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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.term;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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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.hibernate.Criteria;
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import org.hibernate.Query;
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import org.hibernate.Session;
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import org.hibernate.criterion.CriteriaSpecification;
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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.springframework.stereotype.Repository;
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import eu.etaxonomy.cdm.model.common.CdmClass;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.term.TermType;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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import eu.etaxonomy.cdm.model.view.AuditEvent;
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import eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase;
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import eu.etaxonomy.cdm.persistence.dao.term.ITermVocabularyDao;
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import eu.etaxonomy.cdm.persistence.dto.FeatureDto;
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import eu.etaxonomy.cdm.persistence.dto.TermCollectionDto;
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import eu.etaxonomy.cdm.persistence.dto.TermDto;
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import eu.etaxonomy.cdm.persistence.dto.TermVocabularyDto;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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/**
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* @author a.mueller
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*/
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@Repository
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public class TermVocabularyDaoImpl extends IdentifiableDaoBase<TermVocabulary> implements
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ITermVocabularyDao {
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@SuppressWarnings("unchecked")
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public TermVocabularyDaoImpl() {
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super(TermVocabulary.class);
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indexedClasses = new Class[2];
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indexedClasses[0] = TermVocabulary.class;
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indexedClasses[1] = OrderedTermVocabulary.class;
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}
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@Override
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public long countTerms(TermVocabulary termVocabulary) {
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AuditEvent auditEvent = getAuditEventFromContext();
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if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
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Query query = getSession().createQuery("select count(term) from DefinedTermBase term where term.vocabulary = :vocabulary");
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query.setParameter("vocabulary", termVocabulary);
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return (Long)query.uniqueResult();
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} else {
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AuditQuery query = makeAuditQuery(null, auditEvent);
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query.addProjection(AuditEntity.id().count());
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query.add(AuditEntity.relatedId("vocabulary").eq(termVocabulary.getId()));
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return (Long)query.getSingleResult();
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}
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}
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@Override
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public <T extends DefinedTermBase> List<T> getTerms(TermVocabulary<T> vocabulary,Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,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 = getCriteria(DefinedTermBase.class);
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criteria.createCriteria("vocabulary").add(Restrictions.idEq(vocabulary.getId()));
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addPageSizeAndNumber(criteria, pageSize, pageNumber);
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this.addOrder(criteria, orderHints);
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@SuppressWarnings("unchecked")
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List<T> result = DefinedTermDaoImpl.deduplicateResult(criteria.list());
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defaultBeanInitializer.initializeAll(result, propertyPaths);
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return result;
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} else {
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AuditQuery query = makeAuditQuery(null, auditEvent);
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query.add(AuditEntity.relatedId("vocabulary").eq(vocabulary.getId()));
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addPageSizeAndNumber(query, pageSize, pageNumber);
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@SuppressWarnings("unchecked")
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List<T> result = DefinedTermDaoImpl.deduplicateResult(query.getResultList());
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defaultBeanInitializer.initializeAll(result, propertyPaths);
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return result;
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}
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}
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@Override
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public <T extends DefinedTermBase> TermVocabulary<T> findByUri(String termSourceUri, Class<T> clazz) {
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AuditEvent auditEvent = getAuditEventFromContext();
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if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
