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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.persistence.dao.hibernate.description;
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import java.util.ArrayList;
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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.ArrayUtils;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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import org.hibernate.Criteria;
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import org.hibernate.criterion.Criterion;
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import org.hibernate.criterion.ProjectionList;
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import org.hibernate.criterion.Projections;
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import org.hibernate.criterion.Restrictions;
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import org.hibernate.envers.query.AuditEntity;
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import org.hibernate.envers.query.AuditQuery;
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import org.hibernate.query.Query;
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import org.springframework.beans.factory.annotation.Qualifier;
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import org.springframework.stereotype.Repository;
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import eu.etaxonomy.cdm.model.common.LSID;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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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.DescriptionType;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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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.location.NamedArea;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.view.AuditEvent;
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import eu.etaxonomy.cdm.persistence.dao.common.OperationNotSupportedInPriorViewException;
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import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;
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import eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase;
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import eu.etaxonomy.cdm.persistence.dto.SortableTaxonNodeQueryResult;
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import eu.etaxonomy.cdm.persistence.dto.TermDto;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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@Repository
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@Qualifier("descriptionDaoImpl")
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public class DescriptionDaoImpl
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extends IdentifiableDaoBase<DescriptionBase>
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implements IDescriptionDao{
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private static final Logger logger = LogManager.getLogger(DescriptionDaoImpl.class);
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public DescriptionDaoImpl() {
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super(DescriptionBase.class);
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indexedClasses = new Class[3];
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indexedClasses[0] = TaxonDescription.class;
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indexedClasses[1] = TaxonNameDescription.class;
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indexedClasses[2] = SpecimenDescription.class;
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}
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// @Override //Override for testing
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// public DescriptionBase load(UUID uuid, List<String> propertyPaths){
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// DescriptionBase bean = findByUuid(uuid);
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// if(bean == null){
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// return bean;
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// }
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// defaultBeanInitializer.initialize(bean, propertyPaths);
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//
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// return bean;
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// }
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@Override
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public long countDescriptionByDistribution(Set<NamedArea> namedAreas, PresenceAbsenceTerm status) {
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checkNotInPriorView("DescriptionDaoImpl.countDescriptionByDistribution(Set<NamedArea> namedAreas, PresenceAbsenceTermBase status)");
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Query<Long> query = null;
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if(status == null) {
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query = getSession().createQuery("select count(distinct description) from TaxonDescription description left join description.descriptionElements element join element.area area where area in (:namedAreas)", Long.class);
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} else {
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query = getSession().createQuery("select count(distinct description) from TaxonDescription description left join description.descriptionElements element join element.area area join element.status status where area in (:namedAreas) and status = :status", Long.class);
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query.setParameter("status", status);
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}
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query.setParameterList("namedAreas", namedAreas);
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return query.uniqueResult();
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}
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@Override
