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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.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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		}
258
		boolean isIso639_1 = iso639.length() == 2;
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		String queryStr;
261
		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();
267
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
268
		    Query query = getSession().createQuery(queryStr);
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		    query.setParameter("isoCode", iso639);
270
		    if (! isIso639_1){
271
		    	query.setParameter("vocUuid", Language.uuidLanguageVocabulary);
272
			}
273
		    return (Language) query.uniqueResult();
274
		} else {
275
			AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(Language.class,auditEvent.getRevisionNumber());
276
			if (isIso639_1){
277
				query.add(AuditEntity.property("iso639_1").eq(iso639));
278
			}else{
279
				query.add(AuditEntity.property("iso639_2").eq(iso639));
280
				query.add(AuditEntity.property("vocabulary.uuid").eq(Language.uuidLanguageVocabulary));
281
			}
282

    
283
			return (Language)query.getSingleResult();
284
		}
285
	}
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287
	/**
288
	 *  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)
290
	 */
291
	@Override
292
    public List<Language> getLanguagesByIso(List<String> iso639List) {
293
		List<Language> languages = new ArrayList<>(iso639List.size());
294
		for (String iso639 : iso639List) {
295
			languages.add(getLanguageByIso(iso639));
296
		}
297
		return languages;
298
	}
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300
	@Override
301
    public List<Language> getLanguagesByLocale(Enumeration<Locale> locales) {
302
		List<Language> languages = new ArrayList<>();
303
		while(locales.hasMoreElements()) {
304
			Locale locale = locales.nextElement();
305
			languages.add(getLanguageByIso(locale.getLanguage()));
306
		}
307
		return languages;
308
	}
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310
	@Override
311
    public long count(NamedAreaLevel level, NamedAreaType type) {
312
		AuditEvent auditEvent = getAuditEventFromContext();
313
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
314
		    Criteria criteria = getCriteria(NamedArea.class);
315

    
316
		    if(level != null) {
317
			    criteria.add(Restrictions.eq("level",level));
318
		    }
319

    
320
		    if(type != null) {
321
			    criteria.add(Restrictions.eq("type", type));
322
		    }
323

    
324
		    criteria.setProjection(Projections.rowCount());
325

    
326
	        return (Long)criteria.uniqueResult();
327
		} else {
328
			AuditQuery query = makeAuditQuery(NamedArea.class, auditEvent);
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330
			if(level != null) {
331
				query.add(AuditEntity.relatedId("level").eq(level.getId()));
332
		    }
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334
		    if(type != null) {
335
		    	query.add(AuditEntity.relatedId("type").eq(type.getId()));
336
		    }
337
		    query.addProjection(AuditEntity.id().count());
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		    return (Long)query.getSingleResult();
339
		}
340
	}
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342
	@Override
343
    public long countMedia(DefinedTermBase definedTerm) {
344
		checkNotInPriorView("DefinedTermDaoImpl.countMedia(DefinedTermBase definedTerm)");
345
		Query query = getSession().createQuery("select count(media) from DefinedTermBase definedTerm join definedTerm.media media where definedTerm = :definedTerm");
346
	    query.setParameter("definedTerm", definedTerm);
347

    
348
		return (Long)query.uniqueResult();
349
	}
350

    
351
	@Override
352
    public List<Media> getMedia(DefinedTermBase definedTerm, Integer pageSize,	Integer pageNumber) {
353
		checkNotInPriorView("DefinedTermDaoImpl.getMedia(DefinedTermBase definedTerm, Integer pageSize,	Integer pageNumber)");
354
		Query query = getSession().createQuery(
355
		           "SELECT media "
356
		        + " FROM DefinedTermBase definedTerm "
357
		        + " JOIN definedTerm.media media "
358
		        + " WHERE definedTerm = :definedTerm");
359
		query.setParameter("definedTerm", definedTerm);
360

    
361
		addPageSizeAndNumber(query, pageSize, pageNumber);
362

    
363
		@SuppressWarnings("unchecked")
364
        List<Media> result = query.list();
365
		return result;
366
	}
367

    
368
	@Override
369
    public List<NamedArea> list(NamedAreaLevel level, NamedAreaType type, Integer pageSize, Integer pageNumber) {
370
		AuditEvent auditEvent = getAuditEventFromContext();
371
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
372
            Criteria criteria = getCriteria(NamedArea.class);
373

