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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.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.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.DefinedTerm;
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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.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.PresenceAbsenceTerm;
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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.IDefinedTermDao;
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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.dao.taxon.ITaxonDao;
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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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* @created 24.06.2008
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* @version 1.0
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*/
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/**
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* @author a.kohlbecker
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* @date Dec 5, 2013
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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 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 IDefinedTermDao definedTermDao;
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protected IStatisticalMeasurementValueDao statisticalMeasurementValueDao;
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protected ITaxonDao taxonDao;
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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 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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/**
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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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@Transactional(readOnly = false)
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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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@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 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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@Override
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public Pager<DescriptionElementBase> pageDescriptionElements(DescriptionBase description, Class<? extends DescriptionBase> descriptionType,
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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, descriptionType, 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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.IDescriptionService#getDescriptionElements(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.Set, java.lang.Class, java.lang.Integer, java.lang.Integer, java.util.List)
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*/
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@Override
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@Deprecated
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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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return pageDescriptionElements(description, null, features, type, pageSize, pageNumber, propertyPaths);
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}
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@Override
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public List<DescriptionElementBase> listDescriptionElements(DescriptionBase description, Class<? extends DescriptionBase> descriptionType,
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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, descriptionType, features, type);
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List<DescriptionElementBase> results = new ArrayList<DescriptionElementBase>();
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if(AbstractPagerImpl.hasResultsInRange(numberOfResults.longValue(), 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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.IDescriptionService#listDescriptionElements(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.Set, java.lang.Class, java.lang.Integer, java.lang.Integer, java.util.List)
