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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.dao.DataAccessException;
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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.common.Restriction;
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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;
264
		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();
270
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
271
		    Query query = getSession().createQuery(queryStr);
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		    query.setParameter("isoCode", iso639);
273
		    if (! isIso639_1){
274
		    	query.setParameter("vocUuid", Language.uuidLanguageVocabulary);
275
			}
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		    return (Language) query.uniqueResult();
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		} else {
278
			AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(Language.class,auditEvent.getRevisionNumber());
279
			if (isIso639_1){
280
				query.add(AuditEntity.property("iso639_1").eq(iso639));
281
			}else{
282
				query.add(AuditEntity.property("iso639_2").eq(iso639));
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				query.add(AuditEntity.property("vocabulary.uuid").eq(Language.uuidLanguageVocabulary));
284
			}
285

    
286
			return (Language)query.getSingleResult();
287
		}
288
	}
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290
	/**
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	 *  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)
293
	 */
294
	@Override
295
    public List<Language> getLanguagesByIso(List<String> iso639List) {
296
		List<Language> languages = new ArrayList<>(iso639List.size());
297
		for (String iso639 : iso639List) {
298
			languages.add(getLanguageByIso(iso639));
299
		}
300
		return languages;
301
	}
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303
	@Override
304
    public List<Language> getLanguagesByLocale(Enumeration<Locale> locales) {
305
		List<Language> languages = new ArrayList<>();
306
		while(locales.hasMoreElements()) {
307
			Locale locale = locales.nextElement();
308
			languages.add(getLanguageByIso(locale.getLanguage()));
309
		}
310
		return languages;
311
	}
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313
	@Override
314
    public long count(NamedAreaLevel level, NamedAreaType type) {
315
		AuditEvent auditEvent = getAuditEventFromContext();
316
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
317
		    Criteria criteria = getCriteria(NamedArea.class);
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319
		    if(level != null) {
320
			    criteria.add(Restrictions.eq("level",level));
321
		    }
322

    
323
		    if(type != null) {
324
			    criteria.add(Restrictions.eq("type", type));
325
		    }
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327
		    criteria.setProjection(Projections.rowCount());
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329
	        return (Long)criteria.uniqueResult();
330
		} else {
331
			AuditQuery query = makeAuditQuery(NamedArea.class, auditEvent);
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333
			if(level != null) {
334
				query.add(AuditEntity.relatedId("level").eq(level.getId()));
335
		    }
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337
		    if(type != null) {
338
		    	query.add(AuditEntity.relatedId("type").eq(type.getId()));
339
		    }
340
		    query.addProjection(AuditEntity.id().count());
341
		    return (Long)query.getSingleResult();
342
		}
343
	}
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345
	@Override
346
    public long countMedia(DefinedTermBase definedTerm) {
347
		checkNotInPriorView("DefinedTermDaoImpl.countMedia(DefinedTermBase definedTerm)");
348
		Query query = getSession().createQuery("select count(media) from DefinedTermBase definedTerm join definedTerm.media media where definedTerm = :definedTerm");
349
	    query.setParameter("definedTerm", definedTerm);
350

    
351
		return (Long)query.uniqueResult();
352
	}
353

    
354
	@Override
355
    public List<Media> getMedia(DefinedTermBase definedTerm, Integer pageSize,	Integer pageNumber) {
356
		checkNotInPriorView("DefinedTermDaoImpl.getMedia(DefinedTermBase definedTerm, Integer pageSize,	Integer pageNumber)");
357
		Query query = getSession().createQuery(
358
		           "SELECT media "
359
		        + " FROM DefinedTermBase definedTerm "
360
		        + " JOIN definedTerm.media media "
361
		        + " WHERE definedTerm = :definedTerm");
362
		query.setParameter("definedTerm", definedTerm);
363

    
364
		addPageSizeAndNumber(query, pageSize, pageNumber);
365

    
366
		@SuppressWarnings("unchecked")
367
        List<Media> result = query.list();
368
		return result;
369
	}
370