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//TODO use clazz
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Query query = getSession().createQuery("select vocabulary from TermVocabulary vocabulary where vocabulary.termSourceUri= :termSourceUri");
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query.setParameter("termSourceUri", termSourceUri);
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@SuppressWarnings("unchecked")
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TermVocabulary<T> result = (TermVocabulary<T>)query.uniqueResult();
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return result;
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} else {
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AuditQuery query = makeAuditQuery(clazz, auditEvent);
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query.add(AuditEntity.property("termSourceUri").eq(termSourceUri));
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@SuppressWarnings("unchecked")
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TermVocabulary<T> result = (TermVocabulary<T>)query.getSingleResult();
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return result;
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}
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}
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@Override
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public <T extends DefinedTermBase> List<T> getTerms(TermVocabulary<T> termVocabulary, Integer pageSize, Integer pageNumber) {
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return getTerms(termVocabulary, pageSize, pageNumber, null, null);
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}
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@Override
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public <T extends DefinedTermBase> List<TermVocabulary<T>> findByTermType(TermType termType, List<String> propertyPaths) {
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Criteria criteria = getSession().createCriteria(type);
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criteria.add(Restrictions.eq("termType", termType));
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criteria.setResultTransformer(CriteriaSpecification.DISTINCT_ROOT_ENTITY);
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//this.addOrder(criteria, orderHints);
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@SuppressWarnings("unchecked")
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List<TermVocabulary<T>> result = DefinedTermDaoImpl.deduplicateResult(criteria.list());
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defaultBeanInitializer.initializeAll(result, propertyPaths);
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return result;
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}
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@Override
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public List<TermVocabulary> listByTermType(TermType termType, boolean includeSubTypes, Integer limit, Integer start,List<OrderHint> orderHints, List<String> propertyPaths) {
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checkNotInPriorView("TermVocabularyDao.listByTermType(TermType termType, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths)");
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Set<TermType> allTermTypes = new HashSet<TermType>();
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allTermTypes.add(termType);
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if (includeSubTypes){
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allTermTypes.addAll(termType.getGeneralizationOf(true));
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}
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Criteria criteria = getSession().createCriteria(type);
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criteria.add(Restrictions.in("termType", allTermTypes));
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if(limit != null) {
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criteria.setMaxResults(limit);
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if(start != null) {
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criteria.setFirstResult(start);
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}
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}
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this.addOrder(criteria, orderHints);
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@SuppressWarnings("unchecked")
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List<TermVocabulary> result = DefinedTermDaoImpl.deduplicateResult(criteria.list());
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defaultBeanInitializer.initializeAll(result, propertyPaths);
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return result;
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}
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@Override
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public void missingTermUuids(
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Map<UUID, Set<UUID>> uuidsRequested,
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Map<UUID, Set<UUID>> uuidMissingTermsRepsonse,
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Map<UUID, TermVocabulary<?>> vocabularyResponse){
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Set<UUID> missingTermCandidateUuids = new HashSet<>();
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for (Set<UUID> uuidsPerVocSet : uuidsRequested.values()){
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missingTermCandidateUuids.addAll(uuidsPerVocSet);
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}
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//search persisted subset of required (usually all)
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String hql = " SELECT terms.uuid " +
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" FROM TermVocabulary voc join voc.terms terms " +
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" WHERE terms.uuid IN (:uuids) " +
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" ORDER BY voc.uuid ";
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Query query = getSession().createQuery(hql);
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int splitSize = 2000;
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List<Collection<UUID>> missingTermCandidates = splitCollection(missingTermCandidateUuids, splitSize);
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List<UUID> persistedUuids = new ArrayList<>();
