTaxonNameDescriptions(name, pageSize, pageNumber,propertyPaths);
|
|
385
|
}
|
|
386
|
|
|
387
|
return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
|
|
388
|
}
|
|
389
|
|
|
390
|
|
|
391
|
@Override
|
|
392
|
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) {
|
|
393
|
long numberOfResults = dao.countDescriptions(type, hasImages, hasText, feature);
|
|
394
|
|
|
395
|
@SuppressWarnings("rawtypes")
|
|
396
|
List<DescriptionBase> results = new ArrayList<>();
|
|
397
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
|
398
|
results = dao.listDescriptions(type, hasImages, hasText, feature, pageSize, pageNumber,orderHints,propertyPaths);
|
|
399
|
}
|
|
400
|
|
|
401
|
return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
|
|
402
|
}
|
|
403
|
|
|
404
|
/**
|
|
405
|
* FIXME Candidate for harmonization
|
|
406
|
* Rename: searchByDistribution
|
|
407
|
*/
|
|
408
|
@Override
|
|
409
|
public Pager<TaxonDescription> searchDescriptionByDistribution(Set<NamedArea> namedAreas, PresenceAbsenceTerm presence, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
410
|
long numberOfResults = dao.countDescriptionByDistribution(namedAreas, presence);
|
|
411
|
|
|
412
|
List<TaxonDescription> results = new ArrayList<>();
|
|
413
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
|
414
|
results = dao.searchDescriptionByDistribution(namedAreas, presence, pageSize, pageNumber,orderHints,propertyPaths);
|
|
415
|
}
|
|
416
|
|
|
417
|
return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
|
|
418
|
}
|
|
419
|
|
|
420
|
/**
|
|
421
|
* FIXME Candidate for harmonization
|
|
422
|
* move: descriptionElementService.search
|
|
423
|
*/
|
|
424
|
@Override
|
|
425
|
// public Pager<T> searchElements(Class<? extends T> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
426
|
public <S extends DescriptionElementBase> Pager<S> searchElements(Class<S> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
427
|
long numberOfResults = descriptionElementDao.count(clazz, queryString);
|
|
428
|
|
|
429
|
List<S> results = new ArrayList<>();
|
|
430
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
|
431
|
results = (List<S>)descriptionElementDao.search(clazz, queryString, pageSize, pageNumber, orderHints, propertyPaths);
|
|
432
|
}
|
|
433
|
|
|
434
|
return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
|
|
435
|
}
|
|
436
|
|
|
437
|
/**
|
|
438
|
* FIXME Candidate for harmonization
|
|
439
|
* descriptionElementService.find
|
|
440
|
*/
|
|
441
|
@Override
|
|
442
|
public DescriptionElementBase getDescriptionElementByUuid(UUID uuid) {
|
|
443
|
return descriptionElementDao.findByUuid(uuid);
|
|
444
|
}
|
|
445
|
|
|
446
|
/**
|
|
447
|
* FIXME Candidate for harmonization
|
|
448
|
* descriptionElementService.load
|
|
449
|
*/
|
|
450
|
@Override
|
|
451
|
public DescriptionElementBase loadDescriptionElement(UUID uuid, List<String> propertyPaths) {
|
|
452
|
return descriptionElementDao.load(uuid, propertyPaths);
|
|
453
|
}
|
|
454
|
|
|
455
|
/**
|
|
456
|
* FIXME Candidate for harmonization
|
|
457
|
* descriptionElementService.save
|
|
458
|
*/
|
|
459
|
@Override
|
|
460
|
@Transactional(readOnly = false)
|
|
461
|
public UUID saveDescriptionElement(DescriptionElementBase descriptionElement) {
|
|
462
|
return descriptionElementDao.save(descriptionElement).getUuid();
|
|
463
|
}
|
|
464
|
|
|
465
|
/**
|
|
466
|
* FIXME Candidate for harmonization
|
|
467
|
* descriptionElementService.save
|
|
468
|
*/
|
|
469
|
@Override
|
|
470
|
@Transactional(readOnly = false)
|
|
471
|
public Map<UUID, DescriptionElementBase> saveDescriptionElement(Collection<DescriptionElementBase> descriptionElements) {
|
|
472
|
return descriptionElementDao.saveAll(descriptionElements);
|
|
473
|
}
|
|
474
|
|
|