    
371
	@Override
372
    public List<NamedArea> list(NamedAreaLevel level, NamedAreaType type, Integer pageSize, Integer pageNumber) {
373
		AuditEvent auditEvent = getAuditEventFromContext();
374
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
375
            Criteria criteria = getCriteria(NamedArea.class);
376

    
377
		    if(level != null) {
378
			    criteria.add(Restrictions.eq("level",level));
379
		    }
380

    
381
		    if(type != null) {
382
			    criteria.add(Restrictions.eq("type", type));
383
		    }
384

    
385
		    addPageSizeAndNumber(criteria, pageSize, pageNumber);
386

    
387
	        @SuppressWarnings("unchecked")
388
	        List<NamedArea> result = deduplicateResult(criteria.list());
389
	        return result;
390
		} else {
391
            AuditQuery query = makeAuditQuery(NamedArea.class, auditEvent);
392

    
393
			if(level != null) {
394
				query.add(AuditEntity.relatedId("level").eq(level.getId()));
395
		    }
396

    
397
		    if(type != null) {
398
		    	query.add(AuditEntity.relatedId("type").eq(type.getId()));
399
		    }
400

    
401
		    @SuppressWarnings("unchecked")
402
            List<NamedArea> result = deduplicateResult(query.getResultList());
403
		    return result;
404
		}
405
	}
406

    
407
	@Override
408
    public List<NamedArea> list(NamedAreaLevel level, NamedAreaType type, Integer pageSize, Integer pageNumber,
409
			List<OrderHint> orderHints, List<String> propertyPaths) {
410

    
411
	    List<NamedArea> result;
412

    
413
		AuditEvent auditEvent = getAuditEventFromContext();
414
		if (auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
415
			Criteria criteria = getCriteria(NamedArea.class);
416

    
417
			if (level != null) {
418
				criteria.add(Restrictions.eq("level", level));
419
			}
420
			if (type != null) {
421
				criteria.add(Restrictions.eq("type", type));
422
			}
423
			addOrder(criteria,orderHints);
424
			addPageSizeAndNumber(criteria, pageSize, pageNumber);
425

    
426
			result = deduplicateResult(criteria.list());
427

    
428
		} else {
429
			AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(NamedArea.class,
430
				auditEvent.getRevisionNumber());
431
			if (level != null) {
432
				query.add(AuditEntity.relatedId("level").eq(level.getId()));
433
			}
434
			if (type != null) {
435
				query.add(AuditEntity.relatedId("type").eq(type.getId()));
436
			}
437
			result = deduplicateResult(query.getResultList());
438
		}
439

    
440
		defaultBeanInitializer.initializeAll(result, propertyPaths);
441

    
442
		return result;
443
	}
444

    
445

    
446
	@Override
447
    public <T extends DefinedTermBase> long countGeneralizationOf(T kindOf) {
448
		AuditEvent auditEvent = getAuditEventFromContext();
449
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
450
		    Query query = getSession().createQuery("select count(term) from DefinedTermBase term where term.kindOf = :kindOf");
451
		    query.setParameter("kindOf", kindOf);
452
		    return (Long)query.uniqueResult();
453
		} else {
454
            AuditQuery query = makeAuditQuery(DefinedTermBase.class,auditEvent);
455
			query.add(AuditEntity.relatedId("kindOf").eq(kindOf.getId()));
456
		    query.addProjection(AuditEntity.id().count());
457
		    return (Long)query.getSingleResult();
458
		}
459
	}
460

    
461
	@Override
462
    public <T extends DefinedTermBase> long countIncludes(Collection<T> partOf) {
463
		if (partOf == null || partOf.isEmpty()){
464
			return 0;
465
		}
466
		AuditEvent auditEvent = getAuditEventFromContext();
467
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
468
    		Query query = getSession().createQuery("select count(term) from DefinedTermBase term where term.partOf in (:partOf)");
469
	    	query.setParameterList("partOf", partOf);
470
		    return (Long)query.uniqueResult();
471
		} else {
472
			long count = 0;
473
			for(T t : partOf) {
474
				AuditQuery query = makeAuditQuery(DefinedTermBase.class, auditEvent);
475
				query.add(AuditEntity.relatedId("partOf").eq(t.getId()));
476
			    query.addProjection(AuditEntity.id().count());
477
			    count += (Long)query.getSingleResult();
478
			}
479
			return count;
480
		}
481
	}
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483
	@Override
484
    public <T extends DefinedTermBase> List<T> getGeneralizationOf(T kindOf, Integer pageSize, Integer pageNumber) {
485
		AuditEvent auditEvent = getAuditEventFromContext();
486
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
487
		    Query query = getSession().createQuery("select term from DefinedTermBase term where term.kindOf = :kindOf");
488
		    query.setParameter("kindOf", kindOf);
489

