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// $Id$
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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.Collection;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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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.security.access.prepost.PreAuthorize;
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import org.springframework.stereotype.Service;
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import org.springframework.transaction.annotation.Propagation;
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import org.springframework.transaction.annotation.Transactional;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
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import eu.etaxonomy.cdm.common.IProgressMonitor;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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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.Distribution;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
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import eu.etaxonomy.cdm.model.description.Scope;
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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.TaxonNameBase;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.persistence.dao.common.ITermVocabularyDao;
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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.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.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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* @created 24.06.2008
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* @version 1.0
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*/
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@Service
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@Transactional(readOnly = true, propagation = Propagation.SUPPORTS)
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public class DescriptionServiceImpl extends IdentifiableServiceBase<DescriptionBase,IDescriptionDao> 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 IFeatureNodeDao featureNodeDao;
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protected IFeatureDao featureDao;
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protected ITermVocabularyDao vocabularyDao;
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protected IStatisticalMeasurementValueDao statisticalMeasurementValueDao;
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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 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 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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/**
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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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
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*/
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@Override
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public void updateTitleCache(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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super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
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}
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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 (TermVocabulary)vocabularyDao.findByUuid(featureUuid);
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}
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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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public int 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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/**
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* FIXME Candidate for harmonization
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* rename -> getElements
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*/
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public Pager<DescriptionElementBase> getDescriptionElements(DescriptionBase description,
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Set<Feature> features, Class<? extends DescriptionElementBase> type, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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List<DescriptionElementBase> results = listDescriptionElements(description, features, type, pageSize, pageNumber, propertyPaths);
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return new DefaultPagerImpl<DescriptionElementBase>(pageNumber, results.size(), pageSize, results);
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}
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public List<DescriptionElementBase> listDescriptionElements(DescriptionBase description,
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Set<Feature> features, Class<? extends DescriptionElementBase> type, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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Integer numberOfResults = dao.countDescriptionElements(description, features, type);
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List<DescriptionElementBase> results = new ArrayList<DescriptionElementBase>();
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.getDescriptionElements(description, features, type, pageSize, pageNumber, propertyPaths);
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}
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return results;
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}
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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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Integer numberOfResults = descriptionElementDao.countAnnotations(annotatedObj, status);
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List<Annotation> results = new ArrayList<Annotation>();
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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<Annotation>(pageNumber, numberOfResults, pageSize, results);
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}
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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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public Pager<TaxonDescription> getTaxonDescriptions(Taxon taxon, Set<Scope> scopes, Set<NamedArea> geographicalScope, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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Integer numberOfResults = dao.countTaxonDescriptions(taxon, scopes, geographicalScope);
