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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.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.TaxonDistributionDTO;
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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.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.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.taxon.Taxon;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.FeatureTree;
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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.IFeatureDao;
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import eu.etaxonomy.cdm.persistence.dao.description.IFeatureNodeDao;
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import eu.etaxonomy.cdm.persistence.dao.description.IFeatureTreeDao;
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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.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 IFeatureTreeDao featureTreeDao;
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protected IDescriptiveDataSetDao descriptiveDataSetDao;
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protected IFeatureNodeDao featureNodeDao;
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protected IFeatureDao featureDao;
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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(IFeatureTreeDao 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 setFeatureNodeDao(IFeatureNodeDao featureNodeDao) {
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this.featureNodeDao = featureNodeDao;
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}
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@Autowired
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protected void setFeatureDao(IFeatureDao featureDao) {
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this.featureDao = featureDao;
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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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return pageTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, 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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return listTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, 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, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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long numberOfResults = dao.countTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes);
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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, 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, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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List<TaxonDescription> results = dao.listTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, 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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List<UUID> uuids = new ArrayList<UUID>();
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for (TaxonDescription taxonDescription : taxonDescriptions) {
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if (! taxonDescription.isImageGallery()){ //image galleries should not have descriptions, but better filter fully on DTYPE of description element
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uuids.add(taxonDescription.getUuid());
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}
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}
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List<DescriptionBase> desclist = dao.list(uuids, null, null, null, propertyPaths);
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for (DescriptionBase desc : desclist) {
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if (desc.isInstanceOf(TaxonDescription.class)){
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Set<DescriptionElementBase> elements = desc.getElements();
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for (DescriptionElementBase element : elements) {
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if (element.isInstanceOf(Distribution.class)) {
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Distribution distribution = (Distribution) element;
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if(distribution.getArea() != null){
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distList.add(distribution);
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}
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}
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}