    
490
		    addPageSizeAndNumber(query, pageSize, pageNumber);
491

    
492
		    @SuppressWarnings("unchecked")
493
            List<T> result = deduplicateResult(query.list());
494
		    return result;
495
		} else {
496
			 AuditQuery query = makeAuditQuery(DefinedTermBase.class, auditEvent);
497
			 query.add(AuditEntity.relatedId("kindOf").eq(kindOf.getId()));
498

    
499
			 addPageSizeAndNumber(query, pageSize, pageNumber);
500

    
501
             @SuppressWarnings("unchecked")
502
             List<T> result = deduplicateResult(query.getResultList());
503
             return result;
504
		}
505
	}
506

    
507
	@Override
508
    public <T extends DefinedTermBase> List<T> getIncludes(Collection<T> partOf,	Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
509
		if (partOf == null || partOf.isEmpty()){
510
			return new ArrayList<>();
511
		}
512
		AuditEvent auditEvent = getAuditEventFromContext();
513
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
514
    		Query query = getSession().createQuery("select term from DefinedTermBase term where term.partOf in (:partOf)");
515
    		query.setParameterList("partOf", partOf);
516

    
517
    		addPageSizeAndNumber(query, pageSize, pageNumber);
518

    
519
		    @SuppressWarnings("unchecked")
520
            List<T> results = deduplicateResult(query.list());
521
		    defaultBeanInitializer.initializeAll(results, propertyPaths);
522
		    return results;
523
		} else {
524
			List<T> result = new ArrayList<>();
525
			for(T t : partOf) {
526
				AuditQuery query = makeAuditQuery(DefinedTermBase.class, auditEvent);
527
				query.add(AuditEntity.relatedId("partOf").eq(t.getId()));
528
				addPageSizeAndNumber(query, pageSize, pageNumber);
529

    
530
			    result.addAll(deduplicateResult(query.getResultList()));
531
			}
532
			defaultBeanInitializer.initializeAll(result, propertyPaths);
533
			return result;
534
		}
535
	}
536

    
537
	@Override
538
    public <T extends DefinedTermBase> long countPartOf(Set<T> definedTerms) {
539
		checkNotInPriorView("DefinedTermDaoImpl.countPartOf(Set<T> definedTerms)");
540
		Query query = getSession().createQuery("select count(distinct definedTerm) from DefinedTermBase definedTerm join definedTerm.includes included where included in (:definedTerms)");
541
		query.setParameterList("definedTerms", definedTerms);
542
		return (Long)query.uniqueResult();
543
	}
544

    
545
	@Override
546
    public <T extends DefinedTermBase> List<T> getPartOf(Set<T> definedTerms, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
547
		checkNotInPriorView("DefinedTermDaoImpl.getPartOf(Set<T> definedTerms, Integer pageSize, Integer pageNumber)");
548
		Query query = getSession().createQuery("select distinct definedTerm from DefinedTermBase definedTerm join definedTerm.includes included where included in (:definedTerms)");
549
		query.setParameterList("definedTerms", definedTerms);
550