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public <T extends DescriptionElementBase> long countDescriptionElements(DescriptionBase description, Set<Feature> features, Class<T> clazz) {
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return countDescriptionElements(description, null, features, clazz);
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}
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@Override
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public <T extends DescriptionElementBase> long countDescriptionElements(DescriptionBase description, Class<? extends DescriptionBase> descriptionType,
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Set<Feature> features, Class<T> clazz) {
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AuditEvent auditEvent = getAuditEventFromContext();
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if (clazz == null){
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clazz = (Class<T>)DescriptionElementBase.class;
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}
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if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
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Criteria criteria = getCriteria(clazz);
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if(description != null) {
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criteria.add(Restrictions.eq("inDescription", description));
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}
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if(descriptionType != null) {
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criteria.createAlias("inDescription", "d").add(Restrictions.eq("d.class", descriptionType));
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}
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if(features != null && !features.isEmpty()) {
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criteria.add(Restrictions.in("feature", features));
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}
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criteria.setProjection(Projections.rowCount());
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return (Long)criteria.uniqueResult();
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} else {
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if(features != null && !features.isEmpty()) {
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long count = 0;
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for(Feature f : features) {
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AuditQuery query = null;
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query = makeAuditQuery(clazz, auditEvent);
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if(description != null) {
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query.add(AuditEntity.relatedId("inDescription").eq(description.getId()));
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}
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if(descriptionType != null) {
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query.add(AuditEntity.property("inDescription.class").eq(descriptionType));
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}
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query.add(AuditEntity.relatedId("feature").eq(f.getId()));
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query.addProjection(AuditEntity.id().count());
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count += (Long)query.getSingleResult();
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}
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return count;
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} else {
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AuditQuery query = makeAuditQuery(clazz, auditEvent);
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if(description != null) {
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query.add(AuditEntity.relatedId("inDescription").eq(description.getId()));
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}
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if(descriptionType != null) {
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query.add(AuditEntity.property("inDescription.class").eq(descriptionType));
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}
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query.addProjection(AuditEntity.id().count());
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return (Long)query.getSingleResult();
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}
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}
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}
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@Override
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public long countDescriptions(Class<? extends DescriptionBase> clazz, Boolean hasImages, Boolean hasText, Set<Feature> features) {
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checkNotInPriorView("DescriptionDaoImpl.countDescriptions(Class<TYPE> type, Boolean hasImages, Boolean hasText, Set<Feature> features)");
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Criteria inner = getCriteria(clazz);
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Criteria elementsCriteria = inner.createCriteria("descriptionElements");
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if(hasText != null) {
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if(hasText) {
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elementsCriteria.add(Restrictions.isNotEmpty("multilanguageText"));
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} else {
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elementsCriteria.add(Restrictions.isEmpty("multilanguageText"));
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}
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}
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if(hasImages != null) {
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if(hasImages) {
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elementsCriteria.add(Restrictions.isNotEmpty("media"));
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} else {