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List<TaxonDescription> results = new ArrayList<TaxonDescription>();
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.getTaxonDescriptions(taxon, scopes, geographicalScope, pageSize, pageNumber, propertyPaths);
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}
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return new DefaultPagerImpl<TaxonDescription>(pageNumber, numberOfResults, pageSize, results);
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}
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public List<TaxonDescription> listTaxonDescriptions(Taxon taxon, Set<Scope> scopes, Set<NamedArea> geographicalScope, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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List<TaxonDescription> results = dao.getTaxonDescriptions(taxon, scopes, geographicalScope, pageSize, pageNumber, propertyPaths);
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return results;
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}
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public DistributionTree getOrderedDistributions(
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Set<TaxonDescription> taxonDescriptions,
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Set<NamedAreaLevel> omitLevels,
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List<String> propertyPaths){
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DistributionTree tree = new DistributionTree();
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List<Distribution> distList = new ArrayList<Distribution>();
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for (TaxonDescription taxonDescription : taxonDescriptions) {
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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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//ordering the areas
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tree.merge(distList, omitLevels);
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tree.sortChildren();
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return tree;
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}
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public Pager<TaxonNameDescription> getTaxonNameDescriptions(TaxonNameBase name, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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Integer numberOfResults = dao.countTaxonNameDescriptions(name);
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List<TaxonNameDescription> results = new ArrayList<TaxonNameDescription>();
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.getTaxonNameDescriptions(name, pageSize, pageNumber,propertyPaths);
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}
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return new DefaultPagerImpl<TaxonNameDescription>(pageNumber, numberOfResults, pageSize, results);
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}
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public Pager<DescriptionBase> page(Class<? extends DescriptionBase> type, Boolean hasImages, Boolean hasText, Set<Feature> feature, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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Integer numberOfResults = dao.countDescriptions(type, hasImages, hasText, feature);
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List<DescriptionBase> results = new ArrayList<DescriptionBase>();
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.listDescriptions(type, hasImages, hasText, feature, pageSize, pageNumber,orderHints,propertyPaths);
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}
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return new DefaultPagerImpl<DescriptionBase>(pageNumber, numberOfResults, pageSize, results);
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}
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/**
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* FIXME Candidate for harmonization
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* Rename: searchByDistribution
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*/
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public Pager<TaxonDescription> searchDescriptionByDistribution(Set<NamedArea> namedAreas, PresenceAbsenceTermBase presence, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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Integer numberOfResults = dao.countDescriptionByDistribution(namedAreas, presence);
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List<TaxonDescription> results = new ArrayList<TaxonDescription>();
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.searchDescriptionByDistribution(namedAreas, presence, pageSize, pageNumber,orderHints,propertyPaths);
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}
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return new DefaultPagerImpl<TaxonDescription>(pageNumber, numberOfResults, pageSize, results);
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}
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/**
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* FIXME Candidate for harmonization
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* move: descriptionElementService.search
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*/
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public Pager<DescriptionElementBase> searchElements(Class<? extends DescriptionElementBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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Integer numberOfResults = descriptionElementDao.count(clazz,queryString);
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List<DescriptionElementBase> results = new ArrayList<DescriptionElementBase>();
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = descriptionElementDao.search(clazz, queryString, pageSize, pageNumber, orderHints, propertyPaths);
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}
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return new DefaultPagerImpl<DescriptionElementBase>(pageNumber, numberOfResults, pageSize, results);
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}
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/**
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* FIXME Candidate for harmonization
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* descriptionElementService.find
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*/
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public DescriptionElementBase getDescriptionElementByUuid(UUID uuid) {
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return descriptionElementDao.findByUuid(uuid);