    
374
		    if(level != null) {
375
			    criteria.add(Restrictions.eq("level",level));
376
		    }
377

    
378
		    if(type != null) {
379
			    criteria.add(Restrictions.eq("type", type));
380
		    }
381

    
382
		    addPageSizeAndNumber(criteria, pageSize, pageNumber);
383

    
384
	        @SuppressWarnings("unchecked")
385
	        List<NamedArea> result = deduplicateResult(criteria.list());
386
	        return result;
387
		} else {
388
            AuditQuery query = makeAuditQuery(NamedArea.class, auditEvent);
389

    
390
			if(level != null) {
391
				query.add(AuditEntity.relatedId("level").eq(level.getId()));
392
		    }
393

    
394
		    if(type != null) {
395
		    	query.add(AuditEntity.relatedId("type").eq(type.getId()));
396
		    }
397

    
398
		    @SuppressWarnings("unchecked")
399
            List<NamedArea> result = deduplicateResult(query.getResultList());
400
		    return result;
401
		}
402
	}
403

    
404
	@Override
405
    public List<NamedArea> list(NamedAreaLevel level, NamedAreaType type, Integer pageSize, Integer pageNumber,
406
			List<OrderHint> orderHints, List<String> propertyPaths) {
407

    
408
	    List<NamedArea> result;
409

    
410
		AuditEvent auditEvent = getAuditEventFromContext();
411
		if (auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
412
			Criteria criteria = getCriteria(NamedArea.class);
413

    
414
			if (level != null) {
415
				criteria.add(Restrictions.eq("level", level));
416
			}
417
			if (type != null) {
418
				criteria.add(Restrictions.eq("type", type));
419
			}
420
			addOrder(criteria,orderHints);
421
			addPageSizeAndNumber(criteria, pageSize, pageNumber);
422

    
423
			result = deduplicateResult(criteria.list());
424

    
425
		} else {
426
			AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(NamedArea.class,
427
				auditEvent.getRevisionNumber());
428
			if (level != null) {
429
				query.add(AuditEntity.relatedId("level").eq(level.getId()));
430
			}
431
			if (type != null) {
432
				query.add(AuditEntity.relatedId("type").eq(type.getId()));
433
			}
434
			result = deduplicateResult(query.getResultList());
435
		}
436

    
437
		defaultBeanInitializer.initializeAll(result, propertyPaths);
438

    
439
		return result;
440
	}
441

    
442

    
443
	@Override
444
    public <T extends DefinedTermBase> long countGeneralizationOf(T kindOf) {
445
		AuditEvent auditEvent = getAuditEventFromContext();
446
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
447
		    Query query = getSession().createQuery("select count(term) from DefinedTermBase term where term.kindOf = :kindOf");
448
		    query.setParameter("kindOf", kindOf);
449
		    return (Long)query.uniqueResult();
450
		} else {
451
            AuditQuery query = makeAuditQuery(DefinedTermBase.class,auditEvent);
452
			query.add(AuditEntity.relatedId("kindOf").eq(kindOf.getId()));
453
		    query.addProjection(AuditEntity.id().count());
454
		    return (Long)query.getSingleResult();
455
		}
456
	}
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458
	@Override
459
    public <T extends DefinedTermBase> long countIncludes(Collection<T> partOf) {
460
		if (partOf == null || partOf.isEmpty()){
461
			return 0;
462
		}
463
		AuditEvent auditEvent = getAuditEventFromContext();
464
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
465
    		Query query = getSession().createQuery("select count(term) from DefinedTermBase term where term.partOf in (:partOf)");
466
	    	query.setParameterList("partOf", partOf);
467
		    return (Long)query.uniqueResult();
468
		} else {
469
			long count = 0;
470
			for(T t : partOf) {
471
				AuditQuery query = makeAuditQuery(DefinedTermBase.class, auditEvent);
472
				query.add(AuditEntity.relatedId("partOf").eq(t.getId()));
473
			    query.addProjection(AuditEntity.id().count());
474
			    count += (Long)query.getSingleResult();
475
			}
476
			return count;
477
		}
478
	}
479