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for (Collection<UUID> uuids : missingTermCandidates){
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query.setParameterList("uuids", uuids);
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@SuppressWarnings("unchecked")
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List<UUID> list = query.list();
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persistedUuids.addAll(list);
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}
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//fully load and initialize vocabularies if required
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if (vocabularyResponse != null){
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String hql2 = " SELECT DISTINCT voc " +
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" FROM TermVocabulary voc " +
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" LEFT JOIN FETCH voc.terms terms " +
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" LEFT JOIN FETCH terms.representations representations " +
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" LEFT JOIN FETCH voc.representations vocReps " +
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" WHERE terms.uuid IN (:termUuids) OR ( voc.uuid IN (:vocUuids) ) " + //was: AND voc.terms is empty, but did not load originally empty vocabularies with user defined terms added
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// " WHERE voc.uuid IN (:vocUuids) AND voc.terms is empty " +
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" ORDER BY voc.uuid ";
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query = getSession().createQuery(hql2);
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query.setParameterList("termUuids", missingTermCandidateUuids);
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query.setParameterList("vocUuids", uuidsRequested.keySet());
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for (Collection<UUID> uuids : missingTermCandidates){
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query.setParameterList("termUuids", uuids);
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@SuppressWarnings("unchecked")
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List<TermVocabulary<?>> o = query.list();
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for (TermVocabulary<?> voc : o){
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vocabularyResponse.put(voc.getUuid(), voc);
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}
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}
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}
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//compute missing terms
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if (missingTermCandidateUuids.size() == persistedUuids.size()){
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missingTermCandidateUuids.clear();
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}else{
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missingTermCandidateUuids.removeAll(persistedUuids);
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//add missing terms to response
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for (UUID vocUUID : uuidsRequested.keySet()){
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for (UUID termUuid : uuidsRequested.get(vocUUID)){
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if (missingTermCandidateUuids.contains(termUuid)){
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Set<UUID> r = uuidMissingTermsRepsonse.get(vocUUID);
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if (r == null){
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r = new HashSet<>();
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uuidMissingTermsRepsonse.put(vocUUID, r);
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}
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r.add(termUuid);
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}
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}
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}
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}
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return;
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}
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@Override
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public Collection<TermDto> getTerms(List<UUID> vocabularyUuids) {
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String queryString = TermDto.getTermDtoSelect()
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+ "where v.uuid in :vocabularyUuids "
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+ "order by a.titleCache";
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Query query = getSession().createQuery(queryString);
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query.setParameterList("vocabularyUuids", vocabularyUuids);
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@SuppressWarnings("unchecked")
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List<Object[]> result = query.list();
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List<TermDto> list = TermDto.termDtoListFrom(result);
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return list;
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}
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@Override
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public Collection<TermDto> getTerms(UUID vocabularyUuid) {
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String queryString = TermDto.getTermDtoSelect()
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+ "where v.uuid = :vocabularyUuid "
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+ "order by a.titleCache";
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Query query = getSession().createQuery(queryString);
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query.setParameter("vocabularyUuid", vocabularyUuid);
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@SuppressWarnings("unchecked")
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List<Object[]> result = query.list();
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List<TermDto> list = TermDto.termDtoListFrom(result);
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return list;
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}
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@Override
