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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.Enumeration;
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import java.util.HashMap;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Locale;
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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.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.Criterion;
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import org.hibernate.criterion.Disjunction;
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import org.hibernate.criterion.Order;
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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.springframework.stereotype.Repository;
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import eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.description.MeasurementUnit;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
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import eu.etaxonomy.cdm.model.description.TextFormat;
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import eu.etaxonomy.cdm.model.location.Country;
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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.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.location.ReferenceSystem;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.RightsType;
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import eu.etaxonomy.cdm.model.metadata.TermSearchField;
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import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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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.IDefinedTermDao;
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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.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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/**
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 * @author a.kohlbecker
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 * @since 29.05.2008
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 */
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@Repository
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public class DefinedTermDaoImpl
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        extends IdentifiableDaoBase<DefinedTermBase>
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        implements IDefinedTermDao{
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    private static final Logger logger = Logger.getLogger(DefinedTermDaoImpl.class);
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	@SuppressWarnings("unchecked")
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    public DefinedTermDaoImpl() {
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		super(DefinedTermBase.class);
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		indexedClasses = new Class[25];
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		indexedClasses[0] = Rank.class;
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		indexedClasses[1] = AnnotationType.class;
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		indexedClasses[2] = ExtensionType.class;
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		indexedClasses[3] = Language.class;
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		indexedClasses[4] = MarkerType.class;
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		indexedClasses[5] = MeasurementUnit.class;
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		indexedClasses[6] = DefinedTerm.class;
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		indexedClasses[7] = PresenceAbsenceTerm.class;
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		indexedClasses[8] = State.class;
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		indexedClasses[9] = StatisticalMeasure.class;
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		indexedClasses[10] = TextFormat.class;
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		indexedClasses[11] = DerivationEventType.class;
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		indexedClasses[12] = NamedArea.class;
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		indexedClasses[13] = NamedAreaLevel.class;
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		indexedClasses[14] = NamedAreaType.class;
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		indexedClasses[15] = ReferenceSystem.class;
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		indexedClasses[16] = Country.class;
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		indexedClasses[17] = RightsType.class;
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		indexedClasses[18] = HybridRelationshipType.class;
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		indexedClasses[19] = NameRelationshipType.class;
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		indexedClasses[20] = NameTypeDesignationStatus.class;
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		indexedClasses[21] = NomenclaturalStatusType.class;
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		indexedClasses[22] = SpecimenTypeDesignationStatus.class;
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		indexedClasses[23] = SynonymType.class;
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		indexedClasses[24] = TaxonRelationshipType.class;
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	}
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	/**
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	 * Searches by Label
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	 */
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	@Override
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    public List<DefinedTermBase> findByLabel(String queryString) {
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		return findByLabel(queryString, null);
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	}
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	/**
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	 * Searches by Label
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	 */
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	@Override
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    public List<DefinedTermBase> findByLabel(String queryString, CdmBase sessionObject) {
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		checkNotInPriorView("DefinedTermDaoImpl.findByTitle(String queryString, CdmBase sessionObject)");
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		Session session = getSession();
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		if ( sessionObject != null ) {//attache the object to the session, TODO needed?
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			session.update(sessionObject);
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		}
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		Query query = session.createQuery("SELECT term "
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		        + " FROM DefinedTermBase term JOIN FETCH term.representations representation "
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		        + " WHERE representation.label = :label");
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		query.setParameter("label", queryString);
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		@SuppressWarnings({ "unchecked", "rawtypes" })
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		List<DefinedTermBase> result = deduplicateResult(query.list());
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		return result;
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	}
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	@Override
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    public List<DefinedTermBase> findByTitle(String queryString, MatchMode matchMode, int page, int pagesize, List<Criterion> criteria) {
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		//FIXME is query parametrised?
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		checkNotInPriorView("DefinedTermDaoImpl.findByTitle(String queryString, ITitledDao.MATCH_MODE matchMode, int page, int pagesize, List<Criterion> criteria)");
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		Criteria crit = getSession().createCriteria(type);
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		crit.add(Restrictions.ilike("titleCache", matchMode.queryStringFrom(queryString)));
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		crit.setMaxResults(pagesize);
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		int firstItem = (page - 1) * pagesize + 1;
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		crit.setFirstResult(firstItem);
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		@SuppressWarnings("unchecked")
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        List<DefinedTermBase> results = deduplicateResult(crit.list());
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		return results;
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	}
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	@Override
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    public Country getCountryByIso(String iso3166) {
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		// If iso639 = "" query returns non-unique result. We prevent this here:
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		if (StringUtils.isBlank(iso3166) || iso3166.length()<2 || iso3166.length()>3) { return null; }
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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("from Country where iso3166_A2 = :isoCode OR idInVocabulary = :isoCode");
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		    query.setParameter("isoCode", iso3166);