    
480
	@Override
481
    public <T extends DefinedTermBase> List<T> getGeneralizationOf(T kindOf, Integer pageSize, Integer pageNumber) {
482
		AuditEvent auditEvent = getAuditEventFromContext();
483
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
484
		    Query query = getSession().createQuery("select term from DefinedTermBase term where term.kindOf = :kindOf");
485
		    query.setParameter("kindOf", kindOf);
486

    
487
		    addPageSizeAndNumber(query, pageSize, pageNumber);
488

    
489
		    @SuppressWarnings("unchecked")
490
            List<T> result = deduplicateResult(query.list());
491
		    return result;
492
		} else {
493
			 AuditQuery query = makeAuditQuery(DefinedTermBase.class, auditEvent);
494
			 query.add(AuditEntity.relatedId("kindOf").eq(kindOf.getId()));
495

    
496
			 addPageSizeAndNumber(query, pageSize, pageNumber);
497

    
498
             @SuppressWarnings("unchecked")
499
             List<T> result = deduplicateResult(query.getResultList());
500
             return result;
501
		}
502
	}
503

    
504
	@Override
505
    public <T extends DefinedTermBase> List<T> getIncludes(Collection<T> partOf,	Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
506
		if (partOf == null || partOf.isEmpty()){
507
			return new ArrayList<>();
508
		}
509
		AuditEvent auditEvent = getAuditEventFromContext();
510
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
511
    		Query query = getSession().createQuery("select term from DefinedTermBase term where term.partOf in (:partOf)");
512
    		query.setParameterList("partOf", partOf);
513

    
514
    		addPageSizeAndNumber(query, pageSize, pageNumber);
515

    
516
		    @SuppressWarnings("unchecked")
517
            List<T> results = deduplicateResult(query.list());
518
		    defaultBeanInitializer.initializeAll(results, propertyPaths);
519
		    return results;
520
		} else {
521
			List<T> result = new ArrayList<>();
522
			for(T t : partOf) {
523
				AuditQuery query = makeAuditQuery(DefinedTermBase.class, auditEvent);
524
				query.add(AuditEntity.relatedId("partOf").eq(t.getId()));
525
				addPageSizeAndNumber(query, pageSize, pageNumber);
526

    
527
			    result.addAll(deduplicateResult(query.getResultList()));
528
			}
529
			defaultBeanInitializer.initializeAll(result, propertyPaths);
530
			return result;
531
		}
532
	}
533

    
534
	@Override
535
    public <T extends DefinedTermBase> long countPartOf(Set<T> definedTerms) {
536
		checkNotInPriorView("DefinedTermDaoImpl.countPartOf(Set<T> definedTerms)");
537
		Query query = getSession().createQuery("select count(distinct definedTerm) from DefinedTermBase definedTerm join definedTerm.includes included where included in (:definedTerms)");
538
		query.setParameterList("definedTerms", definedTerms);
539
		return (Long)query.uniqueResult();
540
	}
541

    
542
	@Override
543
    public <T extends DefinedTermBase> List<T> getPartOf(Set<T> definedTerms, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
544
		checkNotInPriorView("DefinedTermDaoImpl.getPartOf(Set<T> definedTerms, Integer pageSize, Integer pageNumber)");
545
		Query query = getSession().createQuery("select distinct definedTerm from DefinedTermBase definedTerm join definedTerm.includes included where included in (:definedTerms)");
546
		query.setParameterList("definedTerms", definedTerms);
547

    
548
		addPageSizeAndNumber(query, pageSize, pageNumber);
549

    
550
		@SuppressWarnings("unchecked")
551
        List<T> r = query.list();
552
		/**
553
		 * For some weird reason, hibernate returns proxies (extending the superclass), not the actual class on this,
554
		 * despite querying the damn database and returning the discriminator along with the rest of the object properties!
555
		 *
556
		 * Probably a bug in hibernate, but we'll manually deproxy for now since the objects are initialized anyway, the
557
		 * performance implications are small (we're swapping one array of references for another, not hitting the db or
558
		 * cache).
559
		 */
560
		List<T> results = new ArrayList<>();
561
		if(!definedTerms.isEmpty()) {
562
		    for(T t : r) {
563
		        T deproxied = CdmBase.deproxy(t);
564
                results.add(deproxied);
565
		    }
566
		    defaultBeanInitializer.initializeAll(results, propertyPaths);
567
		}
568
		return results;
569
	}
570