    
551
		addPageSizeAndNumber(query, pageSize, pageNumber);
552

    
553
		@SuppressWarnings("unchecked")
554
        List<T> r = query.list();
555
		/**
556
		 * For some weird reason, hibernate returns proxies (extending the superclass), not the actual class on this,
557
		 * despite querying the damn database and returning the discriminator along with the rest of the object properties!
558
		 *
559
		 * Probably a bug in hibernate, but we'll manually deproxy for now since the objects are initialized anyway, the
560
		 * performance implications are small (we're swapping one array of references for another, not hitting the db or
561
		 * cache).
562
		 */
563
		List<T> results = new ArrayList<>();
564
		if(!definedTerms.isEmpty()) {
565
		    for(T t : r) {
566
		        T deproxied = CdmBase.deproxy(t);
567
                results.add(deproxied);
568
		    }
569
		    defaultBeanInitializer.initializeAll(results, propertyPaths);
570
		}
571
		return results;
572
	}
573

    
574
	@Override
575
    public DefinedTermBase findByUri(URI uri) {
576
		AuditEvent auditEvent = getAuditEventFromContext();
577
		if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
578
		    Query query = getSession().createQuery("select term from DefinedTermBase term where term.uri = :uri");
579
		    query.setParameter("uri", uri);
580
		    return (DefinedTermBase<?>)query.uniqueResult();
581
		} else {
582
			AuditQuery query = makeAuditQuery(DefinedTermBase.class, auditEvent);
583
			query.add(AuditEntity.property("uri").eq(uri));
584
		    return (DefinedTermBase<?>)query.getSingleResult();
585
		}
586
	}
587

    
588
	@Override
589
	public <T extends DefinedTermBase> List<T> listByTermType(TermType termType, Integer limit, Integer start,
590
	        List<OrderHint> orderHints, List<String> propertyPaths) {
591
	    Query query = getSession().createQuery("SELECT term FROM DefinedTermBase term WHERE term.termType = :termType");
592
	    query.setParameter("termType", termType);
593

    
594
	    @SuppressWarnings("unchecked")
595
        List<T> result = deduplicateResult(query.list());
596

    
597
	    defaultBeanInitializer.initializeAll(result, propertyPaths);
598
        return result;
599
	}
600

    
601
	@Override
602
    public <TERM extends DefinedTermBase> List<TERM> listByTermClass(Class<TERM> clazz, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
603
//		checkNotInPriorView("DefinedTermDaoImpl.listByTermClass(Class<TERM> clazz, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths)");
604

    
605
		Query query = getSession().createQuery("FROM " + clazz.getSimpleName());
606

    
607
	    @SuppressWarnings("unchecked")
608
        List<TERM> result = deduplicateResult(query.list());
609

    
610
	    defaultBeanInitializer.initializeAll(result, propertyPaths);
611

    
612
	    return result;
613
	}
614

    
615
    @Override
616
    public <S extends DefinedTermBase> List<S> list(Class<S> type, Integer limit, Integer start,
617
            List<OrderHint> orderHints, List<String> propertyPath) {
618

    
619
        return deduplicateResult(super.list(type, limit, start, orderHints, propertyPath));
620
    }
621

    
622
    /**
623
     * Workaround for https://dev.e-taxonomy.eu/redmine/issues/5871 and #5945
624
     * Terms with multiple representations return identical duplicates
625
     * due to eager representation loading. We expect these duplicates to appear
626
     * in line wo we only compare one term with its predecessor. If it already
627
     * exists we remove it from the result.
628
     * @param orginals
629
     * @return
630
     */
631
    protected static <S extends CdmBase> List<S> deduplicateResult(List<S> orginals) {
632
        List<S> result = new ArrayList<>();
633
        Iterator<S> it = orginals.iterator();
634
        S last = null;
635
        while (it.hasNext()){
636
            S a = it.next();
637
            if (a != last){
638
                //AM: why is this necessary?
639
                if (!result.contains(a)){
640
                    result.add(a);
641
                }
642
            }
643
            last = a;
644
        }
645
        return result;
646
    }
647

    
648
    @Override
649
    public <S extends DefinedTermBase> List<S> list(Class<S> clazz, List<TermVocabulary> vocs, Integer limit, String pattern) {
650
        return list(clazz, vocs, 0, limit, pattern, MatchMode.BEGINNING);
651
    }
652