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elementsCriteria.add(Restrictions.isEmpty("media"));
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}
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}
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if(features != null && !features.isEmpty()) {
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elementsCriteria.add(Restrictions.in("feature", features));
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}
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inner.setProjection(Projections.countDistinct("id"));
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return (Long)inner.uniqueResult();
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}
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@Override
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public long countTaxonDescriptions(Taxon taxon, Set<DefinedTerm> scopes,
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Set<NamedArea> geographicalScopes, Set<MarkerType> markerTypes, Set<DescriptionType> descriptionTypes) {
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AuditEvent auditEvent = getAuditEventFromContext();
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if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
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Criteria criteria = getCriteria(TaxonDescription.class);
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if(taxon != null) {
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criteria.add(Restrictions.eq("taxon", taxon));
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}
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if(scopes != null && !scopes.isEmpty()) {
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Set<Integer> scopeIds = new HashSet<>();
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for(DefinedTerm s : scopes) {
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scopeIds.add(s.getId());
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}
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criteria.createCriteria("scopes").add(Restrictions.in("id", scopeIds));
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}
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if(geographicalScopes != null && !geographicalScopes.isEmpty()) {
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Set<Integer> geoScopeIds = new HashSet<>();
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for(NamedArea n : geographicalScopes) {
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geoScopeIds.add(n.getId());
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}
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criteria.createCriteria("geoScopes").add(Restrictions.in("id", geoScopeIds));
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}
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addMarkerTypesCriterion(markerTypes, criteria);
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addDescriptionTypesCriterion(descriptionTypes, criteria);
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criteria.setProjection(Projections.rowCount());
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return (Long)criteria.uniqueResult();
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} else {
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if((scopes == null || scopes.isEmpty())&& (geographicalScopes == null || geographicalScopes.isEmpty()) && (markerTypes == null || markerTypes.isEmpty())) {
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AuditQuery query = makeAuditQuery(TaxonDescription.class,auditEvent);
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if(taxon != null) {
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query.add(AuditEntity.relatedId("taxon").eq(taxon.getId()));
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}
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query.addProjection(AuditEntity.id().count());
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return (Long)query.getSingleResult();
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} else {
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throw new OperationNotSupportedInPriorViewException("countTaxonDescriptions(Taxon taxon, Set<Scope> scopes,Set<NamedArea> geographicalScopes)");
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}
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}
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}
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private void addDescriptionTypesCriterion(Set<DescriptionType> descriptionTypes, Criteria criteria) {
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if(descriptionTypes != null && !descriptionTypes.isEmpty()) {
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Set<Criterion> typeCriteria = new HashSet<>();
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for (DescriptionType descriptionType : descriptionTypes) {
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typeCriteria.add(Restrictions.sqlRestriction("{alias}.types like '%"+descriptionType.getKey()+"%'"));
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}
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criteria.add(Restrictions.and(typeCriteria.toArray(new Criterion[]{})));
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}
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}
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/**
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* @param markerTypes
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* @param criteria
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*
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*/
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//TODO move to AnnotatableEntityDao(?)
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private void addMarkerTypesCriterion(Set<MarkerType> markerTypes, Criteria criteria) {
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if(markerTypes != null && !markerTypes.isEmpty()) {
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Set<Integer> markerTypeIds = new HashSet<Integer>();