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public Collection<TermDto> getNamedAreaTerms(List<UUID> vocabularyUuids) {
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String queryString = TermDto.getTermDtoSelectNamedArea()
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+ "where v.uuid in :vocabularyUuids "
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+ "order by a.titleCache";
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Query query = getSession().createQuery(queryString);
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query.setParameterList("vocabularyUuids", vocabularyUuids);
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@SuppressWarnings("unchecked")
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List<Object[]> result = query.list();
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List<TermDto> list = TermDto.termDtoListFrom(result);
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return list;
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}
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@Override
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public Collection<TermDto> getTopLevelTerms(UUID vocabularyUuid) {
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String queryString = TermDto.getTermDtoSelect()
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+ "where v.uuid = :vocabularyUuid "
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+ "and a.partOf is null "
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+ "and a.kindOf is null";
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Query query = getSession().createQuery(queryString);
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query.setParameter("vocabularyUuid", vocabularyUuid);
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@SuppressWarnings("unchecked")
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List<Object[]> result = query.list();
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List<TermDto> list = TermDto.termDtoListFrom(result);
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return list;
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}
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@Override
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public Collection<TermDto> getTopLevelTerms(UUID vocabularyUuid, TermType type) {
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String queryString;
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if (type.equals(TermType.NamedArea)){
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queryString = TermDto.getTermDtoSelectNamedArea();
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}else if (type.equals(TermType.Feature) || type.isKindOf(TermType.Feature)){
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queryString = FeatureDto.getTermDtoSelect();
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}else{
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queryString = TermDto.getTermDtoSelect();
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}
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queryString = queryString
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+ "where v.uuid = :vocabularyUuid "
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+ "and a.partOf is null "
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+ "and a.kindOf is null";
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Query query = getSession().createQuery(queryString);
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query.setParameter("vocabularyUuid", vocabularyUuid);
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@SuppressWarnings("unchecked")
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List<Object[]> result = query.list();
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List<TermDto> list = null;
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if (type.equals(TermType.Feature)|| type.isKindOf(TermType.Feature)){
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list = FeatureDto.termDtoListFrom(result);
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}else{
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list = TermDto.termDtoListFrom(result);
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}
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return list;
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}
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@Override
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public List<TermVocabularyDto> findVocabularyDtoByTermTypes(Set<TermType> termTypes) {
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return findVocabularyDtoByTermTypes(termTypes, true);
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}
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@Override
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public List<TermVocabularyDto> findVocabularyDtoByTermTypes(Set<TermType> termTypes, boolean includeSubtypes) {
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return findVocabularyDtoByTermTypes(termTypes, null, includeSubtypes);
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}
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@Override
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public List<TermVocabularyDto> findVocabularyDtoByAvailableFor(Set<CdmClass> availableForSet) {
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String queryVocWithFittingTerms = "SELECT DISTINCT(v.uuid) FROM DefinedTermBase term JOIN term.vocabulary as v WHERE " ;
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for (CdmClass availableFor: availableForSet){
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queryVocWithFittingTerms += " term.availableFor like '%"+availableFor.getKey()+"%' AND term.termType = :feature";
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}
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String queryString = TermCollectionDto.getTermCollectionDtoSelect()
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+ " WHERE a.uuid in "
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+ " (" + queryVocWithFittingTerms + ")";
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Query query = getSession().createQuery(queryString);
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query.setParameter("feature", TermType.Feature);
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@SuppressWarnings("unchecked")
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List<Object[]> result = query.list();
