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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.reference;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.hibernate.Criteria;
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import org.hibernate.Hibernate;
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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.Restrictions;
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import org.hibernate.search.FullTextSession;
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import org.hibernate.search.Search;
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import org.springframework.beans.factory.annotation.Qualifier;
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import org.springframework.stereotype.Repository;
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import eu.etaxonomy.cdm.model.reference.IArticle;
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import eu.etaxonomy.cdm.model.reference.IBookSection;
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import eu.etaxonomy.cdm.model.reference.IInProceedings;
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import eu.etaxonomy.cdm.model.reference.IPrintedUnitBase;
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import eu.etaxonomy.cdm.model.reference.IReport;
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import eu.etaxonomy.cdm.model.reference.IThesis;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceType;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase;
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import eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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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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import eu.etaxonomy.cdm.strategy.cache.reference.DefaultReferenceCacheStrategy;
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/**
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* @author a.mueller
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*
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*/
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@Repository
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@Qualifier("referenceDaoHibernateImpl")
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public class ReferenceDaoHibernateImpl extends IdentifiableDaoBase<Reference> implements IReferenceDao {
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private static final Logger logger = Logger.getLogger(ReferenceDaoHibernateImpl.class);
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public ReferenceDaoHibernateImpl() {
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super(Reference.class);
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}
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@Override
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public void rebuildIndex() {
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FullTextSession fullTextSession = Search.getFullTextSession(getSession());
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for(Reference reference : list(null,null)) { // re-index all agents
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Hibernate.initialize(reference.getAuthorship());
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if(reference.getType().equals(ReferenceType.Article)) {
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Hibernate.initialize(((IArticle)reference).getInJournal());
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} else if(reference.getType().equals(ReferenceType.BookSection)) {
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Hibernate.initialize(((IBookSection)reference).getInBook());
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} else if(reference.getType().equals(ReferenceType.InProceedings)) {
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Hibernate.initialize(((IInProceedings)reference).getInProceedings());
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}else if(reference.getType().equals(ReferenceType.Thesis)) {
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Hibernate.initialize(((IThesis)reference).getSchool());
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} else if(reference.getType().equals(ReferenceType.Report)) {
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Hibernate.initialize(((IReport)reference).getInstitution());
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} else if(reference.getType().isPrintedUnit()) {
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Hibernate.initialize(((IPrintedUnitBase)reference).getInSeries());
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}
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fullTextSession.index(reference);
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}
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fullTextSession.flushToIndexes();
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}
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@Override
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public List<UuidAndTitleCache<Reference>> getUuidAndTitle(){
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List<UuidAndTitleCache<Reference>> list = new ArrayList<UuidAndTitleCache<Reference>>();
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Session session = getSession();
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Query query = session.createQuery("select uuid, id, titleCache from " + type.getSimpleName());
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@SuppressWarnings("unchecked")
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List<Object[]> result = query.list();
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for(Object[] object : result){
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list.add(new UuidAndTitleCache<Reference>(type, (UUID) object[0], (Integer)object[1], (String) object[2]));
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}
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return list;
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}
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@Override
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public List<UuidAndTitleCache<Reference>> getUuidAndTitle(Set<UUID> uuids){
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return getUuidAndTitle(uuids, null);
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}
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@Override
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public List<UuidAndTitleCache<Reference>> getUuidAndTitle(Set<UUID> uuids, ReferenceType refType) {
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List<Reference> result = getReferenceListForUuids(uuids, refType);
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List<UuidAndTitleCache<Reference>> list = new ArrayList<>();
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for(Reference object : result){
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list.add(new UuidAndTitleCache<Reference>(type, object.getUuid(), object.getId(), object.getTitleCache()));
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}
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return list;
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}
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private List<Reference> getReferenceListForUuids(Set<UUID> uuids, ReferenceType refType){
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if (uuids.isEmpty()){