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}
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/**
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* FIXME Candidate for harmonization
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* descriptionElementService.load
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*/
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public DescriptionElementBase loadDescriptionElement(UUID uuid, List<String> propertyPaths) {
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return descriptionElementDao.load(uuid, propertyPaths);
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}
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/**
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* FIXME Candidate for harmonization
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* descriptionElementService.save
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*/
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@Transactional(readOnly = false)
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@PreAuthorize("hasRole('ALL.ADMIN') or hasPermission(#descriptionElement, 'CREATE')" )
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public UUID saveDescriptionElement(DescriptionElementBase descriptionElement) {
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return descriptionElementDao.save(descriptionElement);
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}
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/**
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* FIXME Candidate for harmonization
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* descriptionElementService.save
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*/
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@Transactional(readOnly = false)
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@PreAuthorize("hasRole('ALL.ADMIN') or hasPermission(#descriptionElements, 'CREATE')" )
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public Map<UUID, DescriptionElementBase> saveDescriptionElement(Collection<DescriptionElementBase> descriptionElements) {
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return descriptionElementDao.saveAll(descriptionElements);
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}
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/**
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* FIXME Candidate for harmonization
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* descriptionElementService.delete
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*/
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public UUID deleteDescriptionElement(DescriptionElementBase descriptionElement) {
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return descriptionElementDao.delete(descriptionElement);
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335
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}
|
|
336
|
|
|
337
|
public TermVocabulary<Feature> getFeatureVocabulary(UUID uuid) {
|
|
338
|
return (TermVocabulary)vocabularyDao.findByUuid(uuid);
|
|
339
|
}
|
|
340
|
|
|
341
|
public <T extends DescriptionElementBase> List<T> getDescriptionElementsForTaxon(
|
|
342
|
Taxon taxon, Set<Feature> features,
|
|
343
|
Class<? extends T> type, Integer pageSize,
|
|
344
|
Integer pageNumber, List<String> propertyPaths) {
|
|
345
|
//FIXME remove cast
|
|
346
|
return (List<T>) dao.getDescriptionElementForTaxon(taxon, features, type, pageSize, pageNumber, propertyPaths);
|
|
347
|
}
|
|
348
|
|
|
349
|
public List<DescriptionElementBase> getDescriptionElementsForTaxon(
|
|
350
|
Taxon taxon, FeatureTree featureTree,
|
|
351
|
Class<? extends DescriptionElementBase> type, Integer pageSize,
|
|
352
|
Integer pageNumber, List<String> propertyPaths) {
|
|
353
|
//FIXME remove cast
|
|
354
|
return (List<DescriptionElementBase>) dao.getDescriptionElementForTaxon(taxon, featureTree.getDistinctFeatures(), type, pageSize, pageNumber, propertyPaths);
|
|
355
|
}
|
|
356
|
|
|
357
|
/* (non-Javadoc)
|
|
358
|
* @see eu.etaxonomy.cdm.api.service.IDescriptionService#generateNaturalLanguageDescription(eu.etaxonomy.cdm.model.description.FeatureTree, eu.etaxonomy.cdm.model.description.TaxonDescription, eu.etaxonomy.cdm.model.common.Language, java.util.List)
|
|
359
|
*/
|
|
360
|
@Override
|
|
361
|
public String generateNaturalLanguageDescription(FeatureTree featureTree,
|
|
362
|
TaxonDescription description, List<Language> preferredLanguages, String separator) {
|
|
363
|
|
|
364
|
Language lang = preferredLanguages.size() > 0 ? preferredLanguages.get(0) : Language.DEFAULT();
|
|
365
|
|
|
366
|
description = (TaxonDescription)load(description.getUuid());
|
|
367
|
featureTree = featureTreeDao.load(featureTree.getUuid());
|
|
368
|
|
|
369
|
StringBuilder naturalLanguageDescription = new StringBuilder();
|
|
370
|
|
|
371
|
if(description.hasStructuredData()){
|
|
372
|
|
|
373
|
|
|
374
|
String lastCategory = null;
|
|
375
|
String categorySeparator = ". ";
|
|
376
|
|
|
377
|
List<TextData> textDataList;
|
|
378
|
TextData naturalLanguageDescriptionText = null;
|
|
379
|
|
|
380
|
boolean useMicroFormatQuantitativeDescriptionBuilder = false;
|
|
381
|
|
|
382
|
if(useMicroFormatQuantitativeDescriptionBuilder){
|
|
383
|
|
|
384
|
MicroFormatQuantitativeDescriptionBuilder micro = new MicroFormatQuantitativeDescriptionBuilder();
|
|
385
|
naturalLanguageGenerator.setQuantitativeDescriptionBuilder(micro);
|
|
386
|
naturalLanguageDescriptionText = naturalLanguageGenerator.generateSingleTextData(featureTree, ((TaxonDescription)description), lang);
|
|
387
|
|
|
388
|
} else {
|
|
389
|
|
|
390
|
naturalLanguageDescriptionText = naturalLanguageGenerator.generateSingleTextData(
|
|
391
|
featureTree,
|
|
392
|
((TaxonDescription)description),
|
|
393
|
lang);
|
|
394
|
}
|
|
395
|
|
|
396
|
return naturalLanguageDescriptionText.getText(lang);
|
|
397
|
|
|
398
|
//
|
|
399
|
// boolean doItBetter = false;
|
|
400
|
//
|
|
401
|
// for (TextData textData : textDataList.toArray(new TextData[textDataList.size()])){
|
|
402
|
// if(textData.getMultilanguageText().size() > 0){
|
|
403
|
//
|
|
404
|
// if (!textData.getFeature().equals(Feature.UNKNOWN())) {
|
|
405
|
// String featureLabel = textData.getFeature().getLabel(lang);
|
|
406
|
//
|
|
407
|
// if(doItBetter){
|
|
408
|
// /*
|
|
409
|
// * WARNING
|
|
410
|
// * The code lines below are desinged to handle
|
|
411
|
// * a special case where as the feature label contains
|
|
412
|
// * hierarchical information on the features. This code
|
|
413
|
// * exist only as a base for discussion, and is not
|
|
414
|
// * intendet to be used in production.