475
|
@Override
|
|
476
|
@Transactional(readOnly = false)
|
|
477
|
public List<MergeResult<DescriptionBase>> mergeDescriptionElements(Collection<TaxonDistributionDTO> descriptionElements, boolean returnTransientEntity) {
|
|
478
|
List<MergeResult<DescriptionBase>> mergedObjects = new ArrayList();
|
|
479
|
|
|
480
|
for(TaxonDistributionDTO obj : descriptionElements) {
|
|
481
|
Iterator<TaxonDescription> iterator = obj.getDescriptionsWrapper().getDescriptions().iterator();
|
|
482
|
List<DescriptionBase> list = new ArrayList(obj.getDescriptionsWrapper().getDescriptions());
|
|
483
|
// Map<UUID, DescriptionBase> map = dao.saveOrUpdateAll(list);
|
|
484
|
// MergeResult<DescriptionBase> mergeResult = new MergeResult<DescriptionBase>(mergedEntity, newEntities)
|
|
485
|
// mergedObjects.add(map.values());
|
|
486
|
while (iterator.hasNext()){
|
|
487
|
TaxonDescription desc = iterator.next();
|
|
488
|
mergedObjects.add(dao.merge(desc, returnTransientEntity));
|
|
489
|
}
|
|
490
|
|
|
491
|
|
|
492
|
}
|
|
493
|
|
|
494
|
return mergedObjects;
|
|
495
|
}
|
|
496
|
//
|
|
497
|
@Override
|
|
498
|
@Transactional(readOnly = false)
|
|
499
|
public UpdateResult mergeDescriptions(Collection<DescriptionBaseDto> descriptions, UUID descriptiveDataSetUuid) {
|
|
500
|
// List<<DescriptionBase>> mergedObjects = new ArrayList();
|
|
501
|
UpdateResult result = new UpdateResult();
|
|
502
|
DescriptiveDataSet dataSet = descriptiveDataSetDao.load(descriptiveDataSetUuid);
|
|
503
|
Set<DescriptionBase> descriptionsOfDataSet = dataSet.getDescriptions();
|
|
504
|
HashMap<UUID, DescriptionBase> descriptionSpecimenMap = new HashMap();
|
|
505
|
|
|
506
|
for (DescriptionBase descriptionBase: descriptionsOfDataSet){
|
|
507
|
if (descriptionBase.getDescribedSpecimenOrObservation() != null){
|
|
508
|
descriptionSpecimenMap.put(descriptionBase.getDescribedSpecimenOrObservation().getUuid(), descriptionBase);
|
|
509
|
}
|
|
510
|
}
|
|
511
|
MergeResult<DescriptionBase> mergeResult = null;
|
|
512
|
for(DescriptionBaseDto descDto : descriptions) {
|
|
513
|
DescriptionBase description = descDto.getDescription();
|
|
514
|
UUID describedObjectUuid = null;
|
|
515
|
if (description instanceof SpecimenDescription){
|
|
516
|
describedObjectUuid = descDto.getSpecimenDto().getUuid();
|
|
517
|
}else if (description instanceof TaxonDescription){
|
|
518
|
describedObjectUuid = descDto.getTaxonDto().getUuid();
|
|
519
|
}else if (description instanceof TaxonNameDescription){
|
|
520
|
describedObjectUuid = descDto.getNameDto().getUuid();
|
|
521
|
}
|
|
522
|
if (descriptionSpecimenMap.get(describedObjectUuid) != null && !descriptionSpecimenMap.get(describedObjectUuid).equals(description)){
|
|
523
|
Set<DescriptionElementBase> elements = new HashSet();
|
|
524
|
for (Object element: description.getElements()){
|
|
525
|
elements.add((DescriptionElementBase)element);
|
|
526
|
}
|
|
527
|
DescriptionBase desc = descriptionSpecimenMap.get(describedObjectUuid);
|
|
528
|
// description.setDescribedSpecimenOrObservation(null);
|
|
529
|
|
|
530
|
for (DescriptionElementBase element: elements){
|
|
531
|
desc.addElement(element);
|
|
532
|
}
|
|
533
|
descriptionSpecimenMap.put(describedObjectUuid, desc);
|
|
534
|
description = desc;
|
|
535
|
}
|
|
536
|
try{
|
|
537
|
mergeResult = dao.merge(description, true);
|
|
538
|
result.addUpdatedObject( mergeResult.getMergedEntity());
|
|
539
|
// if (description instanceof SpecimenDescription){
|
|
540
|
// result.addUpdatedObject(mergeResult.getMergedEntity().getDescribedSpecimenOrObservation());
|
|
541
|
// }else if (description instanceof TaxonDescription){
|
|
542
|
// result.addUpdatedObject(((TaxonDescription)mergeResult.getMergedEntity()).getTaxon());
|
|
543
|