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return new ArrayList<>();
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}
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Criteria criteria = null;
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criteria = getSession().createCriteria(Reference.class);
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if (refType != null){
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criteria.add(Restrictions.and(Restrictions.in("uuid", uuids ),Restrictions.eq("type", refType)));
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}else{
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criteria.add(Restrictions.in("uuid", uuids ) );
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}
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@SuppressWarnings("unchecked")
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List<Reference> result = criteria.list();
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return result;
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}
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@Override
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public List<UuidAndTitleCache<Reference>> getUuidAndTitleCache(Integer limit, String pattern, ReferenceType refType) {
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List<UuidAndTitleCache<Reference>> list = new ArrayList<>();
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Session session = getSession();
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String queryString = "SELECT " +"r.uuid, r.id, r.titleCache, ab.titleCache "
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+ " FROM " + type.getSimpleName() + " AS r LEFT OUTER JOIN r.authorship AS ab ";
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if (refType != null || pattern != null){
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queryString += " WHERE (1=1) ";
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if (refType != null ){
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queryString += " AND (r.type = :type) ";// OR r.type = :genericType) " ;
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}
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if (pattern != null){
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queryString += " AND (r.titleCache LIKE :pattern) OR (r.abbrevTitleCache LIKE :pattern) ";
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}
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}
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Query query;
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//if (pattern != null){
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query = session.createQuery(queryString);
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// }else{
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// query = session.createQuery("SELECT " +"r.uuid, r.id, r.titleCache, ab.titleCache FROM " + type.getSimpleName() + " AS r LEFT OUTER JOIN r.authorship AS ab ");//"select uuid, titleCache from " + type.getSimpleName());
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// }
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if (limit != null){
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query.setMaxResults(limit);
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}
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if (pattern != null){
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pattern = pattern.replace("*", "%");
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pattern = pattern.replace("?", "_");
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pattern = pattern + "%";
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query.setParameter("pattern", pattern);
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}
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if (refType != null){
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query.setParameter("type", refType);
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// query.setParameter("genericType", ReferenceType.Generic);
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}
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@SuppressWarnings("unchecked")
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List<Object[]> result = query.list();
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for(Object[] object : result){
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String referenceTitle = (String) object[2];
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if(referenceTitle != null){
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String teamTitle = (String) object[3];
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referenceTitle = DefaultReferenceCacheStrategy.putAuthorToEndOfString(referenceTitle, teamTitle);
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list.add(new UuidAndTitleCache<Reference>(Reference.class, (UUID) object[0],(Integer)object[1], referenceTitle));
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}else{
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logger.warn("Title cache of reference is null. This should not happen. Please fix data. UUID: " + object[0]);
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}
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}
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return list;
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}
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@Override
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public List<Object[]> findByIdentifierAbbrev(String identifier, DefinedTermBase identifierType,
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MatchMode matchmode,Integer limit){
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checkNotInPriorView("IdentifiableDaoBase.findByIdentifier(T clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)");
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String queryString = "SELECT ids.type, ids.identifier, %s FROM %s as c " +
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" INNER JOIN c.identifiers as ids " +
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" WHERE (1=1) ";
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queryString = String.format(queryString, "c.uuid, c.titleCache, c.abbrevTitleCache" , "Reference");
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//Matchmode and identifier
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if (identifier != null){
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if (matchmode == null || matchmode == MatchMode.EXACT){
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queryString += " AND ids.identifier = '" + identifier + "'";
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}else {
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queryString += " AND ids.identifier LIKE '" + matchmode.queryStringFrom(identifier) + "'";
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}
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}
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if (identifierType != null){
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queryString += " AND ids.type = :type";
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}
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//order
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queryString +=" ORDER BY ids.type.uuid, ids.identifier, c.uuid ";
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Query query = getSession().createQuery(queryString);