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		    return (Country) query.uniqueResult();
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		} else {
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			AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(Country.class,auditEvent.getRevisionNumber());
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			query.add(AuditEntity.property("iso3166_A2").eq(iso3166));
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			query.add(AuditEntity.property("idInVocabulary").eq(iso3166));
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			return (Country) 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> getDefinedTermByRepresentationText(String text, Class<T> clazz ) {
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		return getDefinedTermByRepresentationText(text,clazz,null,null);
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	}
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	@Override
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    public <T extends DefinedTermBase> List<T> getDefinedTermByRepresentationText(String text, Class<T> clazz, Integer pageSize,Integer  pageNumber) {
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		checkNotInPriorView("DefinedTermDaoImpl.getDefinedTermByRepresentationText(String text, Class<T> clazz, Integer pageSize,Integer  pageNumber)");
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		Criteria criteria = getCriteria(clazz);
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		criteria.createAlias("representations", "r").add(Restrictions.like("r.text", text));
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		addPageSizeAndNumber(criteria, pageSize, pageNumber);
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		@SuppressWarnings("unchecked")
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        List<T> result = deduplicateResult(criteria.list());
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		return result;
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	}
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	@Override
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    public long countDefinedTermByRepresentationText(String text, Class<? extends DefinedTermBase> clazz) {
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	    checkNotInPriorView("DefinedTermDaoImpl.countDefinedTermByRepresentationText(String text, Class<? extends DefinedTermBase> clazz)");
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		Criteria criteria = getCriteria(clazz);
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		criteria.createAlias("representations", "r").add(Restrictions.like("r.text", text));
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		criteria.setProjection(Projections.rowCount());
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		return (Long)criteria.uniqueResult();
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	}
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	@Override
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	public <T extends DefinedTermBase> List<T> getDefinedTermByIdInVocabulary(String label, UUID vocUuid, Class<T> clazz, Integer pageSize, Integer pageNumber) {
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		checkNotInPriorView("DefinedTermDaoImpl.getDefinedTermByIdInVocabulary(String label, UUID vocUuid, Class<T> clazz, Integer pageSize, Integer pageNumber)");
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		Criteria criteria = getCriteria(clazz);
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		criteria.createAlias("vocabulary", "voc")
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		    .add(Restrictions.like("voc.uuid", vocUuid))
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			.add(Restrictions.like("idInVocabulary", label, org.hibernate.criterion.MatchMode.EXACT));
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		addPageSizeAndNumber(criteria, pageSize, pageNumber);
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		@SuppressWarnings("unchecked")
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        List<T> result = deduplicateResult(criteria.list());
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		return result;
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	}
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    @Override
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	public <T extends DefinedTermBase> List<T> getDefinedTermByRepresentationAbbrev(String text, Class<T> clazz, Integer pageSize,Integer  pageNumber) {
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		checkNotInPriorView("DefinedTermDaoImpl.getDefinedTermByRepresentationAbbrev(String abbrev, Class<T> clazz, Integer pageSize,Integer  pageNumber)");
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		Criteria criteria = getCriteria(clazz);
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		criteria.createAlias("representations", "r").add(Restrictions.like("r.abbreviatedLabel", text));
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		addPageSizeAndNumber(criteria, pageSize, pageNumber);
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		@SuppressWarnings("unchecked")
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		List<T> result = deduplicateResult(criteria.list());
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		return result;
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	}
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	@Override
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	public long countDefinedTermByRepresentationAbbrev(String text, Class<? extends DefinedTermBase> clazz) {
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	    checkNotInPriorView("DefinedTermDaoImpl.countDefinedTermByRepresentationAbbrev(String abbrev, Class<? extends DefinedTermBase> clazz)");
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		Criteria criteria = getCriteria(clazz);
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		criteria.createAlias("representations", "r").add(Restrictions.like("r.abbreviatedLabel", text));
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		criteria.setProjection(Projections.rowCount());
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        return (Long)criteria.uniqueResult();
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	}
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	@Override
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    public Language getLanguageByIso(String iso639) {
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		if (iso639.length() < 2 || iso639.length() > 3) {
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			logger.warn("Invalid length " + iso639.length() + " of ISO code. Length must be 2 or 3.");
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			return null;
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		}
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		boolean isIso639_1 = iso639.length() == 2;
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		String queryStr;
262
		if (isIso639_1){
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			queryStr = "FROM Language WHERE iso639_1 = :isoCode";
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		}else{
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			queryStr = "FROM Language WHERE idInVocabulary = :isoCode AND vocabulary.uuid = :vocUuid";
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		}
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		AuditEvent auditEvent = getAuditEventFromContext();
268
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
269
		    Query query = getSession().createQuery(queryStr);
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		    query.setParameter("isoCode", iso639);
271
		    if (! isIso639_1){
272
		    	query.setParameter("vocUuid", Language.uuidLanguageVocabulary);
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			}
274
		    return (Language) query.uniqueResult();
275
		} else {
276
			AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(Language.class,auditEvent.getRevisionNumber());
277
			if (isIso639_1){
278
				query.add(AuditEntity.property("iso639_1").eq(iso639));
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			}else{
280
				query.add(AuditEntity.property("iso639_2").eq(iso639));
281
				query.add(AuditEntity.property("vocabulary.uuid").eq(Language.uuidLanguageVocabulary));
282
			}
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284
			return (Language)query.getSingleResult();
285
		}
286
	}
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288
	/**
289
	 *  FIXME this will result in a query per language - could you, given that iso codes
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	 *  are unique, use from Language where iso639_1 in (:isoCode) or iso639_2 in (:isoCode)
291
	 */
292
	@Override
293
    public List<Language> getLanguagesByIso(List<String> iso639List) {
294
		List<Language> languages = new ArrayList<>(iso639List.size());
295
		for (String iso639 : iso639List) {
296
			languages.add(getLanguageByIso(iso639));
297
		}
298
		return languages;
299
	}
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301
	@Override
302
    public List<Language> getLanguagesByLocale(Enumeration<Locale> locales) {
303
		List<Language> languages = new ArrayList<>();
304
		while(locales.hasMoreElements()) {
305
			Locale locale = locales.nextElement();
306
			languages.add(getLanguageByIso(locale.getLanguage()));
307
		}
308
		return languages;
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	}
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311
	@Override
312
    public long count(NamedAreaLevel level, NamedAreaType type) {
313
		AuditEvent auditEvent = getAuditEventFromContext();
314
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
315
		    Criteria criteria = getCriteria(NamedArea.class);
316