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}
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}
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//old
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// for (TaxonDescription taxonDescription : taxonDescriptions) {
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// if (logger.isDebugEnabled()){ logger.debug("load taxon description " + taxonDescription.getUuid());}
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// //TODO why not loading all description via .list ? This may improve performance
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// taxonDescription = (TaxonDescription) dao.load(taxonDescription.getUuid(), propertyPaths);
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// Set<DescriptionElementBase> elements = taxonDescription.getElements();
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// for (DescriptionElementBase element : elements) {
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// if (element.isInstanceOf(Distribution.class)) {
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// Distribution distribution = (Distribution) element;
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// if(distribution.getArea() != null){
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// distList.add(distribution);
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// }
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// }
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// }
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// }
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if (logger.isDebugEnabled()){logger.debug("filter tree for " + distList.size() + " distributions ...");}
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// filter distributions
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Collection<Distribution> filteredDistributions = DescriptionUtility.filterDistributions(distList, hiddenAreaMarkerTypes, true, statusOrderPreference, false);
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distList.clear();
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distList.addAll(filteredDistributions);
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return DescriptionUtility.orderDistributions(definedTermDao, omitLevels, distList, hiddenAreaMarkerTypes, null);
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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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380
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
381
|
results = dao.getTaxonNameDescriptions(name, pageSize, pageNumber,propertyPaths);
|
382
|
}
|
383
|
|
384
|
return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
|
385
|
}
|
386
|
|
387
|
|
388
|
@Override
|
389
|
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) {
|
390
|
long numberOfResults = dao.countDescriptions(type, hasImages, hasText, feature);
|
391
|
|
392
|
@SuppressWarnings("rawtypes")
|
393
|
List<DescriptionBase> results = new ArrayList<>();
|
394
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
395
|
results = dao.listDescriptions(type, hasImages, hasText, feature, pageSize, pageNumber,orderHints,propertyPaths);
|
396
|
}
|
397
|
|
398
|
return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
|
399
|
}
|
400
|
|
401
|
/**
|
402
|
* FIXME Candidate for harmonization
|
403
|
* Rename: searchByDistribution
|
404
|
*/
|
405
|
@Override
|
406
|
public Pager<TaxonDescription> searchDescriptionByDistribution(Set<NamedArea> namedAreas, PresenceAbsenceTerm presence, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
407
|
long numberOfResults = dao.countDescriptionByDistribution(namedAreas, presence);
|
408
|
|
409
|
List<TaxonDescription> results = new ArrayList<>();
|
410
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
411
|
results = dao.searchDescriptionByDistribution(namedAreas, presence, pageSize, pageNumber,orderHints,propertyPaths);
|
412
|
}
|
413
|
|
414
|
return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
|
415
|
}
|
416
|
|
417
|
/**
|
418
|
* FIXME Candidate for harmonization
|
419
|
* move: descriptionElementService.search
|
420
|
*/
|
421
|
@Override
|
422
|
// public Pager<T> searchElements(Class<? extends T> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
423
|
public <S extends DescriptionElementBase> Pager<S> searchElements(Class<S> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
424
|
long numberOfResults = descriptionElementDao.count(clazz, queryString);
|
425
|
|
426
|
List<S> results = new ArrayList<>();
|
427
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
428
|
results = (List<S>)descriptionElementDao.search(clazz, queryString, pageSize, pageNumber, orderHints, propertyPaths);