// }else if (description instanceof TaxonNameDescription){
|
|
544
|
// result.addUpdatedObject(((TaxonNameDescription)mergeResult.getMergedEntity()).getTaxonName());
|
|
545
|
// }
|
|
546
|
}catch(Exception e){
|
|
547
|
e.printStackTrace();
|
|
548
|
}
|
|
549
|
|
|
550
|
}
|
|
551
|
|
|
552
|
return result;
|
|
553
|
}
|
|
554
|
|
|
555
|
/**
|
|
556
|
* FIXME Candidate for harmonization
|
|
557
|
* descriptionElementService.delete
|
|
558
|
*/
|
|
559
|
@Override
|
|
560
|
public UUID deleteDescriptionElement(DescriptionElementBase descriptionElement) {
|
|
561
|
return descriptionElementDao.delete(descriptionElement);
|
|
562
|
}
|
|
563
|
|
|
564
|
@Override
|
|
565
|
public UUID deleteDescriptionElement(UUID descriptionElementUuid) {
|
|
566
|
return deleteDescriptionElement(descriptionElementDao.load(descriptionElementUuid));
|
|
567
|
}
|
|
568
|
|
|
569
|
@Override
|
|
570
|
@Transactional(readOnly = false)
|
|
571
|
public DeleteResult deleteDescription(DescriptionBase description) {
|
|
572
|
|
|
573
|
DeleteResult deleteResult = new DeleteResult();
|
|
574
|
if (description == null){
|
|
575
|
return deleteResult;
|
|
576
|
}
|
|
577
|
description = load(description.getId(), Arrays.asList("descriptiveDataSets"));
|
|
578
|
//avoid lazy init exception
|
|
579
|
|
|
580
|
deleteResult = isDeletable(description.getUuid());
|
|
581
|
if (deleteResult.getRelatedObjects() != null && deleteResult.getRelatedObjects().size() == 1){
|
|
582
|
Iterator<CdmBase> relObjects = deleteResult.getRelatedObjects().iterator();
|
|
583
|
CdmBase next = relObjects.next();
|
|
584
|
if (next instanceof CdmLinkSource){
|
|
585
|
CdmLinkSource source = (CdmLinkSource)next;
|
|
586
|
ICdmTarget target = source.getTarget();
|
|
587
|
|
|
588
|
|
|
589
|
}
|
|
590
|
}
|
|
591
|
if (deleteResult.isOk() ){
|
|
592
|
if (description instanceof TaxonDescription){
|
|
593
|
TaxonDescription taxDescription = HibernateProxyHelper.deproxy(description, TaxonDescription.class);
|
|
594
|
Taxon tax = taxDescription.getTaxon();
|
|
595
|
tax.removeDescription(taxDescription, true);
|
|
596
|
deleteResult.addUpdatedObject(tax);
|
|
597
|
}
|
|
598
|
else if (HibernateProxyHelper.isInstanceOf(description, SpecimenDescription.class)){
|
|
599
|
SpecimenDescription specimenDescription = HibernateProxyHelper.deproxy(description, SpecimenDescription.class);
|
|
600
|
SpecimenOrObservationBase<?> specimen = specimenDescription.getDescribedSpecimenOrObservation();
|
|
601
|
specimen.removeDescription(specimenDescription);
|
|
602
|
deleteResult.addUpdatedObject(specimen);
|
|
603
|
}
|
|
604
|
|
|
605
|
Set<DescriptiveDataSet> descriptiveDataSets = description.getDescriptiveDataSets();
|
|
606
|
for (Iterator<DescriptiveDataSet> iterator = descriptiveDataSets.iterator(); iterator.hasNext();) {
|
|
607
|
iterator.next().removeDescription(description);
|
|
608
|
}
|
|
609
|
|
|
610
|
dao.delete(description);
|
|
611
|
deleteResult.addDeletedObject(description);
|
|
612
|
deleteResult.setCdmEntity(description);
|
|
613
|
}else{
|
|
614
|
logger.info(deleteResult.getExceptions().toString());
|
|
615
|
}
|
|
616
|
|
|
617
|
return deleteResult;
|
|
618
|
}
|
|
619
|
|
|
620
|
@Override
|
|
621
|
@Transactional(readOnly = false)
|
|
622
|
public DeleteResult deleteDescription(UUID descriptionUuid) {
|
|
623
|
return deleteDescription(dao.load(descriptionUuid));
|
|
624
|
}
|
|
625
|
|
|
626
|
@Override
|
|
627
|
public DeleteResult isDeletable(UUID descriptionUuid){
|
|
628
|
DeleteResult result = new DeleteResult();
|
|
629
|
DescriptionBase<?> description = this.load(descriptionUuid);
|
|
630
|
Set<CdmBase> references = commonService.getReferencingObjectsForDeletion(description);
|
|
631
|
|
|
632
|
if (references == null || references.isEmpty()){
|
|
633
|
return result;