    
317
		    if(level != null) {
318
			    criteria.add(Restrictions.eq("level",level));
319
		    }
320

    
321
		    if(type != null) {
322
			    criteria.add(Restrictions.eq("type", type));
323
		    }
324

    
325
		    criteria.setProjection(Projections.rowCount());
326

    
327
	        return (Long)criteria.uniqueResult();
328
		} else {
329
			AuditQuery query = makeAuditQuery(NamedArea.class, auditEvent);
330

    
331
			if(level != null) {
332
				query.add(AuditEntity.relatedId("level").eq(level.getId()));
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		    }
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335
		    if(type != null) {
336
		    	query.add(AuditEntity.relatedId("type").eq(type.getId()));
337
		    }
338
		    query.addProjection(AuditEntity.id().count());
339
		    return (Long)query.getSingleResult();
340
		}
341
	}
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343
	@Override
344
    public long countMedia(DefinedTermBase definedTerm) {
345
		checkNotInPriorView("DefinedTermDaoImpl.countMedia(DefinedTermBase definedTerm)");
346
		Query query = getSession().createQuery("select count(media) from DefinedTermBase definedTerm join definedTerm.media media where definedTerm = :definedTerm");
347
	    query.setParameter("definedTerm", definedTerm);
348

    
349
		return (Long)query.uniqueResult();
350
	}
351

    
352
	@Override
353
    public List<Media> getMedia(DefinedTermBase definedTerm, Integer pageSize,	Integer pageNumber) {
354
		checkNotInPriorView("DefinedTermDaoImpl.getMedia(DefinedTermBase definedTerm, Integer pageSize,	Integer pageNumber)");
355
		Query query = getSession().createQuery(
356
		           "SELECT media "
357
		        + " FROM DefinedTermBase definedTerm "
358
		        + " JOIN definedTerm.media media "
359
		        + " WHERE definedTerm = :definedTerm");
360
		query.setParameter("definedTerm", definedTerm);
361

    
362
		addPageSizeAndNumber(query, pageSize, pageNumber);
363

    
364
		@SuppressWarnings("unchecked")
365
        List<Media> result = query.list();
366
		return result;
367
	}
368

    
369
	@Override
370
    public List<NamedArea> list(NamedAreaLevel level, NamedAreaType type, Integer pageSize, Integer pageNumber) {
371
		AuditEvent auditEvent = getAuditEventFromContext();
372
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
373
            Criteria criteria = getCriteria(NamedArea.class);
374

    
375
		    if(level != null) {
376
			    criteria.add(Restrictions.eq("level",level));
377
		    }
378

    
379
		    if(type != null) {
380
			    criteria.add(Restrictions.eq("type", type));
381
		    }
382

    
383
		    addPageSizeAndNumber(criteria, pageSize, pageNumber);
384

    
385
	        @SuppressWarnings("unchecked")
386
	        List<NamedArea> result = deduplicateResult(criteria.list());
387
	        return result;
388
		} else {
389
            AuditQuery query = makeAuditQuery(NamedArea.class, auditEvent);
390

    
391
			if(level != null) {
392
				query.add(AuditEntity.relatedId("level").eq(level.getId()));
393
		    }
394

    
395
		    if(type != null) {
396
		    	query.add(AuditEntity.relatedId("type").eq(type.getId()));
397
		    }
398

    
399
		    @SuppressWarnings("unchecked")
400
            List<NamedArea> result = deduplicateResult(query.getResultList());
401
		    return result;
402
		}
403
	}
404