    
653
    @Override
654
    public <S extends DefinedTermBase> List<S> list(Class<S> clazz, List<TermVocabulary> vocs, Integer pageNumber, Integer limit, String pattern, MatchMode matchmode){
655
        if (clazz == null){
656
            clazz = (Class)type;
657
        }
658
        Criteria crit = getSession().createCriteria(clazz, "term");
659
        if (!StringUtils.isBlank(pattern)){
660
            crit.createAlias("term.representations", "reps");
661
            Disjunction or = Restrictions.disjunction();
662
            if (matchmode == MatchMode.EXACT) {
663
                or.add(Restrictions.eq("titleCache", matchmode.queryStringFrom(pattern)));
664
                or.add(Restrictions.eq("reps.label", matchmode.queryStringFrom(pattern)));
665
            } else {
666
                or.add(Restrictions.like("titleCache", matchmode.queryStringFrom(pattern)));
667
                or.add(Restrictions.like("reps.label", matchmode.queryStringFrom(pattern)));
668
            }
669
            crit.add(or);
670
        }
671

    
672
        if (limit != null && limit >= 0) {
673
            crit.setMaxResults(limit);
674
        }
675

    
676
        if (vocs != null &&!vocs.isEmpty()){
677
            crit.createAlias("term.vocabulary", "voc");
678
            Disjunction or = Restrictions.disjunction();
679
            for (TermVocabulary<?> voc: vocs){
680
                Criterion criterion = Restrictions.eq("voc.id", voc.getId());
681
                or.add(criterion);
682
            }
683
            crit.add(or);
684
        }
685

    
686
        crit.addOrder(Order.asc("titleCache"));
687
        if (limit == null){
688
            limit = 1;
689
        }
690
        crit.setFirstResult(0);
691
        @SuppressWarnings("unchecked")
692
        List<S> results = deduplicateResult(crit.list());
693
        return results;
694
    }
695

    
696
    @Override
697
    public <S extends DefinedTermBase> List<S> listByAbbrev(Class<S> clazz, List<TermVocabulary> vocs, Integer limit, String pattern, TermSearchField type) {
698
        return listByAbbrev(clazz, vocs, 0, limit, pattern, MatchMode.BEGINNING, type);
699
    }
700

    
701
    @Override
702
    public <S extends DefinedTermBase> List<S> listByAbbrev(Class<S> clazz, List<TermVocabulary> vocs, Integer pageNumber, Integer limit, String pattern, MatchMode matchmode, TermSearchField abbrevType){
703

    
704
        if (clazz == null){
705
            clazz = (Class)type;
706
        }
707
        Criteria crit = getSession().createCriteria(clazz, "type");
708
        if (!StringUtils.isBlank(pattern)){
709
            if (matchmode == MatchMode.EXACT) {
710
                crit.add(Restrictions.eq(abbrevType.getKey(), matchmode.queryStringFrom(pattern)));
711
            } else {
712
                crit.add(Restrictions.like(abbrevType.getKey(), matchmode.queryStringFrom(pattern)));
713
            }
714
        }
715
        if (limit != null && limit >= 0) {
716
            crit.setMaxResults(limit);
717
        }
718

    
719
        if (vocs != null &&!vocs.isEmpty()){
720
            crit.createAlias("type.vocabulary", "voc");
721
            Disjunction or = Restrictions.disjunction();
722
            for (TermVocabulary<?> voc: vocs){
723
                Criterion criterion = Restrictions.eq("voc.id", voc.getId());
724
                or.add(criterion);
725
            }
726
            crit.add(or);
727
        }
728

    
729
        crit.addOrder(Order.asc(abbrevType.getKey()));
730
        if (limit == null){
731
            limit = 1;
732
        }
733
//        int firstItem = (pageNumber - 1) * limit;
734

    
735
        crit.setFirstResult(0);
736
        @SuppressWarnings("unchecked")
737
        List<S> results = deduplicateResult(crit.list());
738
        return results;
739
    }
740

    
741

    
742
    @Override
743
    public Collection<TermDto> getIncludesAsDto(
744
            TermDto parentTerm) {
745
        String queryString;
746
        if (parentTerm.getTermType().equals(TermType.NamedArea)){
747
            queryString = TermDto.getTermDtoSelectNamedArea();
748
        }else{
749
            queryString = TermDto.getTermDtoSelect();
750
        }
751
        queryString = queryString
752
                + "where a.partOf.uuid = :parentUuid";
753
        Query query =  getSession().createQuery(queryString);
754
        query.setParameter("parentUuid", parentTerm.getUuid());
755