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for(MarkerType markerType : markerTypes) {
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markerTypeIds.add(markerType.getId());
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}
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criteria.createCriteria("markers").add(Restrictions.eq("flag", true))
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.createAlias("markerType", "mt")
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.add(Restrictions.in("mt.id", markerTypeIds));
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} else if (markerTypes != null && markerTypes.isEmpty()){
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//AT: added in case the projects requires an third state description, An empty Marker type set
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}
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}
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@Override
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public <T extends DescriptionElementBase> List<T> getDescriptionElements(
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DescriptionBase description, Set<Feature> features,
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Class<T> clazz, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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return getDescriptionElements(description, null, features, clazz, pageSize, pageNumber, propertyPaths);
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}
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@Override
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public <T extends DescriptionElementBase> List<T> getDescriptionElements(
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DescriptionBase description, Class<? extends DescriptionBase> descriptionType,
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Set<Feature> features,
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Class<T> clazz,
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Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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AuditEvent auditEvent = getAuditEventFromContext();
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if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
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Criteria criteria = null;
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if(clazz == null) {
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criteria = getSession().createCriteria(DescriptionElementBase.class);
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} else {
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criteria = getSession().createCriteria(clazz);
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}
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if(description != null) {
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criteria.add(Restrictions.eq("inDescription", description));
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}
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if(descriptionType != null) {
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criteria.createAlias("inDescription", "d").add(Restrictions.eq("d.class", descriptionType));
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}
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if(features != null && !features.isEmpty()) {
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criteria.add(Restrictions.in("feature", features));
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}
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if(pageSize != null) {
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criteria.setMaxResults(pageSize);
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if(pageNumber != null) {
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criteria.setFirstResult(pageNumber * pageSize);
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}
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}
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List<T> results = criteria.list();
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defaultBeanInitializer.initializeAll(results, propertyPaths);
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return results;
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} else {
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List<T> result = new ArrayList<T>();
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if(features != null && !features.isEmpty()) {
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for(Feature f : features) {
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AuditQuery query = null;
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if(clazz == null) {
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query = getAuditReader().createQuery().forEntitiesAtRevision(DescriptionElementBase.class,auditEvent.getRevisionNumber());
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} else {
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query = getAuditReader().createQuery().forEntitiesAtRevision(clazz,auditEvent.getRevisionNumber());
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}
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if(description != null) {
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query.add(AuditEntity.relatedId("inDescription").eq(description.getId()));
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}
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if(descriptionType != null) {
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query.add(AuditEntity.property("inDescription.class").eq(descriptionType));
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}
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query.add(AuditEntity.relatedId("feature").eq(f.getId()));
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result.addAll(query.getResultList());
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}
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} else {
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AuditQuery query = null;