    
571
	@Override
572
    public DefinedTermBase findByUri(URI uri) {
573
		AuditEvent auditEvent = getAuditEventFromContext();
574
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
575
		    Query query = getSession().createQuery("select term from DefinedTermBase term where term.uri = :uri");
576
		    query.setParameter("uri", uri);
577
		    return (DefinedTermBase<?>)query.uniqueResult();
578
		} else {
579
			AuditQuery query = makeAuditQuery(DefinedTermBase.class, auditEvent);
580
			query.add(AuditEntity.property("uri").eq(uri));
581
		    return (DefinedTermBase<?>)query.getSingleResult();
582
		}
583
	}
584

    
585
	@Override
586
	public <T extends DefinedTermBase> List<T> listByTermType(TermType termType, Integer limit, Integer start,
587
	        List<OrderHint> orderHints, List<String> propertyPaths) {
588
	    Query query = getSession().createQuery("SELECT term FROM DefinedTermBase term WHERE term.termType = :termType");
589
	    query.setParameter("termType", termType);
590

    
591
	    @SuppressWarnings("unchecked")
592
        List<T> result = deduplicateResult(query.list());
593

    
594
	    defaultBeanInitializer.initializeAll(result, propertyPaths);
595
        return result;
596
	}
597

    
598
	@Override
599
    public <TERM extends DefinedTermBase> List<TERM> listByTermClass(Class<TERM> clazz, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
600
//		checkNotInPriorView("DefinedTermDaoImpl.listByTermClass(Class<TERM> clazz, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths)");
601

    
602
		Query query = getSession().createQuery("FROM " + clazz.getSimpleName());
603

    
604
	    @SuppressWarnings("unchecked")
605
        List<TERM> result = deduplicateResult(query.list());
606

    
607
	    defaultBeanInitializer.initializeAll(result, propertyPaths);
608

    
609
	    return result;
610
	}
611

    
612
    @Override
613
    public <S extends DefinedTermBase> List<S> list(Class<S> type, Integer limit, Integer start,
614
            List<OrderHint> orderHints, List<String> propertyPath) {
615

    
616
        return deduplicateResult(super.list(type, limit, start, orderHints, propertyPath));
617
    }
618

    
619
    /**
620
     * Workaround for https://dev.e-taxonomy.eu/redmine/issues/5871 and #5945
621
     * Terms with multiple representations return identical duplicates
622
     * due to eager representation loading. We expect these duplicates to appear
623
     * in line wo we only compare one term with its predecessor. If it already
624
     * exists we remove it from the result.
625
     * @param orginals
626
     * @return
627
     */
628
    protected static <S extends CdmBase> List<S> deduplicateResult(List<S> orginals) {
629
        List<S> result = new ArrayList<>();
630
        Iterator<S> it = orginals.iterator();
631
        S last = null;
632
        while (it.hasNext()){
633
            S a = it.next();
634
            if (a != last){
635
                if (!result.contains(a)){
636
                    result.add(a);
637
                }
638
            }
639
            last = a;
640
        }
641
        return result;
642
    }
643

    
644
    @Override
645
    public <S extends DefinedTermBase> List<S> list(Class<S> clazz, List<TermVocabulary> vocs, Integer limit, String pattern) {
646
        return list(clazz, vocs, 0, limit, pattern, MatchMode.BEGINNING);
647
    }
648

    
649
    @Override
650
    public <S extends DefinedTermBase> List<S> list(Class<S> clazz, List<TermVocabulary> vocs, Integer pageNumber, Integer limit, String pattern, MatchMode matchmode){
651
        Session session = getSession();
652
        if (clazz == null){
653
            clazz = (Class)type;
654
        }
655
        Criteria crit = getSession().createCriteria(clazz, "term");
656
        if (!StringUtils.isBlank(pattern)){
657
            crit.createAlias("term.representations", "reps");
658
            Disjunction or = Restrictions.disjunction();
659
            if (matchmode == MatchMode.EXACT) {
660
                or.add(Restrictions.eq("titleCache", matchmode.queryStringFrom(pattern)));
661
                or.add(Restrictions.eq("reps.label", matchmode.queryStringFrom(pattern)));
662
            } else {
663
                or.add(Restrictions.like("titleCache", matchmode.queryStringFrom(pattern)));
664
                or.add(Restrictions.like("reps.label", matchmode.queryStringFrom(pattern)));
665
            }
666
            crit.add(or);
667
        }
668