|
429
|
}
|
430
|
|
431
|
return new DefaultPagerImpl<>(pageNumber, numberOfResults, pageSize, results);
|
432
|
}
|
433
|
|
434
|
/**
|
435
|
* FIXME Candidate for harmonization
|
436
|
* descriptionElementService.find
|
437
|
*/
|
438
|
@Override
|
439
|
public DescriptionElementBase getDescriptionElementByUuid(UUID uuid) {
|
440
|
return descriptionElementDao.findByUuid(uuid);
|
441
|
}
|
442
|
|
443
|
/**
|
444
|
* FIXME Candidate for harmonization
|
445
|
* descriptionElementService.load
|
446
|
*/
|
447
|
@Override
|
448
|
public DescriptionElementBase loadDescriptionElement(UUID uuid, List<String> propertyPaths) {
|
449
|
return descriptionElementDao.load(uuid, propertyPaths);
|
450
|
}
|
451
|
|
452
|
/**
|
453
|
* FIXME Candidate for harmonization
|
454
|
* descriptionElementService.save
|
455
|
*/
|
456
|
@Override
|
457
|
@Transactional(readOnly = false)
|
458
|
public UUID saveDescriptionElement(DescriptionElementBase descriptionElement) {
|
459
|
return descriptionElementDao.save(descriptionElement).getUuid();
|
460
|
}
|
461
|
|
462
|
/**
|
463
|
* FIXME Candidate for harmonization
|
464
|
* descriptionElementService.save
|
465
|
*/
|
466
|
@Override
|
467
|
@Transactional(readOnly = false)
|
468
|
public Map<UUID, DescriptionElementBase> saveDescriptionElement(Collection<DescriptionElementBase> descriptionElements) {
|
469
|
return descriptionElementDao.saveAll(descriptionElements);
|
470
|
}
|
471
|
|
472
|
@Override
|
473
|
@Transactional(readOnly = false)
|
474
|
public List<MergeResult<DescriptionBase>> mergeDescriptionElements(Collection<TaxonDistributionDTO> descriptionElements, boolean returnTransientEntity) {
|
475
|
List<MergeResult<DescriptionBase>> mergedObjects = new ArrayList();
|
476
|
List<Distribution> toDelete = new ArrayList<>();
|
477
|
for(TaxonDistributionDTO obj : descriptionElements) {
|
478
|
Iterator<TaxonDescription> iterator = obj.getDescriptionsWrapper().getDescriptions().iterator();
|
479
|
while (iterator.hasNext()){
|
480
|
TaxonDescription desc = iterator.next();
|
481
|
mergedObjects.add(dao.merge(desc, returnTransientEntity));
|
482
|
}
|
483
|
|
484
|
|
485
|
}
|
486
|
|
487
|
return mergedObjects;
|
488
|
}
|
489
|
|
490
|
/**
|
491
|
* FIXME Candidate for harmonization
|
492
|
* descriptionElementService.delete
|
493
|
*/
|
494
|
@Override
|
495
|
public UUID deleteDescriptionElement(DescriptionElementBase descriptionElement) {
|
496
|
return descriptionElementDao.delete(descriptionElement);
|
497
|
}
|
498
|
|
499
|
|
500
|
/* (non-Javadoc)
|
501
|
* @see eu.etaxonomy.cdm.api.service.IDescriptionService#deleteDescriptionElement(java.util.UUID)
|
502
|
*/
|
503
|
@Override
|
504
|
public UUID deleteDescriptionElement(UUID descriptionElementUuid) {
|
505
|
return deleteDescriptionElement(descriptionElementDao.load(descriptionElementUuid));
|
506
|
}
|
507
|
|
508
|
@Override
|
509
|
@Transactional(readOnly = false)
|
510
|
public DeleteResult deleteDescription(DescriptionBase description) {
|
511
|
DeleteResult deleteResult = new DeleteResult();
|
512
|
description = load(description.getId(), Arrays.asList("descriptiveDataSets"));//avoid lazy init exception
|
513
|
|
514
|
if (description instanceof TaxonDescription){
|
515
|
TaxonDescription taxDescription = HibernateProxyHelper.deproxy(description, TaxonDescription.class);
|
516
|
Taxon tax = taxDescription.getTaxon();
|
517
|
tax.removeDescription(taxDescription, true);
|
518
|
deleteResult.addUpdatedObject(tax);
|
519
|
}
|
520
|
else if (HibernateProxyHelper.isInstanceOf(description, SpecimenDescription.class)){
|
521
|
SpecimenDescription specimenDescription = HibernateProxyHelper.deproxy(description, SpecimenDescription.class);
|
522
|
SpecimenOrObservationBase specimen = specimenDescription.getDescribedSpecimenOrObservation();
|
523
|
specimen.removeDescription(specimenDescription);
|
524
|
deleteResult.addUpdatedObject(specimen);
|
525
|
}
|
526
|
|
527
|
Set<DescriptiveDataSet> descriptiveDataSets = description.getDescriptiveDataSets();
|
528
|
for (Iterator<DescriptiveDataSet> iterator = descriptiveDataSets.iterator(); iterator.hasNext();) {
|
529
|
iterator.next().removeDescription(description);
|
530
|
}
|
531
|
|
532
|
dao.delete(description);
|
533
|
deleteResult.addDeletedObject(description);
|
534
|
deleteResult.setCdmEntity(description);
|
535
|
|
536
|
|
537
|
return deleteResult;
|
538
|
}
|
539
|
|
540
|
|
541
|
/* (non-Javadoc)
|
542
|
* @see eu.etaxonomy.cdm.api.service.IDescriptionService#deleteDescription(java.util.UUID)
|
543
|
*/
|
544
|
@Override
|
545
|
@Transactional(readOnly = false)
|
546
|
public DeleteResult deleteDescription(UUID descriptionUuid) {
|
547
|