|
|
634
|
}
|
|
635
|
for (CdmBase ref: references){
|
|
636
|
String message = null;
|
|
637
|
if (description instanceof TaxonDescription && ref instanceof Taxon && ((TaxonDescription)description).getTaxon().equals(ref)){
|
|
638
|
continue;
|
|
639
|
} else if (description instanceof TaxonNameDescription && ref instanceof TaxonName && ((TaxonNameDescription)description).getTaxonName().equals(ref)){
|
|
640
|
continue;
|
|
641
|
} else if (description instanceof SpecimenDescription && ref instanceof SpecimenOrObservationBase && ((SpecimenDescription)description).getDescribedSpecimenOrObservation().equals(ref)){
|
|
642
|
continue;
|
|
643
|
} else if (ref instanceof DescriptionElementBase){
|
|
644
|
continue;
|
|
645
|
}else {
|
|
646
|
message = "The description can't be completely deleted because it is referenced by " + ref.getUserFriendlyTypeName() ;
|
|
647
|
result.setAbort();
|
|
648
|
}
|
|
649
|
if (message != null){
|
|
650
|
result.addException(new ReferencedObjectUndeletableException(message));
|
|
651
|
result.addRelatedObject(ref);
|
|
652
|
}
|
|
653
|
}
|
|
654
|
|
|
655
|
return result;
|
|
656
|
}
|
|
657
|
|
|
658
|
@Override
|
|
659
|
public TermVocabulary<Feature> getFeatureVocabulary(UUID uuid) {
|
|
660
|
return vocabularyDao.findByUuid(uuid);
|
|
661
|
}
|
|
662
|
|
|
663
|
@Override
|
|
664
|
@Deprecated
|
|
665
|
public <T extends DescriptionElementBase> List<T> getDescriptionElementsForTaxon(
|
|
666
|
Taxon taxon, Set<Feature> features,
|
|
667
|
Class<T> type, Integer pageSize,
|
|
668
|
Integer pageNumber, List<String> propertyPaths) {
|
|
669
|
return listDescriptionElementsForTaxon(taxon, features, type, pageSize, pageNumber, propertyPaths);
|
|
670
|
}
|
|
671
|
|
|
672
|
@Override
|
|
673
|
public <T extends DescriptionElementBase> List<T> listDescriptionElementsForTaxon(
|
|
674
|
Taxon taxon, Set<Feature> features,
|
|
675
|
Class<T> type, Integer pageSize,
|
|
676
|
Integer pageNumber, List<String> propertyPaths) {
|
|
677
|
return dao.getDescriptionElementForTaxon(taxon.getUuid(), features, type, pageSize, pageNumber, propertyPaths);
|
|
678
|
}
|
|
679
|
|
|
680
|
@Override
|
|
681
|
public <T extends DescriptionElementBase> Pager<T> pageDescriptionElementsForTaxon(
|
|
682
|
Taxon taxon, Set<Feature> features,
|
|
683
|
Class<T> type, Integer pageSize,
|
|
684
|
Integer pageNumber, List<String> propertyPaths) {
|
|
685
|
if (logger.isDebugEnabled()){logger.debug(" get count ...");}
|
|
686
|
Long count = dao.countDescriptionElementForTaxon(taxon.getUuid(), features, type);
|
|
687
|
List<T> descriptionElements;
|
|
688
|
if(AbstractPagerImpl.hasResultsInRange(count, pageNumber, pageSize)){ // no point checking again
|
|
689
|
if (logger.isDebugEnabled()){logger.debug(" get list ...");}
|
|
690
|
descriptionElements = listDescriptionElementsForTaxon(taxon, features, type, pageSize, pageNumber, propertyPaths);
|
|
691
|
} else {
|
|
692
|
descriptionElements = new ArrayList<T>(0);
|
|
693
|
}
|
|
694
|
if (logger.isDebugEnabled()){logger.debug(" service - DONE ...");}
|
|
695
|
return new DefaultPagerImpl<T>(pageNumber, count, pageSize, descriptionElements);
|
|
696
|
}
|
|
697
|
|
|
698
|
@Override
|
|
699
|
public String generateNaturalLanguageDescription(TermTree featureTree,
|
|
700
|
TaxonDescription description, List<Language> preferredLanguages, String separator) {
|
|
701
|
|
|
702
|
Language lang = preferredLanguages.size() > 0 ? preferredLanguages.get(0) : Language.DEFAULT();
|
|
703
|
|
|
704
|
description = (TaxonDescription)load(description.getUuid());
|
|
705
|
featureTree = featureTreeDao.load(featureTree.getUuid());
|
|
706
|
|
|
707
|
StringBuilder naturalLanguageDescription = new StringBuilder();
|
|
708
|
|
|
709
|