    
405
	@Override
406
    public List<NamedArea> list(NamedAreaLevel level, NamedAreaType type, Integer pageSize, Integer pageNumber,
407
			List<OrderHint> orderHints, List<String> propertyPaths) {
408

    
409
	    List<NamedArea> result;
410

    
411
		AuditEvent auditEvent = getAuditEventFromContext();
412
		if (auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
413
			Criteria criteria = getCriteria(NamedArea.class);
414

    
415
			if (level != null) {
416
				criteria.add(Restrictions.eq("level", level));
417
			}
418
			if (type != null) {
419
				criteria.add(Restrictions.eq("type", type));
420
			}
421
			addOrder(criteria,orderHints);
422
			addPageSizeAndNumber(criteria, pageSize, pageNumber);
423

    
424
			result = deduplicateResult(criteria.list());
425

    
426
		} else {
427
			AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(NamedArea.class,
428
				auditEvent.getRevisionNumber());
429
			if (level != null) {
430
				query.add(AuditEntity.relatedId("level").eq(level.getId()));
431
			}
432
			if (type != null) {
433
				query.add(AuditEntity.relatedId("type").eq(type.getId()));
434
			}
435
			result = deduplicateResult(query.getResultList());
436
		}
437

    
438
		defaultBeanInitializer.initializeAll(result, propertyPaths);
439

    
440
		return result;
441
	}
442

    
443

    
444
	@Override
445
    public <T extends DefinedTermBase> long countGeneralizationOf(T kindOf) {
446
		AuditEvent auditEvent = getAuditEventFromContext();
447
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
448
		    Query query = getSession().createQuery("select count(term) from DefinedTermBase term where term.kindOf = :kindOf");
449
		    query.setParameter("kindOf", kindOf);
450
		    return (Long)query.uniqueResult();
451
		} else {
452
            AuditQuery query = makeAuditQuery(DefinedTermBase.class,auditEvent);
453
			query.add(AuditEntity.relatedId("kindOf").eq(kindOf.getId()));
454
		    query.addProjection(AuditEntity.id().count());
455
		    return (Long)query.getSingleResult();
456
		}
457
	}
458

    
459
	@Override
460
    public <T extends DefinedTermBase> long countIncludes(Collection<T> partOf) {
461
		if (partOf == null || partOf.isEmpty()){
462
			return 0;
463
		}
464
		AuditEvent auditEvent = getAuditEventFromContext();
465
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
466
    		Query query = getSession().createQuery("select count(term) from DefinedTermBase term where term.partOf in (:partOf)");
467
	    	query.setParameterList("partOf", partOf);
468
		    return (Long)query.uniqueResult();
469
		} else {
470
			long count = 0;
471
			for(T t : partOf) {
472
				AuditQuery query = makeAuditQuery(DefinedTermBase.class, auditEvent);
473
				query.add(AuditEntity.relatedId("partOf").eq(t.getId()));
474
			    query.addProjection(AuditEntity.id().count());
475
			    count += (Long)query.getSingleResult();
476
			}
477
			return count;
478
		}
479
	}
480

    
481
	@Override
482
    public <T extends DefinedTermBase> List<T> getGeneralizationOf(T kindOf, Integer pageSize, Integer pageNumber) {
483
		AuditEvent auditEvent = getAuditEventFromContext();
484
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
485
		    Query query = getSession().createQuery("select term from DefinedTermBase term where term.kindOf = :kindOf");
486
		    query.setParameter("kindOf", kindOf);
487

    
488
		    addPageSizeAndNumber(query, pageSize, pageNumber);
489

    
490
		    @SuppressWarnings("unchecked")
491
            List<T> result = deduplicateResult(query.list());
492
		    return result;
493
		} else {
494
			 AuditQuery query = makeAuditQuery(DefinedTermBase.class, auditEvent);
495
			 query.add(AuditEntity.relatedId("kindOf").eq(kindOf.getId()));
496

    
497
			 addPageSizeAndNumber(query, pageSize, pageNumber);
498

    
499
             @SuppressWarnings("unchecked")
500
             List<T> result = deduplicateResult(query.getResultList());
501
             return result;
502
		}
503
	}
504

    
505
	@Override
506
    public <T extends DefinedTermBase> List<T> getIncludes(Collection<T> partOf,	Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
507
		if (partOf == null || partOf.isEmpty()){
508
			return new ArrayList<>();
509
		}
510
		AuditEvent auditEvent = getAuditEventFromContext();
511
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
512
    		Query query = getSession().createQuery("select term from DefinedTermBase term where term.partOf in (:partOf)");
513
    		query.setParameterList("partOf", partOf);
514

    
515
    		addPageSizeAndNumber(query, pageSize, pageNumber);
516

    
517
		    @SuppressWarnings("unchecked")
518
            List<T> results = deduplicateResult(query.list());
519
		    defaultBeanInitializer.initializeAll(results, propertyPaths);
520
		    return results;
521
		} else {
522
			List<T> result = new ArrayList<>();
523
			for(T t : partOf) {
524
				AuditQuery query = makeAuditQuery(DefinedTermBase.class, auditEvent);
525
				query.add(AuditEntity.relatedId("partOf").eq(t.getId()));
526
				addPageSizeAndNumber(query, pageSize, pageNumber);
527