    
756
        @SuppressWarnings("unchecked")
757
        List<Object[]> result = query.list();
758

    
759
        List<TermDto> list = TermDto.termDtoListFrom(result);
760
        return list;
761
    }
762

    
763
    @Override
764
    public Collection<TermDto> getKindOfsAsDto(TermDto parentTerm) {
765

    
766
        String queryString;
767
        if (parentTerm.getTermType().equals(TermType.NamedArea)){
768
            queryString = TermDto.getTermDtoSelectNamedArea();
769
        }else{
770
            queryString = TermDto.getTermDtoSelect();
771
        }
772
        queryString = queryString + "where a.kindOf.uuid = :parentUuid";
773
        Query query =  getSession().createQuery(queryString);
774
        query.setParameter("parentUuid", parentTerm.getUuid());
775

    
776
        @SuppressWarnings("unchecked")
777
        List<Object[]> result = query.list();
778

    
779
        List<TermDto> list = TermDto.termDtoListFrom(result);
780
        return list;
781
    }
782

    
783
    @Override
784
    public Collection<TermDto> findByTitleAsDtoWithVocDto(String title, TermType termType) {
785

    
786
        //terms
787
        String termQueryString = TermDto.getTermDtoSelect()
788
                + " where a.titleCache like :title "
789
                + (termType!=null?" and a.termType = :termType ":"");
790

    
791
        title = title.replace("*", "%");
792
        Query termQuery =  getSession().createQuery(termQueryString);
793
        termQuery.setParameter("title", "%"+title+"%");
794
        if(termType!=null){
795
            termQuery.setParameter("termType", termType);
796
        }
797

    
798
        @SuppressWarnings("unchecked")
799
        List<Object[]> termArrayResult = termQuery.list();
800
        List<TermDto> list = TermDto.termDtoListFrom(termArrayResult);
801

    
802
        //vocabularies
803
        String vocQueryString = TermCollectionDto.getTermCollectionDtoSelect() + " where a.uuid = :uuid";
804
        Query vocQuery = getSession().createQuery(vocQueryString);
805
        Map<UUID,TermVocabularyDto> vocMap = new HashMap<>();
806
        for (TermDto dto: list){
807
            UUID vocUuid = dto.getVocabularyUuid();
808
            TermVocabularyDto vocDto = vocMap.get(vocUuid);
809
            if (vocDto == null){
810
                vocQuery.setParameter("uuid", dto.getVocabularyUuid());
811
                @SuppressWarnings("unchecked")
812
                List<Object[]> vocArrayResult = vocQuery.list();
813
                List<TermVocabularyDto> vocs = TermVocabularyDto.termVocabularyDtoListFrom(vocArrayResult);
814
                if (!vocs.isEmpty()){
815
                    vocDto = vocs.get(0);
816
                    vocMap.put(vocUuid, vocs.get(0));
817
                }
818
            }
819
            dto.setVocabularyDto(vocDto);
820
        }
821

    
822
        return list;
823
    }
824

    
825
    @Override
826
    public TermDto findByUUIDAsDto(UUID uuid) {
827
        String queryString = TermDto.getTermDtoSelect()
828
                + " where a.uuid like :uuid ";
829

    
830

    
831
        Query query =  getSession().createQuery(queryString);
832
        query.setParameter("uuid", uuid);
833

    
834

    
835
        @SuppressWarnings("unchecked")
836
        List<Object[]> result = query.list();
837

    
838
        List<TermDto> list = TermDto.termDtoListFrom(result);
839
        if (list.size()== 1){
840
            return list.get(0);
841
        }else{
842
            return null;
843
        }
844

    
845
    }
846

    
847

    
848
    @Override
849
    public Collection<TermDto> findByTypeAsDto(TermType termType) {
850
        if (termType == null){
851
            return null;
852
        }
853
        String queryString = TermDto.getTermDtoSelect()
854
                + " where a.termType = :termType ";
855
        Query query =  getSession().createQuery(queryString);
856