MarkerType useMarkerType = (MarkerType) definedTermDao.load(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
|
710
|
boolean isUseDescription = false;
|
|
711
|
if(!description.getMarkers().isEmpty()) {
|
|
712
|
for (Marker marker: description.getMarkers()) {
|
|
713
|
MarkerType markerType = marker.getMarkerType();
|
|
714
|
if (markerType.equals(useMarkerType)) {
|
|
715
|
isUseDescription = true;
|
|
716
|
}
|
|
717
|
|
|
718
|
}
|
|
719
|
}
|
|
720
|
|
|
721
|
if(description.hasStructuredData() && !isUseDescription){
|
|
722
|
|
|
723
|
|
|
724
|
String lastCategory = null;
|
|
725
|
String categorySeparator = ". ";
|
|
726
|
|
|
727
|
List<TextData> textDataList;
|
|
728
|
TextData naturalLanguageDescriptionText = null;
|
|
729
|
|
|
730
|
boolean useMicroFormatQuantitativeDescriptionBuilder = false;
|
|
731
|
|
|
732
|
if(useMicroFormatQuantitativeDescriptionBuilder){
|
|
733
|
|
|
734
|
MicroFormatQuantitativeDescriptionBuilder micro = new MicroFormatQuantitativeDescriptionBuilder();
|
|
735
|
naturalLanguageGenerator.setQuantitativeDescriptionBuilder(micro);
|
|
736
|
naturalLanguageDescriptionText = naturalLanguageGenerator.generateSingleTextData(featureTree, (description), lang);
|
|
737
|
|
|
738
|
} else {
|
|
739
|
|
|
740
|
naturalLanguageDescriptionText = naturalLanguageGenerator.generateSingleTextData(
|
|
741
|
featureTree,
|
|
742
|
(description),
|
|
743
|
lang);
|
|
744
|
}
|
|
745
|
|
|
746
|
return naturalLanguageDescriptionText.getText(lang);
|
|
747
|
|
|
748
|
//
|
|
749
|
// boolean doItBetter = false;
|
|
750
|
//
|
|
751
|
// for (TextData textData : textDataList.toArray(new TextData[textDataList.size()])){
|
|
752
|
// if(textData.getMultilanguageText().size() > 0){
|
|
753
|
//
|
|
754
|
// if (!textData.getFeature().equals(Feature.UNKNOWN())) {
|
|
755
|
// String featureLabel = textData.getFeature().getLabel(lang);
|
|
756
|
//
|
|
757
|
// if(doItBetter){
|
|
758
|
// /*
|
|
759
|
// * WARNING
|
|
760
|
// * The code lines below are desinged to handle
|
|
761
|
// * a special case where as the feature label contains
|
|
762
|
// * hierarchical information on the features. This code
|
|
763
|
// * exist only as a base for discussion, and is not
|
|
764
|
// * intendet to be used in production.
|
|
765
|
// */
|
|
766
|
// featureLabel = StringUtils.remove(featureLabel, '>');
|
|
767
|
//
|
|
768
|
// String[] labelTokens = StringUtils.split(featureLabel, '<');
|
|
769
|
// if(labelTokens[0].equals(lastCategory) && labelTokens.length > 1){
|
|
770
|
// if(naturalLanguageDescription.length() > 0){
|
|
771
|
// naturalLanguageDescription.append(separator);
|
|
772
|
// }
|
|
773
|
// naturalLanguageDescription.append(labelTokens[1]);
|
|
774
|
// } else {
|
|
775
|
// if(naturalLanguageDescription.length() > 0){
|
|
776
|
// naturalLanguageDescription.append(categorySeparator);
|
|
777
|
// }
|
|
778
|
// naturalLanguageDescription.append(StringUtils.join(labelTokens));
|
|
779
|
// }
|
|
780
|
// lastCategory = labelTokens[0];
|
|
781
|
// // end of demo code
|
|
782
|
// } else {
|
|
783
|
// if(naturalLanguageDescription.length() > 0){
|
|
784
|
// naturalLanguageDescription.append(separator);
|
|
785
|
// }
|
|
786
|
// naturalLanguageDescription.append(textData.getFeature().getLabel(lang));
|
|
787
|
// }
|
|
788
|
// } else {
|
|
789
|
// if(naturalLanguageDescription.length() > 0){
|
|
790
|
// naturalLanguageDescription.append(separator);
|
|
791
|
// }
|
|
792
|
// }
|
|
793
|
// String text = textData.getMultilanguageText().values().iterator().next().getText();
|
|
794
|
// naturalLanguageDescription.append(text);
|
|
795
|
//
|
|
796
|
// }
|
|
797
|
// }
|
|
798
|
|
|
799
|
}
|
|
800
|
else if (isUseDescription) {
|
|
801
|
//AT: Left Blank in case we need to generate a Natural language text string.