    
528
			    result.addAll(deduplicateResult(query.getResultList()));
529
			}
530
			defaultBeanInitializer.initializeAll(result, propertyPaths);
531
			return result;
532
		}
533
	}
534

    
535
	@Override
536
    public <T extends DefinedTermBase> long countPartOf(Set<T> definedTerms) {
537
		checkNotInPriorView("DefinedTermDaoImpl.countPartOf(Set<T> definedTerms)");
538
		Query query = getSession().createQuery("select count(distinct definedTerm) from DefinedTermBase definedTerm join definedTerm.includes included where included in (:definedTerms)");
539
		query.setParameterList("definedTerms", definedTerms);
540
		return (Long)query.uniqueResult();
541
	}
542

    
543
	@Override
544
    public <T extends DefinedTermBase> List<T> getPartOf(Set<T> definedTerms, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
545
		checkNotInPriorView("DefinedTermDaoImpl.getPartOf(Set<T> definedTerms, Integer pageSize, Integer pageNumber)");
546
		Query query = getSession().createQuery("select distinct definedTerm from DefinedTermBase definedTerm join definedTerm.includes included where included in (:definedTerms)");
547
		query.setParameterList("definedTerms", definedTerms);
548

    
549
		addPageSizeAndNumber(query, pageSize, pageNumber);
550

    
551
		@SuppressWarnings("unchecked")
552
        List<T> r = query.list();
553
		/**
554
		 * For some weird reason, hibernate returns proxies (extending the superclass), not the actual class on this,
555
		 * despite querying the damn database and returning the discriminator along with the rest of the object properties!
556
		 *
557
		 * Probably a bug in hibernate, but we'll manually deproxy for now since the objects are initialized anyway, the
558
		 * performance implications are small (we're swapping one array of references for another, not hitting the db or
559
		 * cache).
560
		 */
561
		List<T> results = new ArrayList<>();
562
		if(!definedTerms.isEmpty()) {
563
		    for(T t : r) {
564
		        T deproxied = CdmBase.deproxy(t);
565
                results.add(deproxied);
566
		    }
567
		    defaultBeanInitializer.initializeAll(results, propertyPaths);
568
		}
569
		return results;
570
	}
571

    
572
	@Override
573
    public DefinedTermBase findByUri(URI uri) {
574
		AuditEvent auditEvent = getAuditEventFromContext();
575
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
576
		    Query query = getSession().createQuery("select term from DefinedTermBase term where term.uri = :uri");
577
		    query.setParameter("uri", uri);
578
		    return (DefinedTermBase<?>)query.uniqueResult();
579
		} else {
580
			AuditQuery query = makeAuditQuery(DefinedTermBase.class, auditEvent);
581
			query.add(AuditEntity.property("uri").eq(uri));
582
		    return (DefinedTermBase<?>)query.getSingleResult();
583
		}
584
	}
585

    
586
	@Override
587
	public <T extends DefinedTermBase> List<T> listByTermType(TermType termType, Integer limit, Integer start,
588
	        List<OrderHint> orderHints, List<String> propertyPaths) {
589
	    Query query = getSession().createQuery("SELECT term FROM DefinedTermBase term WHERE term.termType = :termType");
590
	    query.setParameter("termType", termType);
591

    
592
	    @SuppressWarnings("unchecked")
593
        List<T> result = deduplicateResult(query.list());
594

    
595
	    defaultBeanInitializer.initializeAll(result, propertyPaths);
596
        return result;
597
	}
598

    
599
	@Override
600
    public <TERM extends DefinedTermBase> List<TERM> listByTermClass(Class<TERM> clazz, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
601
//		checkNotInPriorView("DefinedTermDaoImpl.listByTermClass(Class<TERM> clazz, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths)");
602

    
603
		Query query = getSession().createQuery("FROM " + clazz.getSimpleName());
604

    
605
	    @SuppressWarnings("unchecked")
606
        List<TERM> result = deduplicateResult(query.list());
607

    
608
	    defaultBeanInitializer.initializeAll(result, propertyPaths);
609

    
610
	    return result;
611
	}
612

    
613
    @Override
614
    public <S extends DefinedTermBase> List<S> list(Class<S> type, Integer limit, Integer start,
615
            List<OrderHint> orderHints, List<String> propertyPath) {
616

    
617
        return deduplicateResult(super.list(type, limit, start, orderHints, propertyPath));
618
    }
619