    
857
        query.setParameter("termType", termType);
858

    
859
        @SuppressWarnings("unchecked")
860
        List<Object[]> result = query.list();
861

    
862
        List<TermDto> list = TermDto.termDtoListFrom(result);
863
        return list;
864
    }
865

    
866
    @Override
867
    public Collection<TermDto> findByUriAsDto(URI uri, String termLabel, TermType termType) {
868
        String queryString = TermDto.getTermDtoSelect()
869
                + " where a.uri like :uri "
870
                + (termType!=null?" and a.termType = :termType ":"")
871
                + (termLabel!=null?" and a.titleCache = :termLabel ":"")
872
                ;
873
        Query query =  getSession().createQuery(queryString);
874
        query.setParameter("uri", uri.toString());
875
        if(termLabel!=null){
876
            query.setParameter("termLabel", "%"+termLabel+"%");
877
        }
878
        if(termType!=null){
879
            query.setParameter("termType", termType);
880
        }
881

    
882
        @SuppressWarnings("unchecked")
883
        List<Object[]> result = query.list();
884

    
885
        List<TermDto> list = TermDto.termDtoListFrom(result);
886
        return list;
887
    }
888

    
889
    @Override
890
    public  Map<UUID, List<TermDto>> getSupportedStatesForFeature(Set<UUID> featureUuids){
891
        Map<UUID, List<TermDto>> map = new HashMap<>();
892
        for (UUID featureUuid: featureUuids){
893
            List<TermDto> list = new ArrayList<>();
894
            String supportedCategoriesQueryString = "SELECT cat.uuid "
895
                    + "from DefinedTermBase t "
896
                    + "join t.supportedCategoricalEnumerations as cat "
897
                    + "where t.uuid = :featureUuid";
898
            Query supportedCategoriesQuery =  getSession().createQuery(supportedCategoriesQueryString);
899
            supportedCategoriesQuery.setParameter("featureUuid", featureUuid);
900
            @SuppressWarnings("unchecked")
901
    		List<UUID> supportedCategories = supportedCategoriesQuery.list();
902
            if(supportedCategories.isEmpty()){
903
                map.put(featureUuid, list);
904
                continue;
905
            }
906

    
907
            String queryString = TermDto.getTermDtoSelect()
908
                    + "where v.uuid in (:supportedCategories) "
909
                    + "order by a.titleCache";
910
            Query query =  getSession().createQuery(queryString);
911
            query.setParameterList("supportedCategories", supportedCategories);
912

    
913
            @SuppressWarnings("unchecked")
914
            List<Object[]> result = query.list();
915

    
916
            list = TermDto.termDtoListFrom(result);
917
            map.put(featureUuid, list);
918
        }
919
        return map;
920
    }
921

    
922
    @Override
923
    public Collection<TermDto> findByUUIDsAsDto(List<UUID> uuidList) {
924
        List<TermDto> list = new ArrayList<>();
925
        if (uuidList == null || uuidList.isEmpty()){
926
            return null;
927
        }
928

    
929
        String queryString = TermDto.getTermDtoSelect()
930
                + "where a.uuid in :uuidList "
931
                + "order by a.titleCache";
932
        Query query =  getSession().createQuery(queryString);
933
        query.setParameterList("uuidList", uuidList);
934

    
935
        @SuppressWarnings("unchecked")
936
        List<Object[]> result = query.list();
937

    
938
        list = TermDto.termDtoListFrom(result);
939
        return list;
940
    }
941

    
942
    @Override
943
    public Collection<TermDto> findFeatureByUUIDsAsDto(List<UUID> uuidList) {
944
        List<TermDto> list = new ArrayList<>();
945
        if (uuidList == null || uuidList.isEmpty()){
946
            return null;
947
        }
948

    
949
        String queryString = FeatureDto.getTermDtoSelect()
950
                + "where a.uuid in :uuidList "
951
                + "order by a.titleCache";
952
        Query query =  getSession().createQuery(queryString);
953
        query.setParameterList("uuidList", uuidList);
954