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List<TermVocabularyDto> dtos = TermVocabularyDto.termVocabularyDtoListFrom(result);
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return dtos;
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}
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@Override
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public List<TermVocabularyDto> findVocabularyDtoByTermTypes(Set<TermType> termTypes, String pattern, boolean includeSubtypes) {
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Set<TermType> termTypeWithSubType = new HashSet<>();
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if (! (termTypes.isEmpty() || (termTypes.size() == 1 && termTypes.iterator().next() == null))){
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termTypeWithSubType = new HashSet<>(termTypes);
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}
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if(includeSubtypes){
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if (!termTypes.isEmpty()){
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for (TermType termType : termTypes) {
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if (termType != null){
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termTypeWithSubType.addAll(termType.getGeneralizationOf(true));
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}
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}
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}
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}
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String queryString = TermVocabularyDto.getTermCollectionDtoSelect();
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if (!termTypeWithSubType.isEmpty()){
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queryString += " where a.termType in (:termTypes) ";
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if (pattern != null){
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queryString += " AND a.titleCache like :pattern";
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}
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}else{
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if (pattern != null){
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396
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queryString += " WHERE a.titleCache like :pattern";
|
397
|
}
|
398
|
}
|
399
|
|
400
|
Query query = getSession().createQuery(queryString);
|
401
|
if (!termTypeWithSubType.isEmpty()){
|
402
|
query.setParameterList("termTypes", termTypeWithSubType);
|
403
|
}
|
404
|
if (pattern != null){
|
405
|
pattern = pattern.replace("*", "%");
|
406
|
pattern = "%"+pattern+"%";
|
407
|
query.setParameter("pattern", pattern);
|
408
|
}
|
409
|
@SuppressWarnings("unchecked")
|
410
|
List<Object[]> result = query.list();
|
411
|
List<TermVocabularyDto> dtos = TermVocabularyDto.termVocabularyDtoListFrom(result);
|
412
|
return dtos;
|
413
|
|
414
|
// Map<UUID, TermVocabularyDto> dtoMap = new HashMap<>(result.size());
|
415
|
// for (Object[] elements : result) {
|
416
|
// UUID uuid = (UUID)elements[0];
|
417
|
// TermType termType = (TermType)elements[1];
|
418
|
// if(dtoMap.containsKey(uuid)){
|
419
|
// dtoMap.get(uuid).addRepresentation((Representation)elements[2]);
|
420
|
// } else {
|
421
|
// Set<Representation> representations = new HashSet<>();
|
422
|
// if(elements[2] instanceof Representation) {
|
423
|
// representations = new HashSet<Representation>();
|
424
|
// representations.add((Representation)elements[2]);
|
425
|
// } else {
|
426
|
// representations = (Set<Representation>)elements[2];
|
427
|
// }
|
428
|
// dtoMap.put(uuid, new TermVocabularyDto(uuid, representations, termType, (String)elements[3]));
|
429
|
// }
|
430
|
// }
|
431
|
// return new ArrayList<>(dtoMap.values());
|
432
|
}
|
433
|
|
434
|
@Override
|
435
|
public List<TermVocabularyDto> findVocabularyDtoByTermType(TermType termType) {
|
436
|
return findVocabularyDtoByTermTypes(Collections.singleton(termType));
|
437
|
}
|
438
|
|
439
|
@Override
|
440
|
public <S extends TermVocabulary> List<UuidAndTitleCache<S>> getUuidAndTitleCache(Class<S> clazz, TermType termType,
|
441
|
Integer limit, String pattern) {
|
442
|
if(termType==null){
|
443
|
return getUuidAndTitleCache(clazz, limit, pattern);
|
444
|
}
|
445
|
Session session = getSession();
|
446
|
Query query = null;
|
447
|
if (pattern != null){
|
448
|
query = session.createQuery(
|
449
|
" SELECT uuid, id, titleCache "
|
450
|
+ " FROM " + clazz.getSimpleName()
|
451
|
+ " WHERE titleCache LIKE :pattern "
|
452
|
+ " AND termType = :termType");
|
453
|
pattern = pattern.replace("*", "%");
|
454
|
pattern = pattern.replace("?", "_");
|
455
|
pattern = pattern + "%";
|
456
|
query.setParameter("pattern", pattern);
|
457
|
} else {
|
458
|
query = session.createQuery(
|
459
|
" SELECT uuid, id, titleCache "
|
460
|
+ " FROM " + clazz.getSimpleName()
|
461
|
+ " WHERE termType = :termType");
|
462
|
}
|
463
|
query.setParameter("termType", termType);
|
464
|
if (limit != null){
|
465
|
query.setMaxResults(limit);
|
466
|
}
|
467
|
return getUuidAndTitleCache(query);
|
468
|
}
|
469
|
|
470
|
@Override
|
471
|
public TermVocabularyDto findVocabularyDtoByUuid(UUID vocUuid) {
|
472
|
if (vocUuid == null ){
|
473
|
return null;
|
474
|
}
|
475
|
|
476
|
String queryString = TermCollectionDto.getTermCollectionDtoSelect()
|
477
|
+ " where a.uuid like :uuid ";
|
478
|
// + "order by a.titleCache";
|
479
|
Query query = getSession().createQuery(queryString);
|
480
|
query.setParameter("uuid", vocUuid);
|
481
|
|
482
|
@SuppressWarnings("unchecked")
|
483
|
List<Object[]> result = query.list();
|
484
|
if (result.size() == 1){
|
485
|
return TermVocabularyDto.termVocabularyDtoListFrom(result).get(0);
|
486
|
}
|
487
|
return null;
|
488
|
}
|
489
|
|
490
|
@Override
|
491
|
public List<TermVocabularyDto> findVocabularyDtoByUuids(List<UUID> vocUuids) {
|
492
|
|
493
|
if (vocUuids == null || vocUuids.isEmpty()){
|
494
|
return null;
|
495
|
}
|
496
|
List<TermVocabularyDto> list = new ArrayList<>();
|
497
|
|
498
|
String queryString = TermCollectionDto.getTermCollectionDtoSelect()
|
499
|
+ "where a.uuid in :uuidList ";
|
500
|
// + "order by a.titleCache";
|
501
|
Query query = getSession().createQuery(queryString);
|
502
|
query.setParameterList("uuidList", vocUuids);
|
503
|
|
504
|
@SuppressWarnings("unchecked")
|
505
|
List<Object[]> result = query.list();
|
506
|
|
507
|
list = TermVocabularyDto.termVocabularyDtoListFrom(result);
|
508
|
return list;
|
509
|
|
510
|
}
|
511
|
}
|