    
620
    /**
621
     * Workaround for https://dev.e-taxonomy.eu/redmine/issues/5871 and #5945
622
     * Terms with multiple representations return identical duplicates
623
     * due to eager representation loading. We expect these duplicates to appear
624
     * in line wo we only compare one term with its predecessor. If it already
625
     * exists we remove it from the result.
626
     * @param orginals
627
     * @return
628
     */
629
    protected static <S extends CdmBase> List<S> deduplicateResult(List<S> orginals) {
630
        List<S> result = new ArrayList<>();
631
        Iterator<S> it = orginals.iterator();
632
        S last = null;
633
        while (it.hasNext()){
634
            S a = it.next();
635
            if (a != last){
636
                if (!result.contains(a)){
637
                    result.add(a);
638
                }
639
            }
640
            last = a;
641
        }
642
        return result;
643
    }
644

    
645
    @Override
646
    public <S extends DefinedTermBase> List<S> list(Class<S> clazz, List<TermVocabulary> vocs, Integer limit, String pattern) {
647
        return list(clazz, vocs, 0, limit, pattern, MatchMode.BEGINNING);
648
    }
649

    
650
    @Override
651
    public <S extends DefinedTermBase> List<S> list(Class<S> clazz, List<TermVocabulary> vocs, Integer pageNumber, Integer limit, String pattern, MatchMode matchmode){
652
        Session session = getSession();
653
        if (clazz == null){
654
            clazz = (Class)type;
655
        }
656
        Criteria crit = getSession().createCriteria(clazz, "term");
657
        if (!StringUtils.isBlank(pattern)){
658
            crit.createAlias("term.representations", "reps");
659
            Disjunction or = Restrictions.disjunction();
660
            if (matchmode == MatchMode.EXACT) {
661
                or.add(Restrictions.eq("titleCache", matchmode.queryStringFrom(pattern)));
662
                or.add(Restrictions.eq("reps.label", matchmode.queryStringFrom(pattern)));
663
            } else {
664
                or.add(Restrictions.like("titleCache", matchmode.queryStringFrom(pattern)));
665
                or.add(Restrictions.like("reps.label", matchmode.queryStringFrom(pattern)));
666
            }
667
            crit.add(or);
668
        }
669

    
670
        if (limit != null && limit >= 0) {
671
            crit.setMaxResults(limit);
672
        }
673

    
674
        if (vocs != null &&!vocs.isEmpty()){
675
            crit.createAlias("term.vocabulary", "voc");
676
            Disjunction or = Restrictions.disjunction();
677
            for (TermVocabulary<?> voc: vocs){
678
                Criterion criterion = Restrictions.eq("voc.id", voc.getId());
679
                or.add(criterion);
680
            }
681
            crit.add(or);
682
        }
683

    
684
        crit.addOrder(Order.asc("titleCache"));
685
        if (limit == null){
686
            limit = 1;
687
        }
688
        crit.setFirstResult(0);
689
        @SuppressWarnings("unchecked")
690
        List<S> results = deduplicateResult(crit.list());
691
        return results;
692
    }
693

    
694
    @Override
695
    public <S extends DefinedTermBase> List<S> listByAbbrev(Class<S> clazz, List<TermVocabulary> vocs, Integer limit, String pattern, TermSearchField type) {
696
        return listByAbbrev(clazz, vocs, 0, limit, pattern, MatchMode.BEGINNING, type);
697
    }
698

    
699
    @Override
700
    public <S extends DefinedTermBase> List<S> listByAbbrev(Class<S> clazz, List<TermVocabulary> vocs, Integer pageNumber, Integer limit, String pattern, MatchMode matchmode, TermSearchField abbrevType){
701

    
702
        if (clazz == null){
703
            clazz = (Class)type;
704
        }
705
        Criteria crit = getSession().createCriteria(clazz, "type");
706
        if (!StringUtils.isBlank(pattern)){
707
            if (matchmode == MatchMode.EXACT) {
708
                crit.add(Restrictions.eq(abbrevType.getKey(), matchmode.queryStringFrom(pattern)));
709
            } else {
710
                crit.add(Restrictions.like(abbrevType.getKey(), matchmode.queryStringFrom(pattern)));
711
            }
712
        }
713
        if (limit != null && limit >= 0) {
714
            crit.setMaxResults(limit);
715
        }
716

    
717
        if (vocs != null &&!vocs.isEmpty()){
718
            crit.createAlias("type.vocabulary", "voc");
719
            Disjunction or = Restrictions.disjunction();
720
            for (TermVocabulary<?> voc: vocs){
721
                Criterion criterion = Restrictions.eq("voc.id", voc.getId());
722
                or.add(criterion);
723
            }
724
            crit.add(or);
725
        }
726

    
727
        crit.addOrder(Order.asc(abbrevType.getKey()));
728
        if (limit == null){
729
            limit = 1;
730
        }
731
//        int firstItem = (pageNumber - 1) * limit;
732

    
733
        crit.setFirstResult(0);
734
        @SuppressWarnings("unchecked")
735
        List<S> results = deduplicateResult(crit.list());
736
        return results;
737
    }
738