    
669
        if (limit != null && limit >= 0) {
670
            crit.setMaxResults(limit);
671
        }
672

    
673
        if (vocs != null &&!vocs.isEmpty()){
674
            crit.createAlias("term.vocabulary", "voc");
675
            Disjunction or = Restrictions.disjunction();
676
            for (TermVocabulary<?> voc: vocs){
677
                Criterion criterion = Restrictions.eq("voc.id", voc.getId());
678
                or.add(criterion);
679
            }
680
            crit.add(or);
681
        }
682

    
683
        crit.addOrder(Order.asc("titleCache"));
684
        if (limit == null){
685
            limit = 1;
686
        }
687
        crit.setFirstResult(0);
688
        @SuppressWarnings("unchecked")
689
        List<S> results = deduplicateResult(crit.list());
690
        return results;
691
    }
692

    
693
    @Override
694
    public <S extends DefinedTermBase> List<S> listByAbbrev(Class<S> clazz, List<TermVocabulary> vocs, Integer limit, String pattern, TermSearchField type) {
695
        return listByAbbrev(clazz, vocs, 0, limit, pattern, MatchMode.BEGINNING, type);
696
    }
697

    
698
    @Override
699
    public <S extends DefinedTermBase> List<S> listByAbbrev(Class<S> clazz, List<TermVocabulary> vocs, Integer pageNumber, Integer limit, String pattern, MatchMode matchmode, TermSearchField abbrevType){
700

    
701
        if (clazz == null){
702
            clazz = (Class)type;
703
        }
704
        Criteria crit = getSession().createCriteria(clazz, "type");
705
        if (!StringUtils.isBlank(pattern)){
706
            if (matchmode == MatchMode.EXACT) {
707
                crit.add(Restrictions.eq(abbrevType.getKey(), matchmode.queryStringFrom(pattern)));
708
            } else {
709
                crit.add(Restrictions.like(abbrevType.getKey(), matchmode.queryStringFrom(pattern)));
710
            }
711
        }
712
        if (limit != null && limit >= 0) {
713
            crit.setMaxResults(limit);
714
        }
715

    
716
        if (vocs != null &&!vocs.isEmpty()){
717
            crit.createAlias("type.vocabulary", "voc");
718
            Disjunction or = Restrictions.disjunction();
719
            for (TermVocabulary<?> voc: vocs){
720
                Criterion criterion = Restrictions.eq("voc.id", voc.getId());
721
                or.add(criterion);
722
            }
723
            crit.add(or);
724
        }
725

    
726
        crit.addOrder(Order.asc(abbrevType.getKey()));
727
        if (limit == null){
728
            limit = 1;
729
        }
730
//        int firstItem = (pageNumber - 1) * limit;
731

    
732
        crit.setFirstResult(0);
733
        @SuppressWarnings("unchecked")
734
        List<S> results = deduplicateResult(crit.list());
735
        return results;
736
    }
737

    
738

    
739
    @Override
740
    public Collection<TermDto> getIncludesAsDto(
741
            TermDto parentTerm) {
742
        String queryString;
743
        if (parentTerm.getTermType().equals(TermType.NamedArea)){
744
            queryString = TermDto.getTermDtoSelectNamedArea();
745
        }else{
746
            queryString = TermDto.getTermDtoSelect();
747
        }
748
        queryString = queryString
749
                + "where a.partOf.uuid = :parentUuid";
750
        Query query =  getSession().createQuery(queryString);
751
        query.setParameter("parentUuid", parentTerm.getUuid());
752

    
753
        @SuppressWarnings("unchecked")
754
        List<Object[]> result = query.list();
755

    
756
        List<TermDto> list = TermDto.termDtoListFrom(result);
757
        return list;
758
    }
759

    
760
    @Override
761
    public Collection<TermDto> getKindOfsAsDto(TermDto parentTerm) {
762