return deleteDescription(dao.load(descriptionUuid));
|
548
|
}
|
549
|
|
550
|
|
551
|
@Override
|
552
|
public TermVocabulary<Feature> getFeatureVocabulary(UUID uuid) {
|
553
|
return vocabularyDao.findByUuid(uuid);
|
554
|
}
|
555
|
|
556
|
@Override
|
557
|
@Deprecated
|
558
|
public <T extends DescriptionElementBase> List<T> getDescriptionElementsForTaxon(
|
559
|
Taxon taxon, Set<Feature> features,
|
560
|
Class<T> type, Integer pageSize,
|
561
|
Integer pageNumber, List<String> propertyPaths) {
|
562
|
return listDescriptionElementsForTaxon(taxon, features, type, pageSize, pageNumber, propertyPaths);
|
563
|
}
|
564
|
|
565
|
@Override
|
566
|
public <T extends DescriptionElementBase> List<T> listDescriptionElementsForTaxon(
|
567
|
Taxon taxon, Set<Feature> features,
|
568
|
Class<T> type, Integer pageSize,
|
569
|
Integer pageNumber, List<String> propertyPaths) {
|
570
|
return dao.getDescriptionElementForTaxon(taxon.getUuid(), features, type, pageSize, pageNumber, propertyPaths);
|
571
|
}
|
572
|
|
573
|
@Override
|
574
|
public <T extends DescriptionElementBase> Pager<T> pageDescriptionElementsForTaxon(
|
575
|
Taxon taxon, Set<Feature> features,
|
576
|
Class<T> type, Integer pageSize,
|
577
|
Integer pageNumber, List<String> propertyPaths) {
|
578
|
if (logger.isDebugEnabled()){logger.debug(" get count ...");}
|
579
|
Long count = dao.countDescriptionElementForTaxon(taxon.getUuid(), features, type);
|
580
|
List<T> descriptionElements;
|
581
|
if(AbstractPagerImpl.hasResultsInRange(count, pageNumber, pageSize)){ // no point checking again
|
582
|
if (logger.isDebugEnabled()){logger.debug(" get list ...");}
|
583
|
descriptionElements = listDescriptionElementsForTaxon(taxon, features, type, pageSize, pageNumber, propertyPaths);
|
584
|
} else {
|
585
|
descriptionElements = new ArrayList<T>(0);
|
586
|
}
|
587
|
if (logger.isDebugEnabled()){logger.debug(" service - DONE ...");}
|
588
|
return new DefaultPagerImpl<T>(pageNumber, count, pageSize, descriptionElements);
|
589
|
}
|
590
|
|
591
|
@Override
|
592
|
public String generateNaturalLanguageDescription(FeatureTree featureTree,
|
593
|
TaxonDescription description, List<Language> preferredLanguages, String separator) {
|
594
|
|
595
|
Language lang = preferredLanguages.size() > 0 ? preferredLanguages.get(0) : Language.DEFAULT();
|
596
|
|
597
|
description = (TaxonDescription)load(description.getUuid());
|
598
|
featureTree = featureTreeDao.load(featureTree.getUuid());
|
599
|
|
600
|
StringBuilder naturalLanguageDescription = new StringBuilder();
|
601
|
|
602
|
MarkerType useMarkerType = (MarkerType) definedTermDao.load(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
603
|
boolean isUseDescription = false;
|
604
|
if(!description.getMarkers().isEmpty()) {
|
605
|
for (Marker marker: description.getMarkers()) {
|
606
|
MarkerType markerType = marker.getMarkerType();
|
607
|
if (markerType.equals(useMarkerType)) {
|
608
|
isUseDescription = true;
|
609
|
}
|
610
|
|
611
|
}
|
612
|
}
|
613
|
|
614
|
if(description.hasStructuredData() && !isUseDescription){
|
615
|
|
616
|
|
617
|
String lastCategory = null;
|
618
|
String categorySeparator = ". ";
|
619
|
|
620
|
List<TextData> textDataList;
|
621
|
TextData naturalLanguageDescriptionText = null;
|
622
|
|
623
|
boolean useMicroFormatQuantitativeDescriptionBuilder = false;
|
624
|
|
625
|
if(useMicroFormatQuantitativeDescriptionBuilder){
|
626
|
|
627
|
MicroFormatQuantitativeDescriptionBuilder micro = new MicroFormatQuantitativeDescriptionBuilder();
|
628
|
naturalLanguageGenerator.setQuantitativeDescriptionBuilder(micro);
|
629
|
naturalLanguageDescriptionText = naturalLanguageGenerator.generateSingleTextData(featureTree, (description), lang);
|
630
|
|
631
|
} else {
|
632
|
|
633
|
naturalLanguageDescriptionText = naturalLanguageGenerator.generateSingleTextData(
|
634
|
featureTree,
|
635
|
(description),
|
636
|
lang);
|
637
|
}
|
638
|
|
639
|
return naturalLanguageDescriptionText.getText(lang);
|
640
|
|
641
|
//
|
642
|
// boolean doItBetter = false;
|
643
|
//
|
644
|
// for (TextData textData : textDataList.toArray(new TextData[textDataList.size()])){
|
645
|
// if(textData.getMultilanguageText().size() > 0){
|
646
|
//
|
647
|
// if (!textData.getFeature().equals(Feature.UNKNOWN())) {
|
648
|
// String featureLabel = textData.getFeature().getLabel(lang);
|
649
|
//
|
650
|
// if(doItBetter){
|
651
|
// /*
|
652
|
// * WARNING
|
653
|
// * The code lines below are desinged to handle
|
654
|
// * a special case where as the feature label contains
|
655
|
// * hierarchical information on the features. This code
|
656
|
// * exist only as a base for discussion, and is not
|
657
|
// * intendet to be used in production.