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*/
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@Override
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@Deprecated
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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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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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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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@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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.IDescriptionService#pageMarkedTaxonDescriptions(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.Set, java.util.Set, java.util.Set, java.lang.Integer, java.lang.Integer, java.util.List)
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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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Integer numberOfResults = dao.countTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes);
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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.listTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, 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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@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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.IDescriptionService#listTaxonDescriptionMedia(UUID, boolean, Set, Integer, Integer, List)
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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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/*
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* @see IDescriptionService#countTaxonDescriptionMedia(UUID, boolean, Set)
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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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.IDescriptionService#getOrderedDistributions(java.util.Set, boolean, boolean, java.util.Set, java.util.List)
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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) {
|
|
325
|
if (element.isInstanceOf(Distribution.class)) {
|
|
326
|
Distribution distribution = (Distribution) element;
|
|
327
|
if(distribution.getArea() != null){
|
|
328
|
distList.add(distribution);
|
|
329
|
}
|
|
330
|
}
|
|
331
|
}
|
|
332
|
}
|
|
333
|
}
|
|
334
|
|
|
335
|
//old
|
|
336
|
// for (TaxonDescription taxonDescription : taxonDescriptions) {
|
|
337
|
// if (logger.isDebugEnabled()){ logger.debug("load taxon description " + taxonDescription.getUuid());}
|
|
338
|
// //TODO why not loading all description via .list ? This may improve performance
|
|
339
|
// taxonDescription = (TaxonDescription) dao.load(taxonDescription.getUuid(), propertyPaths);
|
|
340
|
// Set<DescriptionElementBase> elements = taxonDescription.getElements();
|
|
341
|
// for (DescriptionElementBase element : elements) {
|
|
342
|
// if (element.isInstanceOf(Distribution.class)) {
|
|
343
|
// Distribution distribution = (Distribution) element;
|
|
344
|
// if(distribution.getArea() != null){
|
|
345
|
// distList.add(distribution);
|
|
346
|
// }
|
|
347
|
// }
|
|
348
|
// }
|
|
349
|
// }
|
|
350
|
|
|
351
|
if (logger.isDebugEnabled()){logger.debug("filter tree for " + distList.size() + " distributions ...");}
|
|
352
|
|
|
353
|
// filter distributions
|
|
354
|
Collection<Distribution> filteredDistributions = DescriptionUtility.filterDistributions(distList, hiddenAreaMarkerTypes, true, statusOrderPreference, false);
|
|
355
|
distList.clear();
|
|
356
|
distList.addAll(filteredDistributions);
|
|
357
|
|
|
358
|
return DescriptionUtility.orderDistributions(definedTermDao, omitLevels, distList, hiddenAreaMarkerTypes);
|
|
359
|
}
|
|
360
|
|
|
361
|
|
|
362
|
@Override
|
|
363
|