    
763
        String queryString;
764
        if (parentTerm.getTermType().equals(TermType.NamedArea)){
765
            queryString = TermDto.getTermDtoSelectNamedArea();
766
        }else{
767
            queryString = TermDto.getTermDtoSelect();
768
        }
769
        queryString = queryString + "where a.kindOf.uuid = :parentUuid";
770
        Query query =  getSession().createQuery(queryString);
771
        query.setParameter("parentUuid", parentTerm.getUuid());
772

    
773
        @SuppressWarnings("unchecked")
774
        List<Object[]> result = query.list();
775

    
776
        List<TermDto> list = TermDto.termDtoListFrom(result);
777
        return list;
778
    }
779

    
780
    @Override
781
    public Collection<TermDto> findByTitleAsDtoWithVocDto(String title, TermType termType) {
782
        String queryString = TermDto.getTermDtoSelect()
783
                + " where a.titleCache like :title "
784
                + (termType!=null?" and a.termType = :termType ":"");
785

    
786
        title = title.replace("*", "%");
787
        Query query =  getSession().createQuery(queryString);
788
        query.setParameter("title", "%"+title+"%");
789
        if(termType!=null){
790
            query.setParameter("termType", termType);
791
        }
792

    
793
        @SuppressWarnings("unchecked")
794
        List<Object[]> result = query.list();
795

    
796
        List<TermDto> list = TermDto.termDtoListFrom(result);
797
        queryString = TermVocabularyDto.getTermCollectionDtoSelect() + " where a.uuid = :uuid";
798

    
799
        query = getSession().createQuery(queryString);
800
        for (TermDto dto: list){
801
            query.setParameter("uuid", dto.getVocabularyUuid());
802
            result = query.list();
803
            List<TermVocabularyDto> vocs = TermVocabularyDto.termVocabularyDtoListFrom(result);
804
            if (!vocs.isEmpty()){
805
                dto.setVocabularyDto(vocs.get(0));
806
            }
807
        }
808

    
809
        return list;
810
    }
811

    
812
    @Override
813
    public TermDto findByUUIDAsDto(UUID uuid) {
814
        String queryString = TermDto.getTermDtoSelect()
815
                + " where a.uuid like :uuid ";
816

    
817

    
818
        Query query =  getSession().createQuery(queryString);
819
        query.setParameter("uuid", uuid);
820

    
821

    
822
        @SuppressWarnings("unchecked")
823
        List<Object[]> result = query.list();
824

    
825
        List<TermDto> list = TermDto.termDtoListFrom(result);
826
        if (list.size()== 1){
827
            return list.get(0);
828
        }else{
829
            return null;
830
        }
831

    
832
    }
833

    
834

    
835
    @Override
836
    public Collection<TermDto> findByTypeAsDto(TermType termType) {
837
        if (termType == null){
838
            return null;
839
        }
840
        String queryString = TermDto.getTermDtoSelect()
841
                + " where a.termType = :termType ";
842
        Query query =  getSession().createQuery(queryString);
843

    
844
        query.setParameter("termType", termType);
845

    
846
        @SuppressWarnings("unchecked")
847
        List<Object[]> result = query.list();
848

    
849
        List<TermDto> list = TermDto.termDtoListFrom(result);
850
        return list;
851
    }
852

    
853
    @Override
854
    public Collection<TermDto> findByUriAsDto(URI uri, String termLabel, TermType termType) {
855
        String queryString = TermDto.getTermDtoSelect()
856
                + " where a.uri like :uri "
857
                + (termType!=null?" and a.termType = :termType ":"")
858
                + (termLabel!=null?" and a.titleCache = :termLabel ":"")
859
                ;
860
        Query query =  getSession().createQuery(queryString);
861
        query.setParameter("uri", uri.toString());
862
        if(termLabel!=null){
863
            query.setParameter("termLabel", "%"+termLabel+"%");
864
        }
865
        if(termType!=null){
866
            query.setParameter("termType", termType);
867
        }
868

    
869
        @SuppressWarnings("unchecked")
870
        List<Object[]> result = query.list();
871