|
658
|
// */
|
659
|
// featureLabel = StringUtils.remove(featureLabel, '>');
|
660
|
//
|
661
|
// String[] labelTokens = StringUtils.split(featureLabel, '<');
|
662
|
// if(labelTokens[0].equals(lastCategory) && labelTokens.length > 1){
|
663
|
// if(naturalLanguageDescription.length() > 0){
|
664
|
// naturalLanguageDescription.append(separator);
|
665
|
// }
|
666
|
// naturalLanguageDescription.append(labelTokens[1]);
|
667
|
// } else {
|
668
|
// if(naturalLanguageDescription.length() > 0){
|
669
|
// naturalLanguageDescription.append(categorySeparator);
|
670
|
// }
|
671
|
// naturalLanguageDescription.append(StringUtils.join(labelTokens));
|
672
|
// }
|
673
|
// lastCategory = labelTokens[0];
|
674
|
// // end of demo code
|
675
|
// } else {
|
676
|
// if(naturalLanguageDescription.length() > 0){
|
677
|
// naturalLanguageDescription.append(separator);
|
678
|
// }
|
679
|
// naturalLanguageDescription.append(textData.getFeature().getLabel(lang));
|
680
|
// }
|
681
|
// } else {
|
682
|
// if(naturalLanguageDescription.length() > 0){
|
683
|
// naturalLanguageDescription.append(separator);
|
684
|
// }
|
685
|
// }
|
686
|
// String text = textData.getMultilanguageText().values().iterator().next().getText();
|
687
|
// naturalLanguageDescription.append(text);
|
688
|
//
|
689
|
// }
|
690
|
// }
|
691
|
|
692
|
}
|
693
|
else if (isUseDescription) {
|
694
|
//AT: Left Blank in case we need to generate a Natural language text string.
|
695
|
}
|
696
|
return naturalLanguageDescription.toString();
|
697
|
}
|
698
|
|
699
|
|
700
|
@Override
|
701
|
public boolean hasStructuredData(DescriptionBase<?> description) {
|
702
|
return load(description.getUuid()).hasStructuredData();
|
703
|
}
|
704
|
|
705
|
|
706
|
@Override
|
707
|
// @Transactional(readOnly = false)
|
708
|
public UpdateResult moveDescriptionElementsToDescription(
|
709
|
Collection<DescriptionElementBase> descriptionElements,
|
710
|
DescriptionBase targetDescription,
|
711
|
boolean isCopy) {
|
712
|
|
713
|
UpdateResult result = new UpdateResult();
|
714
|
if (descriptionElements.isEmpty() || descriptionElements.iterator().next() == null){
|
715
|
result.setAbort();
|
716
|
return result;
|
717
|
}
|
718
|
|
719
|
|
720
|
if (! isCopy && descriptionElements == descriptionElements.iterator().next().getInDescription().getElements()){
|
721
|
//if the descriptionElements collection is the elements set of a description, put it in a separate set before to avoid concurrent modification exceptions
|
722
|
descriptionElements = new HashSet<DescriptionElementBase>(descriptionElements);
|
723
|
// descriptionElementsTmp.addAll(descriptionElements);
|
724
|
// descriptionElements = descriptionElementsTmp;
|
725
|
}
|
726
|
for (DescriptionElementBase element : descriptionElements){
|
727
|
DescriptionBase<?> description = element.getInDescription();
|
728
|
description = dao.load(description.getUuid());
|
729
|
try {
|
730
|
DescriptionElementBase newElement = (DescriptionElementBase)element.clone();
|
731
|
targetDescription.addElement(newElement);
|
732
|
} catch (CloneNotSupportedException e) {
|
733
|
throw new RuntimeException ("Clone not yet implemented for class " + element.getClass().getName(), e);
|
734
|
}
|
735
|
if (! isCopy){
|
736
|
description.removeElement(element);
|
737
|
if (description.getElements().isEmpty()){
|
738
|
if (description instanceof TaxonDescription){
|
739
|
TaxonDescription taxDescription = HibernateProxyHelper.deproxy(description, TaxonDescription.class);
|
740
|
if (taxDescription.getTaxon() != null){
|
741
|
taxDescription.getTaxon().removeDescription((TaxonDescription)description);
|
742
|
}
|
743
|
}
|
744
|
dao.delete(description);
|
745
|
|
746
|
}//else{
|
747
|
// dao.saveOrUpdate(description);