|
|
802
|
}
|
|
803
|
return naturalLanguageDescription.toString();
|
|
804
|
}
|
|
805
|
|
|
806
|
|
|
807
|
@Override
|
|
808
|
public boolean hasStructuredData(DescriptionBase<?> description) {
|
|
809
|
return load(description.getUuid()).hasStructuredData();
|
|
810
|
}
|
|
811
|
|
|
812
|
|
|
813
|
@Override
|
|
814
|
// @Transactional(readOnly = false)
|
|
815
|
public UpdateResult moveDescriptionElementsToDescription(
|
|
816
|
Collection<DescriptionElementBase> descriptionElements,
|
|
817
|
DescriptionBase targetDescription,
|
|
818
|
boolean isCopy,
|
|
819
|
boolean setNameInSource) {
|
|
820
|
|
|
821
|
UpdateResult result = new UpdateResult();
|
|
822
|
if (descriptionElements.isEmpty() || descriptionElements.iterator().next() == null){
|
|
823
|
result.setAbort();
|
|
824
|
return result;
|
|
825
|
}
|
|
826
|
|
|
827
|
|
|
828
|
if (! isCopy && descriptionElements == descriptionElements.iterator().next().getInDescription().getElements()){
|
|
829
|
//if the descriptionElements collection is the elements set of a description, put it in a separate set before to avoid concurrent modification exceptions
|
|
830
|
descriptionElements = new HashSet<DescriptionElementBase>(descriptionElements);
|
|
831
|
// descriptionElementsTmp.addAll(descriptionElements);
|
|
832
|
// descriptionElements = descriptionElementsTmp;
|
|
833
|
}
|
|
834
|
for (DescriptionElementBase element : descriptionElements){
|
|
835
|
DescriptionBase<?> description = element.getInDescription();
|
|
836
|
description = HibernateProxyHelper.deproxy(dao.load(description.getUuid()));
|
|
837
|
Taxon taxon;
|
|
838
|
TaxonName name = null;
|
|
839
|
if (description instanceof TaxonDescription){
|
|
840
|
TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(description, TaxonDescription.class);
|
|
841
|
if (taxonDescription.getTaxon() != null){
|
|
842
|
taxon = (Taxon) taxonDao.load(taxonDescription.getTaxon().getUuid());
|
|
843
|
name = taxon.getName();
|
|
844
|
}
|
|
845
|
|
|
846
|
|
|
847
|
}
|
|
848
|
try {
|
|
849
|
DescriptionElementBase newElement = (DescriptionElementBase)element.clone();
|
|
850
|
if (setNameInSource) {
|
|
851
|
for (DescriptionElementSource source: newElement.getSources()){
|
|
852
|
if (source.getNameUsedInSource() == null){
|
|
853
|
source.setNameUsedInSource(name);
|
|
854
|
}
|
|
855
|
}
|
|
856
|
|
|
857
|
}
|
|
858
|
targetDescription.addElement(newElement);
|
|
859
|
} catch (CloneNotSupportedException e) {
|
|
860
|
throw new RuntimeException ("Clone not yet implemented for class " + element.getClass().getName(), e);
|
|
861
|
}
|
|
862
|
if (! isCopy){
|
|
863
|
description.removeElement(element);
|
|
864
|
dao.saveOrUpdate(description);
|
|
865
|
result.addUpdatedObject(description);
|
|
866
|
// if (description.getElements().isEmpty()){
|
|
867
|
// if (description instanceof TaxonDescription){
|
|
868
|
// TaxonDescription taxDescription = HibernateProxyHelper.deproxy(description, TaxonDescription.class);
|
|
869
|
// if (taxDescription.getTaxon() != null){
|
|
870
|
// taxDescription.getTaxon().removeDescription((TaxonDescription)description);
|
|
871
|
// }
|
|
872
|
// }
|
|
873
|
// dao.delete(description);
|
|
874
|
//
|
|
875
|
// }//else{
|
|
876
|
// dao.saveOrUpdate(description);
|
|
877
|
// result.addUpdatedObject(description);
|
|
878
|
// }
|
|
879
|
}
|
|
880
|
|
|
881
|
|
|
882
|
}
|
|
883
|
dao.saveOrUpdate(targetDescription);
|
|
884
|
result.addUpdatedObject(targetDescription);
|
|
885
|
if (targetDescription instanceof TaxonDescription){
|
|
886
|
result.addUpdatedObject(((TaxonDescription)targetDescription).getTaxon());
|
|
887
|
}
|
|
888
|
return result;
|
|
889
|
}
|
|
890
|
|
|
891
|
@Override
|
|
892
|
@Transactional(readOnly = false)
|
|
893
|
public UpdateResult moveDescriptionElementsToDescription(
|
|
894
|