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if(clazz == null) {
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query = getAuditReader().createQuery().forEntitiesAtRevision(DescriptionElementBase.class,auditEvent.getRevisionNumber());
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} else {
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query = getAuditReader().createQuery().forEntitiesAtRevision(clazz,auditEvent.getRevisionNumber());
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}
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if(description != null) {
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355
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query.add(AuditEntity.relatedId("inDescription").eq(description.getId()));
|
|
356
|
}
|
|
357
|
|
|
358
|
if(descriptionType != null) {
|
|
359
|
query.add(AuditEntity.property("inDescription.class").eq(descriptionType));
|
|
360
|
}
|
|
361
|
|
|
362
|
result = query.getResultList();
|
|
363
|
}
|
|
364
|
|
|
365
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
366
|
return result;
|
|
367
|
}
|
|
368
|
}
|
|
369
|
|
|
370
|
@Override
|
|
371
|
public List<TaxonDescription> listTaxonDescriptions(Taxon taxon, Set<DefinedTerm> scopes, Set<NamedArea> geographicalScopes, Set<MarkerType> markerTypes, Set<DescriptionType> descriptionTypes, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
|
|
372
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
373
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
374
|
Criteria criteria = getSession().createCriteria(TaxonDescription.class);
|
|
375
|
|
|
376
|
if(taxon != null) {
|
|
377
|
criteria.add(Restrictions.eq("taxon", taxon));
|
|
378
|
}
|
|
379
|
|
|
380
|
if(scopes != null && !scopes.isEmpty()) {
|
|
381
|
Set<Integer> scopeIds = new HashSet<Integer>();
|
|
382
|
for(DefinedTerm s : scopes) {
|
|
383
|
scopeIds.add(s.getId());
|
|
384
|
}
|
|
385
|
criteria.createCriteria("scopes").add(Restrictions.in("id", scopeIds));
|
|
386
|
}
|
|
387
|
|
|
388
|
if(geographicalScopes != null && !geographicalScopes.isEmpty()) {
|
|
389
|
Set<Integer> geoScopeIds = new HashSet<Integer>();
|
|
390
|
for(NamedArea n : geographicalScopes) {
|
|
391
|
geoScopeIds.add(n.getId());
|
|
392
|
}
|
|
393
|
criteria.createCriteria("geoScopes").add(Restrictions.in("id", geoScopeIds));
|
|
394
|
}
|
|
395
|
|
|
396
|
addMarkerTypesCriterion(markerTypes, criteria);
|
|
397
|
addDescriptionTypesCriterion(descriptionTypes, criteria);
|
|
398
|
|
|
399
|
if(pageSize != null) {
|
|
400
|
criteria.setMaxResults(pageSize);
|
|
401
|
if(pageNumber != null) {
|
|
402
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
403
|
}
|
|
404
|
}
|
|
405
|
|
|
406
|
List<TaxonDescription> results = criteria.list();
|
|
407
|
|
|
408
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
409
|
|
|
410
|
return results;
|
|
411
|
} else {
|
|
412
|
if((scopes == null || scopes.isEmpty())&& (geographicalScopes == null || geographicalScopes.isEmpty())&& (markerTypes == null || markerTypes.isEmpty())) {
|
|
413
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonDescription.class,auditEvent.getRevisionNumber());
|
|
414
|
if(taxon != null) {
|
|
415
|
query.add(AuditEntity.relatedId("taxon").eq(taxon.getId()));
|
|
416
|
}
|
|
417
|
|
|
418
|
if(pageSize != null) {
|
|
419
|
query.setMaxResults(pageSize);
|
|
420
|
if(pageNumber != null) {
|
|
421
|
query.setFirstResult(pageNumber * pageSize);
|
|
422
|
} else {
|
|
423
|
query.setFirstResult(0);
|
|
424
|
}
|
|
425
|
}
|
|
426
|
|
|
427
|
List<TaxonDescription> results = query.getResultList();
|
|
428
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
429
|
return results;
|
|
430
|
} else {
|
|
431
|
throw new OperationNotSupportedInPriorViewException("countTaxonDescriptions(Taxon taxon, Set<Scope> scopes,Set<NamedArea> geographicalScopes)");
|
|
432
|
}
|
|
433
|
}
|
|
434
|
}
|
|
435
|
|
|
436
|
@Override
|
|
437
|
public List<TaxonNameDescription> getTaxonNameDescriptions(TaxonName name, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
|
|
438
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
439
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
440
|
Criteria criteria = getSession().createCriteria(TaxonNameDescription.class);
|
|
441
|
|
|
442
|
if(name != null) {
|
|
443
|
criteria.add(Restrictions.eq("taxonName", name));
|
|
444
|
}
|
|
445
|
|
|
446
|
if(pageSize != null) {
|
|
447
|
criteria.setMaxResults(pageSize);
|
|
448
|
if(pageNumber != null) {
|
|
449
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
450
|
}
|
|
451
|
}
|
|
452
|
|
|
453
|
List<TaxonNameDescription> results = criteria.list();
|
|
454
|
|
|
455
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
456
|
|
|
457
|
return results;
|
|
458
|
} else {
|
|
459
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonNameDescription.class,auditEvent.getRevisionNumber());
|
|
460
|
|
|
461
|
if(name != null) {
|
|
462
|
query.add(AuditEntity.relatedId("taxonName").eq(name.getId()));
|
|
463
|
}
|
|
464
|
|
|
465
|
if(pageSize != null) {
|
|
466
|
query.setMaxResults(pageSize);
|
|
467
|
if(pageNumber != null) {
|
|
468
|
query.setFirstResult(pageNumber * pageSize);
|
|
469
|
}
|
|
470
|
}
|
|
471
|
|
|
472
|
List<TaxonNameDescription> results = query.getResultList();
|
|
473
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
474
|
return results;
|
|
475
|
}
|
|
476
|
}
|
|
477
|
|
|
478
|
@Override
|
|
479
|
public long countTaxonNameDescriptions(TaxonName name) {
|
|
480
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
481
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
482
|
Criteria criteria = getCriteria(TaxonNameDescription.class);
|
|
483
|
|
|
484
|
if(name != null) {
|
|
485
|
criteria.add(Restrictions.eq("taxonName", name));
|
|
486
|
}
|
|
487
|
|
|
488
|
criteria.setProjection(Projections.rowCount());
|
|
489
|
|
|
490
|
return (Long)criteria.uniqueResult();
|
|
491
|
} else {
|
|
492
|
AuditQuery query = makeAuditQuery(TaxonNameDescription.class,auditEvent);
|
|
493
|
|
|
494
|
if(name != null) {
|
|
495
|
query.add(AuditEntity.relatedId("taxonName").eq(name.getId()));
|
|
496
|
}
|
|
497
|
|
|
498
|