|
748
|
// result.addUpdatedObject(description);
|
749
|
// }
|
750
|
}
|
751
|
|
752
|
|
753
|
}
|
754
|
dao.saveOrUpdate(targetDescription);
|
755
|
result.addUpdatedObject(targetDescription);
|
756
|
if (targetDescription instanceof TaxonDescription){
|
757
|
result.addUpdatedObject(((TaxonDescription)targetDescription).getTaxon());
|
758
|
}
|
759
|
return result;
|
760
|
}
|
761
|
|
762
|
@Override
|
763
|
@Transactional(readOnly = false)
|
764
|
public UpdateResult moveDescriptionElementsToDescription(
|
765
|
Set<UUID> descriptionElementUUIDs,
|
766
|
UUID targetDescriptionUuid,
|
767
|
boolean isCopy) {
|
768
|
Set<DescriptionElementBase> descriptionElements = new HashSet<DescriptionElementBase>();
|
769
|
for(UUID deUuid : descriptionElementUUIDs) {
|
770
|
DescriptionElementBase element = descriptionElementDao.load(deUuid);
|
771
|
if (element != null){
|
772
|
descriptionElements.add(element);
|
773
|
}
|
774
|
}
|
775
|
DescriptionBase targetDescription = dao.load(targetDescriptionUuid);
|
776
|
|
777
|
return moveDescriptionElementsToDescription(descriptionElements, targetDescription, isCopy);
|
778
|
}
|
779
|
|
780
|
@Override
|
781
|
@Transactional(readOnly = false)
|
782
|
public UpdateResult moveDescriptionElementsToDescription(
|
783
|
Set<UUID> descriptionElementUUIDs,
|
784
|
DescriptionBase targetDescription,
|
785
|
boolean isCopy) {
|
786
|
Set<DescriptionElementBase> descriptionElements = new HashSet<DescriptionElementBase>();
|
787
|
for(UUID deUuid : descriptionElementUUIDs) {
|
788
|
DescriptionElementBase element = descriptionElementDao.load(deUuid);
|
789
|
if (element != null){
|
790
|
descriptionElements.add(element);
|
791
|
}
|
792
|
}
|
793
|
DescriptionBase newTargetDescription;
|
794
|
if (targetDescription.isPersited()){
|
795
|
newTargetDescription = dao.load(targetDescription.getUuid());
|
796
|
}else{
|
797
|
if (targetDescription instanceof TaxonDescription){
|
798
|
Taxon taxon = (Taxon)taxonDao.load(((TaxonDescription)targetDescription).getTaxon().getUuid());
|
799
|
|
800
|
newTargetDescription = TaxonDescription.NewInstance(taxon, targetDescription.isImageGallery());
|
801
|
|
802
|
}else if (targetDescription instanceof TaxonNameDescription){
|
803
|
TaxonName name = nameDao.load(((TaxonNameDescription)targetDescription).getTaxonName().getUuid());
|
804
|
newTargetDescription = TaxonNameDescription.NewInstance(name);
|
805
|
}else {
|
806
|
SpecimenOrObservationBase specimen = occurrenceDao.load(((SpecimenDescription)targetDescription).getDescribedSpecimenOrObservation().getUuid());
|
807
|
newTargetDescription = SpecimenDescription.NewInstance(specimen);
|
808
|
}
|
809
|
|
810
|
newTargetDescription.addSources(targetDescription.getSources());
|
811
|
newTargetDescription.setTitleCache(targetDescription.getTitleCache(), targetDescription.isProtectedTitleCache());
|
812
|
|
813
|
}
|
814
|
return moveDescriptionElementsToDescription(descriptionElements, newTargetDescription, isCopy);
|
815
|
}
|
816
|
|
817
|
|
818
|
@Override
|
819
|
@Transactional(readOnly = false)
|
820
|
public UpdateResult moveDescriptionElementsToDescription(
|
821
|
Set<UUID> descriptionElementUUIDs,
|
822
|
UUID targetTaxonUuid,
|
823
|
String moveMessage,
|
824
|
boolean isCopy) {
|
825
|
Taxon targetTaxon = CdmBase.deproxy(taxonDao.load(targetTaxonUuid), Taxon.class);
|
826
|
DescriptionBase targetDescription = TaxonDescription.NewInstance(targetTaxon);
|
827
|
targetDescription.setTitleCache(moveMessage, true);
|
828
|
Annotation annotation = Annotation.NewInstance(moveMessage, Language.getDefaultLanguage());
|
829
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
830
|
targetDescription.addAnnotation(annotation);
|
831
|
|
832
|
targetDescription = dao.save(targetDescription);