    
739

    
740
    @Override
741
    public Collection<TermDto> getIncludesAsDto(
742
            TermDto parentTerm) {
743
        String queryString;
744
        if (parentTerm.getTermType().equals(TermType.NamedArea)){
745
            queryString = TermDto.getTermDtoSelectNamedArea();
746
        }else{
747
            queryString = TermDto.getTermDtoSelect();
748
        }
749
        queryString = queryString
750
                + "where a.partOf.uuid = :parentUuid";
751
        Query query =  getSession().createQuery(queryString);
752
        query.setParameter("parentUuid", parentTerm.getUuid());
753

    
754
        @SuppressWarnings("unchecked")
755
        List<Object[]> result = query.list();
756

    
757
        List<TermDto> list = TermDto.termDtoListFrom(result);
758
        return list;
759
    }
760

    
761
    @Override
762
    public Collection<TermDto> getKindOfsAsDto(TermDto parentTerm) {
763

    
764
        String queryString;
765
        if (parentTerm.getTermType().equals(TermType.NamedArea)){
766
            queryString = TermDto.getTermDtoSelectNamedArea();
767
        }else{
768
            queryString = TermDto.getTermDtoSelect();
769
        }
770
        queryString = queryString + "where a.kindOf.uuid = :parentUuid";
771
        Query query =  getSession().createQuery(queryString);
772
        query.setParameter("parentUuid", parentTerm.getUuid());
773

    
774
        @SuppressWarnings("unchecked")
775
        List<Object[]> result = query.list();
776

    
777
        List<TermDto> list = TermDto.termDtoListFrom(result);
778
        return list;
779
    }
780

    
781
    @Override
782
    public Collection<TermDto> findByTitleAsDtoWithVocDto(String title, TermType termType) {
783

    
784
        //terms
785
        String termQueryString = TermDto.getTermDtoSelect()
786
                + " where a.titleCache like :title "
787
                + (termType!=null?" and a.termType = :termType ":"");
788

    
789
        title = title.replace("*", "%");
790
        Query termQuery =  getSession().createQuery(termQueryString);
791
        termQuery.setParameter("title", "%"+title+"%");
792
        if(termType!=null){
793
            termQuery.setParameter("termType", termType);
794
        }
795

    
796
        @SuppressWarnings("unchecked")
797
        List<Object[]> termArrayResult = termQuery.list();
798
        List<TermDto> list = TermDto.termDtoListFrom(termArrayResult);
799

    
800
        //vocabularies
801
        String vocQueryString = TermCollectionDto.getTermCollectionDtoSelect() + " where a.uuid = :uuid";
802
        Query vocQuery = getSession().createQuery(vocQueryString);
803
        Map<UUID,TermVocabularyDto> vocMap = new HashMap<>();
804
        for (TermDto dto: list){
805
            UUID vocUuid = dto.getVocabularyUuid();
806
            TermVocabularyDto vocDto = vocMap.get(vocUuid);
807
            if (vocDto == null){
808
                vocQuery.setParameter("uuid", dto.getVocabularyUuid());
809
                @SuppressWarnings("unchecked")
810
                List<Object[]> vocArrayResult = vocQuery.list();
811
                List<TermVocabularyDto> vocs = TermVocabularyDto.termVocabularyDtoListFrom(vocArrayResult);
812
                if (!vocs.isEmpty()){
813
                    vocDto = vocs.get(0);
814
                    vocMap.put(vocUuid, vocs.get(0));
815
                }
816
            }
817
            dto.setVocabularyDto(vocDto);
818
        }
819

    
820
        return list;
821
    }
822

    
823
    @Override
824
    public TermDto findByUUIDAsDto(UUID uuid) {
825
        String queryString = TermDto.getTermDtoSelect()
826
                + " where a.uuid like :uuid ";
827

    
828

    
829
        Query query =  getSession().createQuery(queryString);
830
        query.setParameter("uuid", uuid);
831

    
832

    
833
        @SuppressWarnings("unchecked")
834
        List<Object[]> result = query.list();
835

    
836
        List<TermDto> list = TermDto.termDtoListFrom(result);
837
        if (list.size()== 1){
838
            return list.get(0);
839
        }else{
840
            return null;
841
        }
842

    
843
    }
844

    
845

    
846
    @Override
847
    public Collection<TermDto> findByTypeAsDto(TermType termType) {
848
        if (termType == null){
849
            return null;
850
        }
851
        String queryString = TermDto.getTermDtoSelect()
852
                + " where a.termType = :termType ";
853
        Query query =  getSession().createQuery(queryString);
854

    
855
        query.setParameter("termType", termType);
856

    
857
        @SuppressWarnings("unchecked")
858
        List<Object[]> result = query.list();
859

    
860
        List<TermDto> list = TermDto.termDtoListFrom(result);
861
        return list;
862
    }
863

    
864
    @Override
865
    public Collection<TermDto> findByUriAsDto(URI uri, String termLabel, TermType termType) {
866
        String queryString = TermDto.getTermDtoSelect()
867
                + " where a.uri like :uri "
868
                + (termType!=null?" and a.termType = :termType ":"")
869
                + (termLabel!=null?" and a.titleCache = :termLabel ":"")
870
                ;
871
        Query query =  getSession().createQuery(queryString);
872
        query.setParameter("uri", uri.toString());
873
        if(termLabel!=null){
874
            query.setParameter("termLabel", "%"+termLabel+"%");
875
        }
876
        if(termType!=null){
877
            query.setParameter("termType", termType);
878
        }
879