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//parameters
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if (identifierType != null){
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query.setEntity("type", identifierType);
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}
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List<Object[]> results = query.list();
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//initialize
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return results;
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}
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@Override
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public List<Reference> getAllReferencesForPublishing(){
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@SuppressWarnings("unchecked")
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List<Reference> references = getSession().createQuery("SELECT r FROM Reference r "+
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"WHERE r.id IN "+
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"(SELECT m.markedObj.id FROM Marker m WHERE "+
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"m.markerType.id = "+
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"(SELECT dtb.id FROM DefinedTermBase dtb, Representation r WHERE r MEMBER OF dtb.representations AND r.text='publish'))").list();
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return references;
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}
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@Override
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public List<Reference> getAllNotNomenclaturalReferencesForPublishing(){
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@SuppressWarnings("unchecked")
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List<Reference> references = getSession().createQuery("select t.nomenclaturalReference from TaxonName t").list();
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String queryString = "from Reference b where b not in (:referenceList) and b in (:publish)" ;
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Query referenceQuery = getSession().createQuery(queryString).setParameterList("referenceList", references);
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referenceQuery.setParameterList("publish", getAllReferencesForPublishing());
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@SuppressWarnings("unchecked")
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List<Reference> resultRefernces =referenceQuery.list();
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return resultRefernces;
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}
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// the result list held doubles therefore I put a "distinct" in the query string
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@Override
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public List<Reference> getAllNomenclaturalReferences() {
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@SuppressWarnings("unchecked")
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List<Reference> references = getSession().createQuery(
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" SELECT DISTINCT ns.citation "
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+ " FROM TaxonName n"
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+ " JOIN n.nomenclaturalSource ns ").list();
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return references;
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}
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@Override
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public List<Reference> getSubordinateReferences(Reference reference) {
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List<Reference> references = new ArrayList<>();
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List<Reference> subordinateReferences = new ArrayList<>();
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Query query = getSession().createQuery("select r from Reference r where r.inReference = (:reference)");
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query.setParameter("reference", reference);
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@SuppressWarnings("unchecked")
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List<Reference> list = query.list();
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references.addAll(list);
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for(Reference ref : references){
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subordinateReferences.addAll(getSubordinateReferences(ref));
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}
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references.addAll(subordinateReferences);
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return references;
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}
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@Override
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public List<TaxonBase> listCoveredTaxa(Reference reference, boolean includeSubordinateReferences,
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List<OrderHint> orderHints, List<String> propertyPaths) {
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/*
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* <li>taxon.name.nomenclaturalSource.citation</li>
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* <li>taxon.descriptions.descriptionElement.sources.citation</li>
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* <li>taxon.descriptions.descriptionSources</li>
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* <li>taxon.name.descriptions.descriptionElement.sources</li>
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* <li>taxon.name.descriptions.descriptionSources</li>
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*/
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//TODO implement search in nameDescriptions
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Set<Reference> referenceSet = new HashSet<>();
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referenceSet.add(reference);
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if(includeSubordinateReferences){
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referenceSet.addAll(getSubordinateReferences(reference));
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}
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StringBuilder taxonDescriptionSql = new StringBuilder();
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taxonDescriptionSql.append(
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"SELECT DISTINCT t from Taxon t " +
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// TaxonDescription
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"LEFT JOIN t.descriptions td " +
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"LEFT JOIN td.descriptionSources td_s " +
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"LEFT JOIN td.descriptionElements td_e " +
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"LEFT JOIN td_e.sources td_e_s " +
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// TaxonNameDescription
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"LEFT JOIN t.name n " +
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"LEFT JOIN n.descriptions nd " +
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"LEFT JOIN nd.descriptionSources nd_s " +