query.addProjection(AuditEntity.id().count());
|
|
499
|
return (Long)query.getSingleResult();
|
|
500
|
}
|
|
501
|
}
|
|
502
|
|
|
503
|
/**
|
|
504
|
* Should use a DetachedCriteria & subquery, but HHH-158 prevents this, for now.
|
|
505
|
*
|
|
506
|
* e.g. DetachedCriteria inner = DestachedCriteria.forClass(type);
|
|
507
|
*
|
|
508
|
* outer.add(Subqueries.propertyIn("id", inner));
|
|
509
|
*/
|
|
510
|
@Override
|
|
511
|
public List<DescriptionBase> listDescriptions(Class<? extends DescriptionBase> clazz, Boolean hasImages, Boolean hasText, Set<Feature> features, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
512
|
checkNotInPriorView("DescriptionDaoImpl.listDescriptions(Class<TYPE> type, Boolean hasImages, Boolean hasText, Set<Feature> features, Integer pageSize, Integer pageNumber)");
|
|
513
|
Criteria inner = getCriteria(clazz);
|
|
514
|
|
|
515
|
Criteria elementsCriteria = inner.createCriteria("descriptionElements");
|
|
516
|
if(hasText != null) {
|
|
517
|
if(hasText) {
|
|
518
|
elementsCriteria.add(Restrictions.isNotEmpty("multilanguageText"));
|
|
519
|
} else {
|
|
520
|
elementsCriteria.add(Restrictions.isEmpty("multilanguageText"));
|
|
521
|
}
|
|
522
|
}
|
|
523
|
|
|
524
|
if(hasImages != null) {
|
|
525
|
if(hasImages) {
|
|
526
|
elementsCriteria.add(Restrictions.isNotEmpty("media"));
|
|
527
|
} else {
|
|
528
|
elementsCriteria.add(Restrictions.isEmpty("media"));
|
|
529
|
}
|
|
530
|
}
|
|
531
|
|
|
532
|
if(features != null && !features.isEmpty()) {
|
|
533
|
elementsCriteria.add(Restrictions.in("feature", features));
|
|
534
|
}
|
|
535
|
|
|
536
|
inner.setProjection(Projections.distinct(Projections.id()));
|
|
537
|
|
|
538
|
@SuppressWarnings("unchecked")
|
|
539
|
List<Object> intermediateResult = inner.list();
|
|
540
|
|
|
541
|
if(intermediateResult.isEmpty()) {
|
|
542
|
return new ArrayList<>();
|
|
543
|
}
|
|
544
|
|
|
545
|
Integer[] resultIds = new Integer[intermediateResult.size()];
|
|
546
|
for(int i = 0; i < resultIds.length; i++) {
|
|
547
|
resultIds[i] = (Integer)intermediateResult.get(i);
|
|
548
|
}
|
|
549
|
|
|
550
|
Criteria outer = getCriteria(clazz);
|
|
551
|
|
|
552
|
outer.add(Restrictions.in("id", resultIds));
|
|
553
|
addOrder(outer, orderHints);
|
|
554
|
|
|
555
|
addPageSizeAndNumber(outer, pageSize, pageNumber);
|
|
556
|
|
|
557
|
@SuppressWarnings({ "unchecked", "rawtypes" })
|
|
558
|
List<DescriptionBase> results = outer.list();
|
|
559
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
560
|
return results;
|
|
561
|
}
|
|
562
|
|
|
563
|
@Override
|
|
564
|
public List<TaxonDescription> searchDescriptionByDistribution(Set<NamedArea> namedAreas, PresenceAbsenceTerm status, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
565
|
checkNotInPriorView("DescriptionDaoImpl.searchDescriptionByDistribution(Set<NamedArea> namedAreas, PresenceAbsenceTermBase status, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)");
|
|
566
|
|
|
567
|
Criteria criteria = getSession().createCriteria(TaxonDescription.class);
|
|
568
|
Criteria elements = criteria.createCriteria("descriptionElements", "descriptionElement", Criteria.LEFT_JOIN);
|
|
569
|
elements.add(Restrictions.in("area", namedAreas.toArray()));
|
|
570
|
|
|
571
|
if(status != null) {
|
|
572
|
elements.add(Restrictions.eq("status", status));
|
|
573
|
}
|
|
574
|
|
|
575
|
ProjectionList projectionList = Projections.projectionList().add(Projections.id());
|
|
576
|
|
|
577
|
if(orderHints != null && !orderHints.isEmpty()) {
|
|
578
|
for(OrderHint orderHint : orderHints) {
|
|
579
|
projectionList = projectionList.add(Projections.property(orderHint.getPropertyName()));
|
|
580
|
}
|
|
581
|
}
|
|
582
|
|
|
583
|
criteria.setProjection(Projections.distinct(projectionList));
|
|
584
|
|
|
585
|
if(pageSize != null) {
|
|
586
|
criteria.setMaxResults(pageSize);
|
|
587
|
if(pageNumber != null) {
|
|
588
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
589
|
}
|
|
590
|
}
|
|
591
|
|
|
592
|
addOrder(criteria,orderHints);
|
|
593
|
|
|
594
|
@SuppressWarnings("unchecked")
|
|
595
|
List<Object> intermediateResult = criteria.list();
|
|
596
|
|
|
597
|
if(intermediateResult.isEmpty()) {
|
|
598
|
return new ArrayList<>();
|
|
599
|
}
|
|
600
|
|
|
601
|
Integer[] resultIds = new Integer[intermediateResult.size()];
|
|
602
|
for(int i = 0; i < resultIds.length; i++) {
|
|
603
|
if(orderHints == null || orderHints.isEmpty()) {
|
|
604
|
resultIds[i] = (Integer)intermediateResult.get(i);
|
|
605
|
} else {
|
|
606
|
resultIds[i] = ((Number)((Object[])intermediateResult.get(i))[0]).intValue();
|
|
607
|
}
|
|
608
|
}
|
|
609
|
|
|
610
|
criteria = getSession().createCriteria(TaxonDescription.class);
|
|
611
|
criteria.add(Restrictions.in("id", resultIds));
|
|
612
|
addOrder(criteria,orderHints);
|
|
613
|
|
|
614
|
@SuppressWarnings("unchecked")
|
|
615
|
List<TaxonDescription> results = criteria.list();
|
|
616
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
617
|
return results;
|
|
618
|
}
|
|
619
|
|
|
620
|
@Override
|
|
621
|
public List<CommonTaxonName> searchDescriptionByCommonName(String queryString, MatchMode matchMode, Integer pageSize, Integer pageNumber) {
|
|
622
|
|
|
623
|
Criteria crit = getSession().createCriteria(CommonTaxonName.class);
|
|
624
|
if (matchMode == MatchMode.EXACT) {
|
|
625
|
crit.add(Restrictions.eq("name", matchMode.queryStringFrom(queryString)));
|
|
626
|
} else {
|
|
627
|
crit.add(Restrictions.ilike("name", matchMode.queryStringFrom(queryString)));
|
|
628
|
}
|
|
629
|
|
|
630
|
if(pageSize != null) {
|
|
631
|
crit.setMaxResults(pageSize);
|
|
632
|
if(pageNumber != null) {
|
|
633
|
crit.setFirstResult(pageNumber * pageSize);
|
|
634
|
}
|
|
635
|
}
|
|
636
|
@SuppressWarnings("unchecked")
|
|
637
|
List<CommonTaxonName> results = crit.list();
|
|
638
|
return results;
|
|
639
|
}
|
|
640
|
|
|
641
|
@Override
|
|
642
|
public Integer countDescriptionByCommonName(String queryString, MatchMode matchMode) {
|
|
643
|
//TODO inprove performance
|
|
644
|
List<CommonTaxonName> results = searchDescriptionByCommonName(queryString, matchMode, null, null);
|
|
645
|
return results.size();
|
|
646
|
}
|
|
647
|
|
|
648
|
@Override
|
|