|
833
|
Set<DescriptionElementBase> descriptionElements = new HashSet<DescriptionElementBase>();
|
834
|
for(UUID deUuid : descriptionElementUUIDs) {
|
835
|
descriptionElements.add(descriptionElementDao.load(deUuid));
|
836
|
}
|
837
|
|
838
|
return moveDescriptionElementsToDescription(descriptionElements, targetDescription, isCopy);
|
839
|
}
|
840
|
|
841
|
@Override
|
842
|
public Pager<TermDto> pageNamedAreasInUse(boolean includeAllParents, Integer pageSize,
|
843
|
Integer pageNumber){
|
844
|
List<TermDto> results = dao.listNamedAreasInUse(includeAllParents, null, null);
|
845
|
int startIndex= pageNumber * pageSize;
|
846
|
int toIndex = Math.min(startIndex + pageSize, results.size());
|
847
|
List<TermDto> page = results.subList(startIndex, toIndex);
|
848
|
return new DefaultPagerImpl<TermDto>(pageNumber, results.size(), pageSize, page);
|
849
|
}
|
850
|
|
851
|
|
852
|
@Override
|
853
|
@Transactional(readOnly = false)
|
854
|
public UpdateResult moveTaxonDescriptions(Taxon sourceTaxon, Taxon targetTaxon) {
|
855
|
List<TaxonDescription> descriptions = new ArrayList(sourceTaxon.getDescriptions());
|
856
|
UpdateResult result = new UpdateResult();
|
857
|
result.addUpdatedObject(sourceTaxon);
|
858
|
result.addUpdatedObject(targetTaxon);
|
859
|
for(TaxonDescription description : descriptions){
|
860
|
|
861
|
String moveMessage = String.format("Description moved from %s", sourceTaxon);
|
862
|
if(description.isProtectedTitleCache()){
|
863
|
String separator = "";
|
864
|
if(!StringUtils.isBlank(description.getTitleCache())){
|
865
|
separator = " - ";
|
866
|
}
|
867
|
description.setTitleCache(description.getTitleCache() + separator + moveMessage, true);
|
868
|
}
|
869
|
Annotation annotation = Annotation.NewInstance(moveMessage, Language.getDefaultLanguage());
|
870
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
871
|
description.addAnnotation(annotation);
|
872
|
targetTaxon.addDescription(description);
|
873
|
}
|
874
|
return result;
|
875
|
}
|
876
|
|
877
|
@Override
|
878
|
@Transactional(readOnly = false)
|
879
|
public UpdateResult moveTaxonDescriptions(UUID sourceTaxonUuid, UUID targetTaxonUuid) {
|
880
|
Taxon sourceTaxon = HibernateProxyHelper.deproxy(taxonDao.load(sourceTaxonUuid), Taxon.class);
|
881
|
Taxon targetTaxon = HibernateProxyHelper.deproxy(taxonDao.load(targetTaxonUuid), Taxon.class);
|
882
|
return moveTaxonDescriptions(sourceTaxon, targetTaxon);
|
883
|
|
884
|
}
|
885
|
|
886
|
@Override
|
887
|
@Transactional(readOnly = false)
|
888
|
public UpdateResult moveTaxonDescription(UUID descriptionUuid, UUID targetTaxonUuid){
|
889
|
UpdateResult result = new UpdateResult();
|
890
|
TaxonDescription description = HibernateProxyHelper.deproxy(dao.load(descriptionUuid), TaxonDescription.class);
|
891
|
|
892
|
Taxon sourceTaxon = description.getTaxon();
|
893
|
String moveMessage = String.format("Description moved from %s", sourceTaxon);
|
894
|
if(description.isProtectedTitleCache()){
|
895
|
String separator = "";
|
896
|
if(!StringUtils.isBlank(description.getTitleCache())){
|
897
|
separator = " - ";
|
898
|
}
|
899
|
description.setTitleCache(description.getTitleCache() + separator + moveMessage, true);
|
900
|
}
|
901
|
Annotation annotation = Annotation.NewInstance(moveMessage, Language.getDefaultLanguage());
|
902
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
903
|
description.addAnnotation(annotation);
|
904
|
Taxon targetTaxon = HibernateProxyHelper.deproxy(taxonDao.load(targetTaxonUuid), Taxon.class);
|
905
|
targetTaxon.addDescription(description);
|
906
|
result.addUpdatedObject(targetTaxon);
|
907
|
result.addUpdatedObject(sourceTaxon);
|
908
|
// dao.merge(description);
|
909
|
return result;
|
910
|
|
911
|
}
|
912
|
|
913
|
|
914
|
}
|