public Pager<TaxonNameDescription> getTaxonNameDescriptions(TaxonNameBase name, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
|
|
364
|
Integer numberOfResults = dao.countTaxonNameDescriptions(name);
|
|
365
|
|
|
366
|
List<TaxonNameDescription> results = new ArrayList<TaxonNameDescription>();
|
|
367
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
|
368
|
results = dao.getTaxonNameDescriptions(name, pageSize, pageNumber,propertyPaths);
|
|
369
|
}
|
|
370
|
|
|
371
|
return new DefaultPagerImpl<TaxonNameDescription>(pageNumber, numberOfResults, pageSize, results);
|
|
372
|
}
|
|
373
|
|
|
374
|
|
|
375
|
@Override
|
|
376
|
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) {
|
|
377
|
Integer numberOfResults = dao.countDescriptions(type, hasImages, hasText, feature);
|
|
378
|
|
|
379
|
List<DescriptionBase> results = new ArrayList<DescriptionBase>();
|
|
380
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
|
381
|
results = dao.listDescriptions(type, hasImages, hasText, feature, pageSize, pageNumber,orderHints,propertyPaths);
|
|
382
|
}
|
|
383
|
|
|
384
|
return new DefaultPagerImpl<DescriptionBase>(pageNumber, numberOfResults, pageSize, results);
|
|
385
|
}
|
|
386
|
|
|
387
|
/**
|
|
388
|
* FIXME Candidate for harmonization
|
|
389
|
* Rename: searchByDistribution
|
|
390
|
*/
|
|
391
|
@Override
|
|
392
|
public Pager<TaxonDescription> searchDescriptionByDistribution(Set<NamedArea> namedAreas, PresenceAbsenceTerm presence, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
393
|
Integer numberOfResults = dao.countDescriptionByDistribution(namedAreas, presence);
|
|
394
|
|
|
395
|
List<TaxonDescription> results = new ArrayList<TaxonDescription>();
|
|
396
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
|
397
|
results = dao.searchDescriptionByDistribution(namedAreas, presence, pageSize, pageNumber,orderHints,propertyPaths);
|
|
398
|
}
|
|
399
|
|
|
400
|
return new DefaultPagerImpl<TaxonDescription>(pageNumber, numberOfResults, pageSize, results);
|
|
401
|
}
|
|
402
|
|
|
403
|
/**
|
|
404
|
* FIXME Candidate for harmonization
|
|
405
|
* move: descriptionElementService.search
|
|
406
|
*/
|
|
407
|
@Override
|
|
408
|
public Pager<DescriptionElementBase> searchElements(Class<? extends DescriptionElementBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
409
|
Integer numberOfResults = descriptionElementDao.count(clazz, queryString);
|
|
410
|
|
|
411
|
List<DescriptionElementBase> results = new ArrayList<DescriptionElementBase>();
|
|
412
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
|
413
|
results = descriptionElementDao.search(clazz, queryString, pageSize, pageNumber, orderHints, propertyPaths);
|
|
414
|
}
|
|
415
|
|
|
416
|
return new DefaultPagerImpl<DescriptionElementBase>(pageNumber, numberOfResults, pageSize, results);
|
|
417
|
}
|
|
418
|
|
|
419
|
/**
|
|
420
|
* FIXME Candidate for harmonization
|
|
421
|
* descriptionElementService.find
|
|
422
|
*/
|
|
423
|
@Override
|
|
424
|
public DescriptionElementBase getDescriptionElementByUuid(UUID uuid) {
|
|
425
|
return descriptionElementDao.findByUuid(uuid);
|
|
426
|
}
|
|
427
|
|
|
428
|
/**
|
|
429
|
* FIXME Candidate for harmonization
|
|
430
|
* descriptionElementService.load
|
|
431
|
*/
|
|
432
|
@Override
|
|
433
|
public DescriptionElementBase loadDescriptionElement(UUID uuid, List<String> propertyPaths) {
|
|
434
|
return descriptionElementDao.load(uuid, propertyPaths);
|
|
435
|
}
|
|
436
|
|
|
437
|
/**
|
|
438
|
* FIXME Candidate for harmonization
|
|
439
|
* descriptionElementService.save
|
|
440
|
*/
|
|
441
|
@Override
|
|
442
|
@Transactional(readOnly = false)
|
|
443
|
public UUID saveDescriptionElement(DescriptionElementBase descriptionElement) {
|
|
444
|
return descriptionElementDao.save(descriptionElement).getUuid();
|
|
445
|
}
|
|
446
|
|
|
447
|
/**
|
|
448
|
* FIXME Candidate for harmonization
|
|
449
|
* descriptionElementService.save
|
|
450
|
*/
|
|
451
|
@Override
|
|
452
|
@Transactional(readOnly = false)
|
|
453
|
public Map<UUID, DescriptionElementBase> saveDescriptionElement(Collection<DescriptionElementBase> descriptionElements) {
|
|
454
|
return descriptionElementDao.saveAll(descriptionElements);