649
|
public DescriptionBase find(LSID lsid) {
|
|
650
|
DescriptionBase<?> descriptionBase = super.find(lsid);
|
|
651
|
if(descriptionBase != null) {
|
|
652
|
List<String> propertyPaths = new ArrayList<>();
|
|
653
|
propertyPaths.add("createdBy");
|
|
654
|
propertyPaths.add("updatedBy");
|
|
655
|
propertyPaths.add("taxon");
|
|
656
|
propertyPaths.add("taxonName");
|
|
657
|
propertyPaths.add("descriptionElements");
|
|
658
|
propertyPaths.add("descriptionElements.createdBy");
|
|
659
|
propertyPaths.add("descriptionElements.updatedBy");
|
|
660
|
propertyPaths.add("descriptionElements.feature");
|
|
661
|
propertyPaths.add("descriptionElements.multilanguageText");
|
|
662
|
propertyPaths.add("descriptionElements.multilanguageText.language");
|
|
663
|
propertyPaths.add("descriptionElements.area");
|
|
664
|
propertyPaths.add("descriptionElements.status");
|
|
665
|
propertyPaths.add("descriptionElements.modifyingText");
|
|
666
|
propertyPaths.add("descriptionElementsmodifyingText.language");
|
|
667
|
propertyPaths.add("descriptionElements.modifiers");
|
|
668
|
|
|
669
|
defaultBeanInitializer.initialize(descriptionBase, propertyPaths);
|
|
670
|
}
|
|
671
|
return descriptionBase;
|
|
672
|
}
|
|
673
|
|
|
674
|
|
|
675
|
@Override
|
|
676
|
public List<Integer> getIndividualAssociationSpecimenIDs(UUID taxonUuid,
|
|
677
|
Set<Feature> features, Integer pageSize,
|
|
678
|
Integer pageNumber, List<String> propertyPaths){
|
|
679
|
Query<Integer> query = prepareGetDescriptionElementForTaxon(taxonUuid, features, IndividualsAssociation.class, pageSize, pageNumber, "de.associatedSpecimenOrObservation.id");
|
|
680
|
List<Integer> results = query.list();
|
|
681
|
return results;
|
|
682
|
}
|
|
683
|
|
|
684
|
@Override
|
|
685
|
public List<SortableTaxonNodeQueryResult> getNodeOfIndividualAssociationForSpecimen(UUID specimenUuid, UUID classificationUuid){
|
|
686
|
String selectString = " new " +SortableTaxonNodeQueryResult.class.getName()+"(n.uuid, n.id, n.treeIndex, t.uuid, t.titleCache, t.name.titleCache, t.name.rank, n.parent.uuid) ";
|
|
687
|
Query<SortableTaxonNodeQueryResult> query = prepareGetIndividualAssociationForSpecimen(specimenUuid, classificationUuid, selectString);
|
|
688
|
@SuppressWarnings("unchecked")
|
|
689
|
List<SortableTaxonNodeQueryResult> results = query.list();
|
|
690
|
return results;
|
|
691
|
}
|
|
692
|
|
|
693
|
@Override
|
|
694
|
public <T extends DescriptionElementBase> List<T> getDescriptionElementForTaxon(
|
|
695
|
UUID taxonUuid, Set<Feature> features,
|
|
696
|
Class<T> type, Integer pageSize,
|
|
697
|
Integer pageNumber, List<String> propertyPaths) {
|
|
698
|
|
|
699
|
// Logger.getLogger("org.hibernate.SQL").setLevel(Level.TRACE);
|
|
700
|
Query<T> query = prepareGetDescriptionElementForTaxon(taxonUuid, features, type, pageSize, pageNumber, "de");
|
|
701
|
|
|
702
|
if (logger.isDebugEnabled()){logger.debug(" dao: get list ...");}
|
|
703
|
List<T> results = query.list();
|
|
704
|
if (logger.isDebugEnabled()){logger.debug(" dao: initialize ...");}
|
|
705
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
706
|
if (logger.isDebugEnabled()){logger.debug(" dao: initialize - DONE");}
|
|
707
|
|
|
708
|
// Logger.getLogger("org.hibernate.SQL").setLevel(Level.WARN);
|
|
709
|
return results;
|
|
710
|
}
|
|
711
|
|
|
712
|
@Override
|
|
713
|
public <T extends DescriptionElementBase> long countDescriptionElementForTaxon(
|
|
714
|
UUID taxonUuid, Set<Feature> features, Class<T> type) {
|
|
715
|
|
|
716
|
Query<Long> query = prepareGetDescriptionElementForTaxon(taxonUuid, features, type, null, null, "count(de)");
|
|
717
|
|
|
718
|
return query.uniqueResult();
|
|
719
|
}
|
|
720
|
|
|
721
|
private <T extends DescriptionElementBase, R extends Object> Query<R> prepareGetDescriptionElementForTaxon(UUID taxonUuid,
|
|
722
|
Set<Feature> features, Class<T> type, Integer pageSize, Integer pageNumber, String selectString) {
|
|
723
|
|
|
724
|
String queryString = "SELECT " + selectString + " FROM DescriptionElementBase AS de" +
|
|
725
|
" LEFT JOIN de.inDescription AS d" +
|
|
726
|
" LEFT JOIN d.taxon AS t" +
|
|
727
|
" WHERE d.class = 'TaxonDescription' AND t.uuid = :taxon_uuid ";
|
|
728
|
|
|
729
|
if(type != null){
|
|
730
|
queryString += " and de.class = :type";
|
|
731
|
}
|
|
732
|
if (features != null && features.size() > 0){
|
|
733
|
queryString += " and de.feature in (:features) ";
|
|
734
|
}
|
|
735
|
Query<R> query = getSession().createQuery(queryString);
|
|
736
|
|
|
737
|
query.setParameter("taxon_uuid", taxonUuid);
|
|
738
|
if(type != null){
|
|
739
|
query.setParameter("type", type.getSimpleName());
|
|
740
|
}
|
|
741
|
if(features != null && features.size() > 0){
|
|
742
|
query.setParameterList("features", features) ;
|
|
743
|
}
|
|
744
|
|
|
745
|
addPageSizeAndNumber(query, pageSize, pageNumber);
|
|
746
|
return query;
|
|
747
|
}
|
|
748
|
|
|
749
|
private Query<SortableTaxonNodeQueryResult> prepareGetIndividualAssociationForSpecimen(UUID specimenUuid, UUID classificationUuid, String selectString) {
|
|
750
|
|
|
751
|
String queryString = "SELECT " + selectString + " FROM DescriptionElementBase AS de" +
|
|
752
|
" LEFT JOIN de.inDescription AS d" +
|
|
753
|
" LEFT JOIN d.taxon AS t" +
|
|
754
|
" LEFT JOIN t.taxonNodes AS n" +
|
|
755
|
" LEFT JOIN de.associatedSpecimenOrObservation AS specimen ";
|
|
756
|
String classificationString = "";
|
|
757
|
if (classificationUuid != null){
|
|
758
|
classificationString = " LEFT JOIN n.classification AS c ";
|
|
759
|
}
|
|
760
|
String whereString = " WHERE specimen.uuid = :specimen_uuid";
|
|
761
|
if (classificationUuid != null){
|
|
762
|
whereString = whereString + " AND c.uuid = :classifcationUuid";
|
|
763
|
}
|
|
764
|
|
|
765
|
Query<SortableTaxonNodeQueryResult> query = getSession().createQuery(queryString + classificationString + whereString, SortableTaxonNodeQueryResult.class);
|
|
766
|
|
|
767
|
query.setParameter("specimen_uuid", specimenUuid);
|
|
768
|
if (classificationUuid != null){
|
|
769
|
query.setParameter("classifcationUuid", classificationUuid);
|
|
770
|
}
|
|
771
|
|
|
772
|
return query;
|
|
773
|
}
|
|
774
|
|
|
775
|
@Override
|
|