    
880
        @SuppressWarnings("unchecked")
881
        List<Object[]> result = query.list();
882

    
883
        List<TermDto> list = TermDto.termDtoListFrom(result);
884
        return list;
885
    }
886

    
887
    @Override
888
    public  Map<UUID, List<TermDto>> getSupportedStatesForFeature(Set<UUID> featureUuids){
889
        Map<UUID, List<TermDto>> map = new HashMap<>();
890
        for (UUID featureUuid: featureUuids){
891
            List<TermDto> list = new ArrayList<>();
892
            String supportedCategoriesQueryString = "SELECT cat.uuid "
893
                    + "from DefinedTermBase t "
894
                    + "join t.supportedCategoricalEnumerations as cat "
895
                    + "where t.uuid = :featureUuid";
896
            Query supportedCategoriesQuery =  getSession().createQuery(supportedCategoriesQueryString);
897
            supportedCategoriesQuery.setParameter("featureUuid", featureUuid);
898
            @SuppressWarnings("unchecked")
899
    		List<UUID> supportedCategories = supportedCategoriesQuery.list();
900
            if(supportedCategories.isEmpty()){
901
                map.put(featureUuid, list);
902
                continue;
903
            }
904

    
905
            String queryString = TermDto.getTermDtoSelect()
906
                    + "where v.uuid in (:supportedCategories) "
907
                    + "order by a.titleCache";
908
            Query query =  getSession().createQuery(queryString);
909
            query.setParameterList("supportedCategories", supportedCategories);
910

    
911
            @SuppressWarnings("unchecked")
912
            List<Object[]> result = query.list();
913

    
914
            list = TermDto.termDtoListFrom(result);
915
            map.put(featureUuid, list);
916
        }
917
        return map;
918
    }
919

    
920
    @Override
921
    public Collection<TermDto> findByUUIDsAsDto(List<UUID> uuidList) {
922
        List<TermDto> list = new ArrayList<>();
923
        if (uuidList == null || uuidList.isEmpty()){
924
            return null;
925
        }
926

    
927
        String queryString = TermDto.getTermDtoSelect()
928
                + "where a.uuid in :uuidList "
929
                + "order by a.titleCache";
930
        Query query =  getSession().createQuery(queryString);
931
        query.setParameterList("uuidList", uuidList);
932

    
933
        @SuppressWarnings("unchecked")
934
        List<Object[]> result = query.list();
935

    
936
        list = TermDto.termDtoListFrom(result);
937
        return list;
938
    }
939

    
940
    @Override
941
    public Collection<TermDto> findFeatureByUUIDsAsDto(List<UUID> uuidList) {
942
        List<TermDto> list = new ArrayList<>();
943
        if (uuidList == null || uuidList.isEmpty()){
944
            return null;
945
        }
946

    
947
        String queryString = FeatureDto.getTermDtoSelect()
948
                + "where a.uuid in :uuidList "
949
                + "order by a.titleCache";
950
        Query query =  getSession().createQuery(queryString);
951
        query.setParameterList("uuidList", uuidList);
952

    
953
        @SuppressWarnings("unchecked")
954
        List<Object[]> result = query.list();
955

    
956
        list = FeatureDto.termDtoListFrom(result);
957
        return list;
958
    }
959

    
960
    @Override
961
    public Collection<TermDto> findFeatureByTitleAsDto(String pattern) {
962
        String queryString = FeatureDto.getTermDtoSelect()
963
                + " where a.titleCache like :title "
964
                +  " and a.termType = :termType ";
965

    
966
        pattern = pattern.replace("*", "%");
967
        Query query =  getSession().createQuery(queryString);
968
        query.setParameter("title", "%"+pattern+"%");
969
        query.setParameter("termType", TermType.Feature);
970

    
971

    
972
        @SuppressWarnings("unchecked")
973
        List<Object[]> result = query.list();
974

    
975
        List<TermDto> list = FeatureDto.termDtoListFrom(result);
976
        return list;
977
    }
978

    
979
    @Override
980
    public TermDto getTermDto(UUID uuid) {
981
        String queryString = TermDto.getTermDtoSelect()
982
                + " where a.uuid = :uuid ";
983

    
984

    
985
        Query query =  getSession().createQuery(queryString);
986
        query.setParameter("uuid", uuid);
987

    
988

    
989

    
990
        @SuppressWarnings("unchecked")
991
        List<Object[]> result = query.list();
992
        TermDto dto = null;
993
        List<TermDto> dtoList = TermDto.termDtoListFrom(result);
994
        if (dtoList != null && !dtoList.isEmpty()){
995
            dto = dtoList.get(0);
996
        }
997
        return dto;
998
    }
999
}
(1-1/6)