Set<UUID> descriptionElementUUIDs,
|
|
895
|
UUID targetDescriptionUuid,
|
|
896
|
boolean isCopy, boolean setNameInSource) {
|
|
897
|
Set<DescriptionElementBase> descriptionElements = new HashSet<DescriptionElementBase>();
|
|
898
|
for(UUID deUuid : descriptionElementUUIDs) {
|
|
899
|
DescriptionElementBase element = descriptionElementDao.load(deUuid);
|
|
900
|
if (element != null){
|
|
901
|
descriptionElements.add(element);
|
|
902
|
}
|
|
903
|
}
|
|
904
|
DescriptionBase targetDescription = dao.load(targetDescriptionUuid);
|
|
905
|
|
|
906
|
return moveDescriptionElementsToDescription(descriptionElements, targetDescription, isCopy, setNameInSource);
|
|
907
|
}
|
|
908
|
|
|
909
|
@Override
|
|
910
|
@Transactional(readOnly = false)
|
|
911
|
public UpdateResult moveDescriptionElementsToDescription(
|
|
912
|
Set<UUID> descriptionElementUUIDs,
|
|
913
|
DescriptionBase targetDescription,
|
|
914
|
boolean isCopy, boolean setNameInSource) {
|
|
915
|
Set<DescriptionElementBase> descriptionElements = new HashSet<DescriptionElementBase>();
|
|
916
|
for(UUID deUuid : descriptionElementUUIDs) {
|
|
917
|
DescriptionElementBase element = descriptionElementDao.load(deUuid);
|
|
918
|
if (element != null){
|
|
919
|
descriptionElements.add(element);
|
|
920
|
}
|
|
921
|
}
|
|
922
|
DescriptionBase newTargetDescription;
|
|
923
|
if (targetDescription.isPersited()){
|
|
924
|
newTargetDescription = dao.load(targetDescription.getUuid());
|
|
925
|
}else{
|
|
926
|
if (targetDescription instanceof TaxonDescription){
|
|
927
|
Taxon taxon = (Taxon)taxonDao.load(((TaxonDescription)targetDescription).getTaxon().getUuid());
|
|
928
|
|
|
929
|
newTargetDescription = TaxonDescription.NewInstance(taxon, targetDescription.isImageGallery());
|
|
930
|
|
|
931
|
}else if (targetDescription instanceof TaxonNameDescription){
|
|
932
|
TaxonName name = nameDao.load(((TaxonNameDescription)targetDescription).getTaxonName().getUuid());
|
|
933
|
newTargetDescription = TaxonNameDescription.NewInstance(name);
|
|
934
|
}else {
|
|
935
|
SpecimenOrObservationBase specimen = occurrenceDao.load(((SpecimenDescription)targetDescription).getDescribedSpecimenOrObservation().getUuid());
|
|
936
|
newTargetDescription = SpecimenDescription.NewInstance(specimen);
|
|
937
|
}
|
|
938
|
|
|
939
|
newTargetDescription.addSources(targetDescription.getSources());
|
|
940
|
newTargetDescription.setTitleCache(targetDescription.getTitleCache(), targetDescription.isProtectedTitleCache());
|
|
941
|
|
|
942
|
}
|
|
943
|
return moveDescriptionElementsToDescription(descriptionElements, newTargetDescription, isCopy, setNameInSource);
|
|
944
|
}
|
|
945
|
|
|
946
|
|
|
947
|
@Override
|
|
948
|
@Transactional(readOnly = false)
|
|
949
|
public UpdateResult moveDescriptionElementsToDescription(
|
|
950
|
Set<UUID> descriptionElementUUIDs,
|
|
951
|
UUID targetTaxonUuid,
|
|
952
|
String moveMessage,
|
|
953
|
boolean isCopy, boolean setNameInSource) {
|
|
954
|
Taxon targetTaxon = CdmBase.deproxy(taxonDao.load(targetTaxonUuid), Taxon.class);
|
|
955
|
DescriptionBase targetDescription = TaxonDescription.NewInstance(targetTaxon);
|
|
956
|
targetDescription.setTitleCache(moveMessage, true);
|
|
957
|
Annotation annotation = Annotation.NewInstance(moveMessage, Language.getDefaultLanguage());
|
|
958
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
|
959
|
targetDescription.addAnnotation(annotation);
|
|
960
|
|
|
961
|
targetDescription = dao.save(targetDescription);
|
|
962
|
Set<DescriptionElementBase> descriptionElements = new HashSet<DescriptionElementBase>();
|
|
963
|
for(UUID deUuid : descriptionElementUUIDs) {
|
|
964
|
descriptionElements.add(descriptionElementDao.load(deUuid));
|
|
965
|
}
|
|
966
|
|
|
967
|
return moveDescriptionElementsToDescription(descriptionElements, targetDescription, isCopy, setNameInSource);