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"LEFT JOIN nd.descriptionElements nd_e " +
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"LEFT JOIN nd_e.sources nd_e_s " +
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//nomenclatural citation
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"LEFT JOIN n.nomenclaturalSource ns " +
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"WHERE td_e_s.citation IN (:referenceBase_1) " +
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" OR td_s IN (:referenceBase_2) " +
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" OR nd_e_s.citation IN (:referenceBase_3) " +
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" OR nd_s IN (:referenceBase_4) " +
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" OR ns.citation IN (:referenceBase_5) " +
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" OR t.sec IN (:referenceBase_6)"
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);
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if (orderHints != null && orderHints.size() > 0){
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taxonDescriptionSql.append(" order by ");
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int i = 0;
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for (OrderHint hint : orderHints) {
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if(i > 0) {
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taxonDescriptionSql.append(", ");
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}
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taxonDescriptionSql.append("t.").append(hint.toHql());
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}
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}
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// TODO include:
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// name relations
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// taxon relations
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Query query = getSession().createQuery(taxonDescriptionSql.toString());
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query.setParameterList("referenceBase_1", referenceSet);
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query.setParameterList("referenceBase_2", referenceSet);
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query.setParameterList("referenceBase_3", referenceSet);
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query.setParameterList("referenceBase_4", referenceSet);
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query.setParameterList("referenceBase_5", referenceSet);
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query.setParameterList("referenceBase_6", referenceSet);
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@SuppressWarnings("unchecked")
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List<TaxonBase> taxonBaseList = query.list();
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defaultBeanInitializer.initializeAll(taxonBaseList, propertyPaths);
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return taxonBaseList;
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}
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@Override
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public List<UuidAndTitleCache<Reference>> getUuidAndAbbrevTitleCache(Integer limit, String pattern, ReferenceType refType) {
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Session session = getSession();
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Query query = null;
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if (pattern != null){
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if (pattern.startsWith("*")){
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query = session.createQuery("select uuid, id, abbrevTitleCache, titleCache from " + type.getSimpleName() +" where abbrevTitleCache like :pattern OR titleCache like :pattern ");
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}else{
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query = session.createQuery("select uuid, id, abbrevTitleCache, titleCache from " + type.getSimpleName() +" where abbrevTitleCache like :pattern ");
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}
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pattern = pattern + "%";
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pattern = pattern.replace("*", "%");
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pattern = pattern.replace("?", "_");
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query.setParameter("pattern", pattern);
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} else {
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query = session.createQuery("select uuid, id, abbrevTitleCache, titleCache from " + type.getSimpleName() );
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}
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if (limit != null){
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query.setMaxResults(limit);
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}
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return getUuidAndAbbrevTitleCache(query);
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}
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@Override
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public List<UuidAndTitleCache<Reference>> getUuidAndAbbrevTitleCacheForAuthor(Integer limit, String pattern, ReferenceType refType) {
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Session session = getSession();
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Query query = null;
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if (pattern != null){
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query = session.createQuery("SELECT uuid, id, abbrevTitleCache, titleCache from " + type.getSimpleName()
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+" as r where r.authorship.nomenclaturalTitle like :pattern ");
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query.setParameter("pattern", pattern);
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} else {
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query = session.createQuery("select uuid, id, abbrevTitleCache, titleCache from " + type.getSimpleName() );
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}
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if (limit != null){
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query.setMaxResults(limit);
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}
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if(pattern != null){
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pattern = pattern.replace("*", "%");
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pattern = pattern.replace("?", "_");
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query.setParameter("pattern", pattern);
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}
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return getUuidAndAbbrevTitleCache(query);
|
414
|
|
415
|
}
|
416
|
|
417
|
@Override
|
418
|
public List<Reference> findByTitleAndAbbrevTitle(Class clazz, String queryString, MatchMode matchmode, List<Criterion> criterion, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
419
|
Set<String> params = new HashSet<>();
|
420
|
params.add("titleCache");
|
421
|
params.add("abbrevTitleCache");
|
422
|
|
423
|
return findByParam(clazz, params, queryString, matchmode, criterion, pageSize, pageNumber, orderHints, propertyPaths);
|
424
|
}
|
425
|
|
426
|
}
|