|
|
455
|
}
|
|
456
|
|
|
457
|
/**
|
|
458
|
* FIXME Candidate for harmonization
|
|
459
|
* descriptionElementService.delete
|
|
460
|
*/
|
|
461
|
@Override
|
|
462
|
public UUID deleteDescriptionElement(DescriptionElementBase descriptionElement) {
|
|
463
|
return descriptionElementDao.delete(descriptionElement);
|
|
464
|
}
|
|
465
|
|
|
466
|
|
|
467
|
/* (non-Javadoc)
|
|
468
|
* @see eu.etaxonomy.cdm.api.service.IDescriptionService#deleteDescriptionElement(java.util.UUID)
|
|
469
|
*/
|
|
470
|
@Override
|
|
471
|
public UUID deleteDescriptionElement(UUID descriptionElementUuid) {
|
|
472
|
return deleteDescriptionElement(descriptionElementDao.load(descriptionElementUuid));
|
|
473
|
}
|
|
474
|
|
|
475
|
@Override
|
|
476
|
@Transactional(readOnly = false)
|
|
477
|
public DeleteResult deleteDescription(DescriptionBase description) {
|
|
478
|
DeleteResult deleteResult = new DeleteResult();
|
|
479
|
|
|
480
|
if (description instanceof TaxonDescription){
|
|
481
|
TaxonDescription taxDescription = HibernateProxyHelper.deproxy(description, TaxonDescription.class);
|
|
482
|
Taxon tax = taxDescription.getTaxon();
|
|
483
|
tax.removeDescription(taxDescription, true);
|
|
484
|
dao.delete(description);
|
|
485
|
|
|
486
|
deleteResult.addUpdatedObject(tax);
|
|
487
|
deleteResult.setCdmEntity(tax);
|
|
488
|
}
|
|
489
|
|
|
490
|
|
|
491
|
return deleteResult;
|
|
492
|
}
|
|
493
|
|
|
494
|
|
|
495
|
/* (non-Javadoc)
|
|
496
|
* @see eu.etaxonomy.cdm.api.service.IDescriptionService#deleteDescription(java.util.UUID)
|
|
497
|
*/
|
|
498
|
@Override
|
|
499
|
@Transactional(readOnly = false)
|
|
500
|
public DeleteResult deleteDescription(UUID descriptionUuid) {
|
|
501
|
return deleteDescription(dao.load(descriptionUuid));
|
|
502
|
}
|
|
503
|
|
|
504
|
|
|
505
|
@Override
|
|
506
|
public TermVocabulary<Feature> getFeatureVocabulary(UUID uuid) {
|
|
507
|
return vocabularyDao.findByUuid(uuid);
|
|
508
|
}
|
|
509
|
|
|
510
|
@Override
|
|
511
|
@Deprecated
|
|
512
|
public <T extends DescriptionElementBase> List<T> getDescriptionElementsForTaxon(
|
|
513
|
Taxon taxon, Set<Feature> features,
|
|
514
|
Class<T> type, Integer pageSize,
|
|
515
|
Integer pageNumber, List<String> propertyPaths) {
|
|
516
|
return listDescriptionElementsForTaxon(taxon, features, type, pageSize, pageNumber, propertyPaths);
|
|
517
|
}
|
|
518
|
|
|
519
|
@Override
|
|
520
|
public <T extends DescriptionElementBase> List<T> listDescriptionElementsForTaxon(
|
|
521
|
Taxon taxon, Set<Feature> features,
|
|
522
|
Class<T> type, Integer pageSize,
|
|
523
|
Integer pageNumber, List<String> propertyPaths) {
|
|
524
|
return dao.getDescriptionElementForTaxon(taxon.getUuid(), features, type, pageSize, pageNumber, propertyPaths);
|
|
525
|
}
|
|
526
|
|
|
527
|
@Override
|
|
528
|
public <T extends DescriptionElementBase> Pager<T> pageDescriptionElementsForTaxon(
|
|
529
|
Taxon taxon, Set<Feature> features,
|
|
530
|
Class<T> type, Integer pageSize,
|
|
531
|
Integer pageNumber, List<String> propertyPaths) {
|
|
532
|
if (logger.isDebugEnabled()){logger.debug(" get count ...");}
|
|
533
|
Long count = dao.countDescriptionElementForTaxon(taxon.getUuid(), features, type);
|
|
534
|
List<T> descriptionElements;
|
|
535
|
if(AbstractPagerImpl.hasResultsInRange(count, pageNumber, pageSize)){ // no point checking again
|
|
536
|
if (logger.isDebugEnabled()){logger.debug(" get list ...");}
|
|
537
|
descriptionElements = listDescriptionElementsForTaxon(taxon, features, type, pageSize, pageNumber, propertyPaths);
|
|
538
|
} else {
|
|
539
|
descriptionElements = new ArrayList<T>(0);
|
|
540
|
}
|
|
541
|
if (logger.isDebugEnabled()){logger.debug(" service - DONE ...");}
|
|
542
|
return new DefaultPagerImpl<T>(pageNumber, count.intValue(), pageSize, descriptionElements);
|
|
543
|
}
|
|
544
|
|
|
545
|
|
|
546
|
/* (non-Javadoc)
|
|
547
|
* @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)
|
|
548
|
*/
|
|
549
|
@Override
|
|
550
|
public String generateNaturalLanguageDescription(FeatureTree featureTree,
|
|
551
|
TaxonDescription description, List<Language> preferredLanguages, String separator) {
|
|
552
|
|
|