|
|
415
|
// */
|
|
416
|
// featureLabel = StringUtils.remove(featureLabel, '>');
|
|
417
|
//
|
|
418
|
// String[] labelTokens = StringUtils.split(featureLabel, '<');
|
|
419
|
// if(labelTokens[0].equals(lastCategory) && labelTokens.length > 1){
|
|
420
|
// if(naturalLanguageDescription.length() > 0){
|
|
421
|
// naturalLanguageDescription.append(separator);
|
|
422
|
// }
|
|
423
|
// naturalLanguageDescription.append(labelTokens[1]);
|
|
424
|
// } else {
|
|
425
|
// if(naturalLanguageDescription.length() > 0){
|
|
426
|
// naturalLanguageDescription.append(categorySeparator);
|
|
427
|
// }
|
|
428
|
// naturalLanguageDescription.append(StringUtils.join(labelTokens));
|
|
429
|
// }
|
|
430
|
// lastCategory = labelTokens[0];
|
|
431
|
// // end of demo code
|
|
432
|
// } else {
|
|
433
|
// if(naturalLanguageDescription.length() > 0){
|
|
434
|
// naturalLanguageDescription.append(separator);
|
|
435
|
// }
|
|
436
|
// naturalLanguageDescription.append(textData.getFeature().getLabel(lang));
|
|
437
|
// }
|
|
438
|
// } else {
|
|
439
|
// if(naturalLanguageDescription.length() > 0){
|
|
440
|
// naturalLanguageDescription.append(separator);
|
|
441
|
// }
|
|
442
|
// }
|
|
443
|
// String text = textData.getMultilanguageText().values().iterator().next().getText();
|
|
444
|
// naturalLanguageDescription.append(text);
|
|
445
|
//
|
|
446
|
// }
|
|
447
|
// }
|
|
448
|
|
|
449
|
}
|
|
450
|
return naturalLanguageDescription.toString();
|
|
451
|
}
|
|
452
|
|
|
453
|
/* (non-Javadoc)
|
|
454
|
* @see eu.etaxonomy.cdm.api.service.IDescriptionService#hasStructuredData(eu.etaxonomy.cdm.model.description.DescriptionBase)
|
|
455
|
*/
|
|
456
|
@Override
|
|
457
|
public boolean hasStructuredData(DescriptionBase<?> description) {
|
|
458
|
return load(description.getUuid()).hasStructuredData();
|
|
459
|
}
|
|
460
|
|
|
461
|
|
|
462
|
/* (non-Javadoc)
|
|
463
|
* @see eu.etaxonomy.cdm.api.service.IDescriptionService#moveDescriptionElementsToDescription(java.util.Collection, eu.etaxonomy.cdm.model.description.DescriptionBase, boolean)
|
|
464
|
*/
|
|
465
|
@Override
|
|
466
|
public void moveDescriptionElementsToDescription(Collection<DescriptionElementBase> descriptionElements,
|
|
467
|
DescriptionBase targetDescription, boolean isCopy) {
|
|
468
|
|
|
469
|
if (descriptionElements.isEmpty() ){
|
|
470
|
return ;
|
|
471
|
}
|
|
472
|
|
|
473
|
if (! isCopy && descriptionElements == descriptionElements.iterator().next().getInDescription().getElements()){
|
|
474
|
//if the descriptionElements collection is the elements set of a description, put it in a separate set before to avoid concurrent modification exceptions
|
|
475
|
descriptionElements = new HashSet<DescriptionElementBase>(descriptionElements);
|
|
476
|
// descriptionElementsTmp.addAll(descriptionElements);
|
|
477
|
// descriptionElements = descriptionElementsTmp;
|
|
478
|
}
|
|
479
|
for (DescriptionElementBase element : descriptionElements){
|
|
480
|
DescriptionBase description = element.getInDescription();
|
|
481
|
try {
|
|
482
|
DescriptionElementBase newElement = (DescriptionElementBase)element.clone();
|
|
483
|
targetDescription.addElement(newElement);
|
|
484
|
} catch (CloneNotSupportedException e) {
|
|
485
|
new RuntimeException ("Clone not yet implemented for class " + element.getClass().getName(), e);
|
|
486
|
}
|
|
487
|
if (! isCopy){
|
|
488
|
description.removeElement(element);
|
|
489
|
}
|
|
490
|
|
|
491
|
}
|
|
492
|
}
|
|
493
|
|
|
494
|
}
|