    
872
        List<TermDto> list = TermDto.termDtoListFrom(result);
873
        return list;
874
    }
875

    
876
    @Override
877
    public  Map<UUID, List<TermDto>> getSupportedStatesForFeature(Set<UUID> featureUuids){
878
        Map<UUID, List<TermDto>> map = new HashMap<>();
879
        for (UUID featureUuid: featureUuids){
880
            List<TermDto> list = new ArrayList<>();
881
            String supportedCategoriesQueryString = "SELECT cat.uuid "
882
                    + "from DefinedTermBase t "
883
                    + "join t.supportedCategoricalEnumerations as cat "
884
                    + "where t.uuid = :featureUuid";
885
            Query supportedCategoriesQuery =  getSession().createQuery(supportedCategoriesQueryString);
886
            supportedCategoriesQuery.setParameter("featureUuid", featureUuid);
887
            @SuppressWarnings("unchecked")
888
    		List<UUID> supportedCategories = supportedCategoriesQuery.list();
889
            if(supportedCategories.isEmpty()){
890
                map.put(featureUuid, list);
891
                continue;
892
            }
893

    
894
            String queryString = TermDto.getTermDtoSelect()
895
                    + "where v.uuid in (:supportedCategories) "
896
                    + "order by a.titleCache";
897
            Query query =  getSession().createQuery(queryString);
898
            query.setParameterList("supportedCategories", supportedCategories);
899

    
900
            @SuppressWarnings("unchecked")
901
            List<Object[]> result = query.list();
902

    
903
            list = TermDto.termDtoListFrom(result);
904
            map.put(featureUuid, list);
905
        }
906
        return map;
907
    }
908

    
909
    @Override
910
    public Collection<TermDto> findByUUIDsAsDto(List<UUID> uuidList) {
911
        List<TermDto> list = new ArrayList<>();
912
        if (uuidList == null || uuidList.isEmpty()){
913
            return null;
914
        }
915

    
916
        String queryString = TermDto.getTermDtoSelect()
917
                + "where a.uuid in :uuidList "
918
                + "order by a.titleCache";
919
        Query query =  getSession().createQuery(queryString);
920
        query.setParameterList("uuidList", uuidList);
921

    
922
        @SuppressWarnings("unchecked")
923
        List<Object[]> result = query.list();
924

    
925
        list = TermDto.termDtoListFrom(result);
926
        return list;
927
    }
928

    
929
    @Override
930
    public Collection<TermDto> findFeatureByUUIDsAsDto(List<UUID> uuidList) {
931
        List<TermDto> list = new ArrayList<>();
932
        if (uuidList == null || uuidList.isEmpty()){
933
            return null;
934
        }
935

    
936
        String queryString = FeatureDto.getTermDtoSelect()
937
                + "where a.uuid in :uuidList "
938
                + "order by a.titleCache";
939
        Query query =  getSession().createQuery(queryString);
940
        query.setParameterList("uuidList", uuidList);
941

    
942
        @SuppressWarnings("unchecked")
943
        List<Object[]> result = query.list();
944

    
945
        list = FeatureDto.termDtoListFrom(result);
946
        return list;
947
    }
948

    
949
    @Override
950
    public Collection<TermDto> findFeatureByTitleAsDto(String pattern) {
951
        String queryString = FeatureDto.getTermDtoSelect()
952
                + " where a.titleCache like :title "
953
                +  " and a.termType = :termType ";
954

    
955
        pattern = pattern.replace("*", "%");
956
        Query query =  getSession().createQuery(queryString);
957
        query.setParameter("title", "%"+pattern+"%");
958
        query.setParameter("termType", TermType.Feature);
959

    
960

    
961
        @SuppressWarnings("unchecked")
962
        List<Object[]> result = query.list();
963

    
964
        List<TermDto> list = FeatureDto.termDtoListFrom(result);
965
        return list;
966
    }
967

    
968
    @Override
969
    public TermDto getTermDto(UUID uuid) {
970
        String queryString = TermDto.getTermDtoSelect()
971
                + " where a.uuid = :uuid ";
972

    
973

    
974
        Query query =  getSession().createQuery(queryString);
975
        query.setParameter("uuid", uuid);
976

    
977

    
978

    
979
        @SuppressWarnings("unchecked")
980
        List<Object[]> result = query.list();
981
        TermDto dto = null;
982
        List<TermDto> dtoList = TermDto.termDtoListFrom(result);
983
        if (dtoList != null && !dtoList.isEmpty()){
984
            dto = dtoList.get(0);
985
        }
986
        return dto;
987
    }
988
}
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