553
|
Language lang = preferredLanguages.size() > 0 ? preferredLanguages.get(0) : Language.DEFAULT();
|
|
554
|
|
|
555
|
description = (TaxonDescription)load(description.getUuid());
|
|
556
|
featureTree = featureTreeDao.load(featureTree.getUuid());
|
|
557
|
|
|
558
|
StringBuilder naturalLanguageDescription = new StringBuilder();
|
|
559
|
|
|
560
|
MarkerType useMarkerType = (MarkerType) definedTermDao.load(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
|
561
|
boolean isUseDescription = false;
|
|
562
|
if(!description.getMarkers().isEmpty()) {
|
|
563
|
for (Marker marker: description.getMarkers()) {
|
|
564
|
MarkerType markerType = marker.getMarkerType();
|
|
565
|
if (markerType.equals(useMarkerType)) {
|
|
566
|
isUseDescription = true;
|
|
567
|
}
|
|
568
|
|
|
569
|
}
|
|
570
|
}
|
|
571
|
|
|
572
|
if(description.hasStructuredData() && !isUseDescription){
|
|
573
|
|
|
574
|
|
|
575
|
String lastCategory = null;
|
|
576
|
String categorySeparator = ". ";
|
|
577
|
|
|
578
|
List<TextData> textDataList;
|
|
579
|
TextData naturalLanguageDescriptionText = null;
|
|
580
|
|
|
581
|
boolean useMicroFormatQuantitativeDescriptionBuilder = false;
|
|
582
|
|
|
583
|
if(useMicroFormatQuantitativeDescriptionBuilder){
|
|
584
|
|
|
585
|
MicroFormatQuantitativeDescriptionBuilder micro = new MicroFormatQuantitativeDescriptionBuilder();
|
|
586
|
naturalLanguageGenerator.setQuantitativeDescriptionBuilder(micro);
|
|
587
|
naturalLanguageDescriptionText = naturalLanguageGenerator.generateSingleTextData(featureTree, (description), lang);
|
|
588
|
|
|
589
|
} else {
|
|
590
|
|
|
591
|
naturalLanguageDescriptionText = naturalLanguageGenerator.generateSingleTextData(
|
|
592
|
featureTree,
|
|
593
|
(description),
|
|
594
|
lang);
|
|
595
|
}
|
|
596
|
|
|
597
|
return naturalLanguageDescriptionText.getText(lang);
|
|
598
|
|
|
599
|
//
|
|
600
|
// boolean doItBetter = false;
|
|
601
|
//
|
|
602
|
// for (TextData textData : textDataList.toArray(new TextData[textDataList.size()])){
|
|
603
|
// if(textData.getMultilanguageText().size() > 0){
|
|
604
|
//
|
|
605
|
// if (!textData.getFeature().equals(Feature.UNKNOWN())) {
|
|
606
|
// String featureLabel = textData.getFeature().getLabel(lang);
|
|
607
|
//
|
|
608
|
// if(doItBetter){
|
|
609
|
// /*
|
|
610
|
// * WARNING
|
|
611
|
// * The code lines below are desinged to handle
|
|
612
|
// * a special case where as the feature label contains
|
|
613
|
// * hierarchical information on the features. This code
|
|
614
|
// * exist only as a base for discussion, and is not
|
|
615
|
// * intendet to be used in production.
|
|
616
|
// */
|
|
617
|
// featureLabel = StringUtils.remove(featureLabel, '>');
|
|
618
|
//
|
|
619
|
// String[] labelTokens = StringUtils.split(featureLabel, '<');
|
|
620
|
// if(labelTokens[0].equals(lastCategory) && labelTokens.length > 1){
|
|
621
|
// if(naturalLanguageDescription.length() > 0){
|
|
622
|
// naturalLanguageDescription.append(separator);
|
|
623
|
// }
|
|
624
|
// naturalLanguageDescription.append(labelTokens[1]);
|
|
625
|
// } else {
|
|
626
|
// if(naturalLanguageDescription.length() > 0){
|
|
627
|
// naturalLanguageDescription.append(categorySeparator);
|
|
628
|
// }
|
|
629
|
// naturalLanguageDescription.append(StringUtils.join(labelTokens));
|
|
630
|
// }
|
|
631
|
// lastCategory = labelTokens[0];
|
|
632
|
// // end of demo code
|
|
633
|
// } else {
|
|
634
|
// if(naturalLanguageDescription.length() > 0){
|
|
635
|
// naturalLanguageDescription.append(separator);
|
|
636
|
// }
|
|
637
|
// naturalLanguageDescription.append(textData.getFeature().getLabel(lang));
|
|
638
|
// }
|
|
639
|
// } else {
|
|
640
|
// if(naturalLanguageDescription.length() > 0){
|
|
641
|
// naturalLanguageDescription.append(separator);
|
|
642
|
// }
|
|
643
|
// }
|
|
644
|
// String text = textData.getMultilanguageText().values().iterator().next().getText();
|
|
645
|
// naturalLanguageDescription.append(text);
|
|
646
|
//
|
|
647
|
// }
|
|
648
|
// }
|
|
649
|
|
|
650
|
}
|
|
651
|
else if (isUseDescription) {
|
|
652
|
//AT: Left Blank in case we need to generate a Natural language text string.