776
|
public List<Media> listTaxonDescriptionMedia(UUID taxonUuid,
|
|
777
|
Boolean limitToGalleries, Set<MarkerType> markerTypes,
|
|
778
|
Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
|
|
779
|
|
|
780
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
781
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
782
|
String queryString = " SELECT media " +
|
|
783
|
getTaxonDescriptionMediaQueryString(
|
|
784
|
taxonUuid, limitToGalleries, markerTypes);
|
|
785
|
queryString +=
|
|
786
|
" GROUP BY media "
|
|
787
|
// " ORDER BY index(media) " //not functional
|
|
788
|
;
|
|
789
|
|
|
790
|
Query<Media> query = getSession().createQuery(queryString, Media.class);
|
|
791
|
|
|
792
|
setTaxonDescriptionMediaParameters(query, taxonUuid, limitToGalleries, markerTypes);
|
|
793
|
// addMarkerTypesCriterion(markerTypes, hql);
|
|
794
|
|
|
795
|
addPageSizeAndNumber(query, pageSize, pageNumber);
|
|
796
|
List<Media> results = query.list();
|
|
797
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
798
|
|
|
799
|
return results;
|
|
800
|
} else {
|
|
801
|
throw new OperationNotSupportedInPriorViewException("countTaxonDescriptionMedia(UUID taxonUuid, boolean restrictToGalleries)");
|
|
802
|
}
|
|
803
|
}
|
|
804
|
|
|
805
|
@Override
|
|
806
|
public int countTaxonDescriptionMedia(UUID taxonUuid,
|
|
807
|
Boolean limitToGalleries, Set<MarkerType> markerTypes) {
|
|
808
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
809
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
810
|
String queryString = " SELECT count(DISTINCT media) " +
|
|
811
|
getTaxonDescriptionMediaQueryString(
|
|
812
|
taxonUuid, limitToGalleries, markerTypes);
|
|
813
|
|
|
814
|
Query<Long> query = getSession().createQuery(queryString, Long.class);
|
|
815
|
setTaxonDescriptionMediaParameters(query, taxonUuid, limitToGalleries, markerTypes);
|
|
816
|
return query.uniqueResult().intValue();
|
|
817
|
}else{
|
|
818
|
throw new OperationNotSupportedInPriorViewException("countTaxonDescriptionMedia(UUID taxonUuid)");
|
|
819
|
}
|
|
820
|
|
|
821
|
}
|
|
822
|
|
|
823
|
private void setTaxonDescriptionMediaParameters(Query query, UUID taxonUuid, Boolean limitToGalleries, Set<MarkerType> markerTypes) {
|
|
824
|
if(taxonUuid != null){
|
|
825
|
query.setParameter("uuid", taxonUuid);
|
|
826
|
}
|
|
827
|
}
|
|
828
|
|
|
829
|
/**
|
|
830
|
* @param taxonUuid
|
|
831
|
* @param restrictToGalleries
|
|
832
|
* @param markerTypes
|
|
833
|
* @return
|
|
834
|
*/
|
|
835
|
private String getTaxonDescriptionMediaQueryString(UUID taxonUuid,
|
|
836
|
Boolean restrictToGalleries, Set<MarkerType> markerTypes) {
|
|
837
|
String fromQueryString =
|
|
838
|
" FROM DescriptionElementBase as deb INNER JOIN " +
|
|
839
|
" deb.inDescription as td "
|
|
840
|
+ " INNER JOIN td.taxon as t "
|
|
841
|
+ " JOIN deb.media as media "
|
|
842
|
+ " LEFT JOIN td.markers marker ";
|
|
843
|
|
|
844
|
String whereQueryString = " WHERE (1=1) ";
|
|
845
|
if (taxonUuid != null){
|
|
846
|
whereQueryString += " AND t.uuid = :uuid ";
|
|
847
|
}
|
|
848
|
if (restrictToGalleries){
|
|
849
|
whereQueryString += " AND td.imageGallery is true ";
|
|
850
|
}
|
|
851
|
if (markerTypes != null && !markerTypes.isEmpty()){
|
|
852
|
whereQueryString += " AND (1=0";
|
|
853
|
for (MarkerType markerType : markerTypes){
|
|
854
|
whereQueryString += " OR ( marker.markerType.id = " + markerType.getId() + " AND marker.flag is true)";
|
|
855
|
|
|
856
|
}
|
|
857
|
whereQueryString += ") ";
|
|
858
|
}
|
|
859
|
|
|
860
|
return fromQueryString + whereQueryString;
|
|
861
|
|
|
862
|
}
|
|
863
|
|
|
864
|
@SuppressWarnings("unchecked")
|
|
865
|
@Override
|
|
866
|
public List<TermDto> listNamedAreasInUse(boolean includeAllParents, Integer pageSize, Integer pageNumber) {
|
|
867
|
|
|
868
|
// Logger.getLogger("org.hibernate.SQL").setLevel(Level.TRACE);
|
|
869
|
|
|
870
|
StringBuilder queryString = new StringBuilder(
|
|
871
|
"SELECT DISTINCT a.id, a.partOf.id"
|
|
872
|
+ " FROM Distribution AS d JOIN d.area AS a");
|
|
873
|
Query<Object[]> query = getSession().createQuery(queryString.toString(), Object[].class);
|
|
874
|
|
|
875
|
List<Object[]> areasInUse = query.list();
|
|
876
|
List<Object[]> parentResults = new ArrayList<>();
|
|
877
|
|
|
878
|
if(!areasInUse.isEmpty()) {
|
|
879
|
Set<Object> allAreaIds = new HashSet<>(areasInUse.size());
|
|
880
|
|
|
881
|
if(includeAllParents) {
|
|
882
|
// find all parent nodes
|
|
883
|
String allAreasQueryStr = "select a.id, a.partOf.id from NamedArea as a";
|
|
884
|
query = getSession().createQuery(allAreasQueryStr, Object[].class);
|
|
885
|
List<Object[]> allAreasResult = query.list();
|
|
886
|
Map<Object, Object> allAreasMap = ArrayUtils.toMap(allAreasResult.toArray());
|
|
887
|
|
|
888
|
Set<Object> parents = new HashSet<>();
|
|
889
|
|
|
890
|
for(Object[] leaf : areasInUse) {
|
|
891
|
allAreaIds.add(leaf[0]);
|
|
892
|
Object parentId = leaf[1];
|
|
893
|
while (parentId != null) {
|
|
894
|
if(parents.contains(parentId)) {
|
|
895
|
// break if the parent already is in the set
|
|
896
|
break;
|
|
897
|
}
|
|
898
|
parents.add(parentId);
|
|
899
|
parentId = allAreasMap.get(parentId);
|
|
900
|
}
|
|
901
|
}
|
|
902
|
allAreaIds.addAll(parents);
|
|
903
|
} else {
|
|
904
|
// only add the ids found so far
|
|
905
|
for(Object[] leaf : areasInUse) {
|
|
906
|
allAreaIds.add(leaf[0]);
|
|
907
|
}
|
|
908
|
}
|
|
909
|
|
|
910
|
// NOTE can't use "select new TermDto(distinct a.uuid, r , a.vocabulary.uuid) since we will get multiple
|
|
911
|
// rows for a term with multiple representations
|
|
912
|
String parentAreasQueryStr = TermDto.getTermDtoSelect("NamedArea")
|
|
913
|
+ "where a.id in (:allAreaIds) order by a.idInVocabulary";
|
|
914
|
query = getSession().createQuery(parentAreasQueryStr, Object[].class);
|
|
915
|
query.setParameterList("allAreaIds", allAreaIds);
|
|
916
|
|
|
917
|
addPageSizeAndNumber(query, pageSize, pageNumber);
|
|
918
|
parentResults = query.list();
|
|
919
|
}
|
|
920
|
List<TermDto> dtoList = TermDto.termDtoListFrom(parentResults);
|
|
921
|
|
|
922
|
return dtoList;
|
|
923
|
}
|
|
924
|
|
|
925
|
|
|
926
|
|
|
927
|
|
|
928
|
|
|
929
|
}
|