    
955
        @SuppressWarnings("unchecked")
956
        List<Object[]> result = query.list();
957

    
958
        list = FeatureDto.termDtoListFrom(result);
959
        return list;
960
    }
961

    
962
    @Override
963
    public Collection<TermDto> findFeatureByTitleAsDto(String pattern) {
964
        String queryString = FeatureDto.getTermDtoSelect()
965
                + " where a.titleCache like :title "
966
                +  " and a.termType = :termType ";
967

    
968
        pattern = pattern.replace("*", "%");
969
        Query query =  getSession().createQuery(queryString);
970
        query.setParameter("title", "%"+pattern+"%");
971
        query.setParameter("termType", TermType.Feature);
972

    
973

    
974
        @SuppressWarnings("unchecked")
975
        List<Object[]> result = query.list();
976

    
977
        List<TermDto> list = FeatureDto.termDtoListFrom(result);
978
        return list;
979
    }
980

    
981
    @Override
982
    public TermDto getTermDto(UUID uuid) {
983
        String queryString = TermDto.getTermDtoSelect()
984
                + " where a.uuid = :uuid ";
985

    
986

    
987
        Query query =  getSession().createQuery(queryString);
988
        query.setParameter("uuid", uuid);
989

    
990

    
991

    
992
        @SuppressWarnings("unchecked")
993
        List<Object[]> result = query.list();
994
        TermDto dto = null;
995
        List<TermDto> dtoList = TermDto.termDtoListFrom(result);
996
        if (dtoList != null && !dtoList.isEmpty()){
997
            dto = dtoList.get(0);
998
        }
999
        return dto;
1000
    }
1001

    
1002
  //***************** Overrides for deduplication *******************************/
1003

    
1004
    @Override
1005
    public List<DefinedTermBase> loadList(Collection<Integer> ids, List<OrderHint> orderHints,
1006
            List<String> propertyPaths) throws DataAccessException {
1007
        return DefinedTermDaoImpl.deduplicateResult(super.loadList(ids, orderHints, propertyPaths));
1008
    }
1009

    
1010
    @Override
1011
    public List<DefinedTermBase> list(Collection<UUID> uuids, Integer pageSize, Integer pageNumber,
1012
            List<OrderHint> orderHints, List<String> propertyPaths) throws DataAccessException {
1013
        return DefinedTermDaoImpl.deduplicateResult(super.list(uuids, pageSize, pageNumber, orderHints, propertyPaths));
1014
    }
1015

    
1016
    @Override
1017
    public <S extends DefinedTermBase> List<S> list(Class<S> clazz, Collection<UUID> uuids, Integer pageSize,
1018
            Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws DataAccessException {
1019
        return DefinedTermDaoImpl.deduplicateResult(super.list(clazz, uuids, pageSize, pageNumber, orderHints, propertyPaths));
1020
    }
1021

    
1022
    @Override
1023
    public <S extends DefinedTermBase> List<S> list(Class<S> type, List<Restriction<?>> restrictions, Integer limit,
1024
            Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
1025
        return DefinedTermDaoImpl.deduplicateResult(super.list(type, restrictions, limit, start, orderHints, propertyPaths));
1026
    }
1027

    
1028
    @Override
1029
    public List<DefinedTermBase> list(Integer limit, Integer start, List<OrderHint> orderHints) {
1030
        return DefinedTermDaoImpl.deduplicateResult(super.list(limit, start, orderHints));
1031
    }
1032

    
1033
    @Override
1034
    public List<DefinedTermBase> list(Integer limit, Integer start, List<OrderHint> orderHints,
1035
            List<String> propertyPaths) {
1036
        return DefinedTermDaoImpl.deduplicateResult(super.list(limit, start, orderHints, propertyPaths));
1037
    }
1038

    
1039
    @Override
1040
    public <S extends DefinedTermBase> List<S> list(Class<S> type, Integer limit, Integer start,
1041
            List<OrderHint> orderHints) {
1042
        return DefinedTermDaoImpl.deduplicateResult(super.list(type, limit, start, orderHints));
1043
    }
1044
}
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