|
|
968
|
}
|
|
969
|
|
|
970
|
@Override
|
|
971
|
public Pager<TermDto> pageNamedAreasInUse(boolean includeAllParents, Integer pageSize,
|
|
972
|
Integer pageNumber){
|
|
973
|
List<TermDto> results = dao.listNamedAreasInUse(includeAllParents, null, null);
|
|
974
|
int startIndex= pageNumber * pageSize;
|
|
975
|
int toIndex = Math.min(startIndex + pageSize, results.size());
|
|
976
|
List<TermDto> page = results.subList(startIndex, toIndex);
|
|
977
|
return new DefaultPagerImpl<TermDto>(pageNumber, results.size(), pageSize, page);
|
|
978
|
}
|
|
979
|
|
|
980
|
|
|
981
|
@Override
|
|
982
|
@Transactional(readOnly = false)
|
|
983
|
public UpdateResult moveTaxonDescriptions(Taxon sourceTaxon, Taxon targetTaxon, boolean setNameInSource) {
|
|
984
|
List<TaxonDescription> descriptions = new ArrayList<>(sourceTaxon.getDescriptions());
|
|
985
|
UpdateResult result = new UpdateResult();
|
|
986
|
result.addUpdatedObject(sourceTaxon);
|
|
987
|
result.addUpdatedObject(targetTaxon);
|
|
988
|
for(TaxonDescription description : descriptions){
|
|
989
|
targetTaxon.addDescription(prepareDescriptionForMove(description, sourceTaxon, setNameInSource));
|
|
990
|
}
|
|
991
|
return result;
|
|
992
|
}
|
|
993
|
|
|
994
|
private TaxonDescription prepareDescriptionForMove(TaxonDescription description, Taxon sourceTaxon, boolean setNameInSource){
|
|
995
|
String moveMessage = String.format("Description moved from %s", sourceTaxon);
|
|
996
|
if(description.isProtectedTitleCache()){
|
|
997
|
String separator = "";
|
|
998
|
if(!StringUtils.isBlank(description.getTitleCache())){
|
|
999
|
separator = " - ";
|
|
1000
|
}
|
|
1001
|
description.setTitleCache(description.getTitleCache() + separator + moveMessage, true);
|
|
1002
|
}
|
|
1003
|
else{
|
|
1004
|
description.setTitleCache(moveMessage, true);
|
|
1005
|
}
|
|
1006
|
Annotation annotation = Annotation.NewInstance(moveMessage, Language.getDefaultLanguage());
|
|
1007
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
|
1008
|
description.addAnnotation(annotation);
|
|
1009
|
if(setNameInSource){
|
|
1010
|
for (DescriptionElementBase element: description.getElements()){
|
|
1011
|
for (DescriptionElementSource source: element.getSources()){
|
|
1012
|
if (source.getNameUsedInSource() == null){
|
|
1013
|
source.setNameUsedInSource(sourceTaxon.getName());
|
|
1014
|
}
|
|
1015
|
}
|
|
1016
|
}
|
|
1017
|
}
|
|
1018
|
return description;
|
|
1019
|
}
|
|
1020
|
|
|
1021
|
@Override
|
|
1022
|
@Transactional(readOnly = false)
|
|
1023
|
public UpdateResult moveTaxonDescriptions(UUID sourceTaxonUuid, UUID targetTaxonUuid, boolean setNameInSource) {
|
|
1024
|
Taxon sourceTaxon = HibernateProxyHelper.deproxy(taxonDao.load(sourceTaxonUuid), Taxon.class);
|
|
1025
|
Taxon targetTaxon = HibernateProxyHelper.deproxy(taxonDao.load(targetTaxonUuid), Taxon.class);
|
|
1026
|
return moveTaxonDescriptions(sourceTaxon, targetTaxon, setNameInSource);
|
|
1027
|
|
|
1028
|
}
|
|
1029
|
|
|
1030
|
@Override
|
|
1031
|
@Transactional(readOnly = false)
|
|
1032
|
public UpdateResult moveTaxonDescription(UUID descriptionUuid, UUID targetTaxonUuid, boolean setNameInSource){
|
|
1033
|
TaxonDescription description = HibernateProxyHelper.deproxy(dao.load(descriptionUuid), TaxonDescription.class);
|
|
1034
|
Taxon targetTaxon = HibernateProxyHelper.deproxy(taxonDao.load(targetTaxonUuid), Taxon.class);
|
|
1035
|
Taxon sourceTaxon = description.getTaxon();
|
|
1036
|
UpdateResult result = new UpdateResult();
|
|
1037
|
result.addUpdatedObject(sourceTaxon);
|
|
1038
|
result.addUpdatedObject(targetTaxon);
|
|
1039
|
|
|
1040
|
targetTaxon.addDescription(prepareDescriptionForMove(description, sourceTaxon, setNameInSource));
|
|
1041
|
return result;
|
|
1042
|
|
|
1043
|
}
|
|
1044
|
|
|
1045
|
|
|
1046
|
}
|