|
|
653
|
}
|
|
654
|
return naturalLanguageDescription.toString();
|
|
655
|
}
|
|
656
|
|
|
657
|
|
|
658
|
@Override
|
|
659
|
public boolean hasStructuredData(DescriptionBase<?> description) {
|
|
660
|
return load(description.getUuid()).hasStructuredData();
|
|
661
|
}
|
|
662
|
|
|
663
|
|
|
664
|
@Override
|
|
665
|
public void moveDescriptionElementsToDescription(
|
|
666
|
Collection<DescriptionElementBase> descriptionElements,
|
|
667
|
DescriptionBase targetDescription,
|
|
668
|
boolean isCopy) {
|
|
669
|
|
|
670
|
if (descriptionElements.isEmpty() ){
|
|
671
|
return ;
|
|
672
|
}
|
|
673
|
|
|
674
|
if (! isCopy && descriptionElements == descriptionElements.iterator().next().getInDescription().getElements()){
|
|
675
|
//if the descriptionElements collection is the elements set of a description, put it in a separate set before to avoid concurrent modification exceptions
|
|
676
|
descriptionElements = new HashSet<DescriptionElementBase>(descriptionElements);
|
|
677
|
// descriptionElementsTmp.addAll(descriptionElements);
|
|
678
|
// descriptionElements = descriptionElementsTmp;
|
|
679
|
}
|
|
680
|
for (DescriptionElementBase element : descriptionElements){
|
|
681
|
DescriptionBase<?> description = element.getInDescription();
|
|
682
|
try {
|
|
683
|
DescriptionElementBase newElement = (DescriptionElementBase)element.clone();
|
|
684
|
targetDescription.addElement(newElement);
|
|
685
|
} catch (CloneNotSupportedException e) {
|
|
686
|
throw new RuntimeException ("Clone not yet implemented for class " + element.getClass().getName(), e);
|
|
687
|
}
|
|
688
|
if (! isCopy){
|
|
689
|
description.removeElement(element);
|
|
690
|
dao.saveOrUpdate(description);
|
|
691
|
}
|
|
692
|
|
|
693
|
}
|
|
694
|
dao.saveOrUpdate(targetDescription);
|
|
695
|
|
|
696
|
}
|
|
697
|
|
|
698
|
@Override
|
|
699
|
public Pager<TermDto> pageNamedAreasInUse(boolean includeAllParents, Integer pageSize,
|
|
700
|
Integer pageNumber){
|
|
701
|
List<TermDto> results = dao.listNamedAreasInUse(includeAllParents, null, null);
|
|
702
|
int startIndex= pageNumber * pageSize;
|
|
703
|
int toIndex = Math.min(startIndex + pageSize, results.size());
|
|
704
|
List<TermDto> page = results.subList(startIndex, toIndex);
|
|
705
|
return new DefaultPagerImpl<TermDto>(pageNumber, results.size(), pageSize, page);
|
|
706
|
}
|
|
707
|
|
|
708
|
|
|
709
|
@Override
|
|
710
|
@Transactional(readOnly = false)
|
|
711
|
public UpdateResult moveTaxonDescriptions(Taxon sourceTaxon, Taxon targetTaxon) {
|
|
712
|
List<TaxonDescription> descriptions = new ArrayList(sourceTaxon.getDescriptions());
|
|
713
|
UpdateResult result = new UpdateResult();
|
|
714
|
result.addUpdatedObject(sourceTaxon);
|
|
715
|
result.addUpdatedObject(targetTaxon);
|
|
716
|
for(TaxonDescription description : descriptions){
|
|
717
|
|
|
718
|
String moveMessage = String.format("Description moved from %s", sourceTaxon);
|
|
719
|
if(description.isProtectedTitleCache()){
|
|
720
|
String separator = "";
|
|
721
|
if(!StringUtils.isBlank(description.getTitleCache())){
|
|
722
|
separator = " - ";
|
|
723
|
}
|
|
724
|
description.setTitleCache(description.getTitleCache() + separator + moveMessage, true);
|
|
725
|
}
|
|
726
|
Annotation annotation = Annotation.NewInstance(moveMessage, Language.getDefaultLanguage());
|
|
727
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
|
728
|
description.addAnnotation(annotation);
|
|
729
|
targetTaxon.addDescription(description);
|
|
730
|
}
|
|
731
|
return result;
|
|
732
|
}
|
|
733
|
|
|
734
|
@Override
|
|
735
|
@Transactional(readOnly = false)
|
|
736
|
public UpdateResult moveTaxonDescriptions(UUID sourceTaxonUuid, UUID targetTaxonUuid) {
|
|
737
|
Taxon sourceTaxon = HibernateProxyHelper.deproxy(taxonDao.load(sourceTaxonUuid), Taxon.class);
|
|
738
|
Taxon targetTaxon = HibernateProxyHelper.deproxy(taxonDao.load(targetTaxonUuid), Taxon.class);
|
|
739
|
return moveTaxonDescriptions(sourceTaxon, targetTaxon);
|
|
740
|
|
|
741
|
}
|
|
742
|
|
|
743
|
|
|
744
|
|
|
745
|
}
|