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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.taxon;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.SortedSet;
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import java.util.TreeSet;
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import java.util.UUID;
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import java.util.stream.Collectors;
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import org.apache.commons.lang.StringUtils;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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import org.hibernate.Criteria;
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import org.hibernate.FetchMode;
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import org.hibernate.Hibernate;
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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.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.hibernate.envers.query.criteria.internal.NotNullAuditExpression;
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import org.hibernate.envers.query.internal.property.EntityPropertyName;
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import org.hibernate.query.Query;
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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.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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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.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.LSID;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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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.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.name.ITaxonNameDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
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import eu.etaxonomy.cdm.persistence.dto.SortableTaxonNodeQueryResult;
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import eu.etaxonomy.cdm.persistence.dto.SortableTaxonNodeQueryResultComparator;
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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.NameSearchOrder;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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import eu.etaxonomy.cdm.persistence.query.TaxonTitleType;
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/**
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* @author a.mueller
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* @since 24.11.2008
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*/
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@Repository
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@Qualifier("taxonDaoHibernateImpl")
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public class TaxonDaoHibernateImpl
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extends IdentifiableDaoBase<TaxonBase>
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implements ITaxonDao {
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// private AlternativeSpellingSuggestionParser<TaxonBase> alternativeSpellingSuggestionParser;
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private static final Logger logger = LogManager.getLogger(TaxonDaoHibernateImpl.class);
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public TaxonDaoHibernateImpl() {
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super(TaxonBase.class);
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indexedClasses = new Class[2];
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indexedClasses[0] = Taxon.class;
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indexedClasses[1] = Synonym.class;
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super.defaultField = "name.titleCache_tokenized";
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}
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@Autowired
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private ITaxonNameDao taxonNameDao;
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//// spelling support currently disabled in appcontext, see spelling.xml ... "
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//// @Autowired(required = false) //TODO switched of because it caused problems when starting CdmApplicationController
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// public void setAlternativeSpellingSuggestionParser(AlternativeSpellingSuggestionParser<TaxonBase> alternativeSpellingSuggestionParser) {
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// this.alternativeSpellingSuggestionParser = alternativeSpellingSuggestionParser;
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// }
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@Override
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public TaxonBase load(UUID uuid, List<String> propertyPaths){
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return load(uuid, INCLUDE_UNPUBLISHED, propertyPaths);
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}
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@Override
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public TaxonBase load(UUID uuid, boolean includeUnpublished, List<String> propertyPaths){
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TaxonBase<?> result = super.load(uuid, includeUnpublished, propertyPaths);
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return result; //(result == null || (!result.isPublish() && !includeUnpublished))? null : result;
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}
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@Override
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public <S extends TaxonBase> List<S> list(Class<S> type, List<Restriction<?>> restrictions, Integer limit,
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Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
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return list(type, restrictions, limit, start, orderHints, propertyPaths, INCLUDE_UNPUBLISHED);
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}
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@Override
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public <S extends TaxonBase> List<S> list(Class<S> type, List<Restriction<?>> restrictions, Integer limit, Integer start,
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List<OrderHint> orderHints, List<String> propertyPaths, boolean includePublished) {
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Criteria criteria = createCriteria(type, restrictions, false);
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if(!includePublished){
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criteria.add(Restrictions.eq("publish", true));
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}
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addLimitAndStart(criteria, limit, start);
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addOrder(criteria, orderHints);
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@SuppressWarnings("unchecked")
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List<S> result = criteria.list();
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defaultBeanInitializer.initializeAll(result, propertyPaths);
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return result;
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}
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@Override
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public long count(Class<? extends TaxonBase> type, List<Restriction<?>> restrictions) {
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return count(type, restrictions, INCLUDE_UNPUBLISHED);
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}
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@Override
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public long count(Class<? extends TaxonBase> type, List<Restriction<?>> restrictions, boolean includePublished) {
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Criteria criteria = createCriteria(type, restrictions, false);
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if(!includePublished){
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criteria.add(Restrictions.eq("publish", true));
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}
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criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));
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return (Long) criteria.uniqueResult();
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}
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@Override
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public List<TaxonBase> getTaxaByName(String queryString, boolean includeUnpublished, Reference sec) {
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return getTaxaByName(queryString, true, includeUnpublished, sec);
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}
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@Override
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public List<TaxonBase> getTaxaByName(String queryString, Boolean accepted, boolean includeUnpublished, Reference sec) {
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checkNotInPriorView("TaxonDaoHibernateImpl.getTaxaByName(String name, Reference sec)");
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Criteria criteria = null;
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if (accepted == true) {
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criteria = getSession().createCriteria(Taxon.class);
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} else {
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criteria = getSession().createCriteria(Synonym.class);
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}
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criteria.setFetchMode( "name", FetchMode.JOIN );
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criteria.createAlias("name", "name");
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if (!includeUnpublished){
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criteria.add(Restrictions.eq("publish", Boolean.TRUE ));
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}
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if (sec != null && sec.getId() != 0) {
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criteria.createCriteria("secSource").add(Restrictions.eq("citation", sec ) );
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}
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if (queryString != null) {
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criteria.add(Restrictions.ilike("name.nameCache", queryString));
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}
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@SuppressWarnings({ "unchecked", "rawtypes" })
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List<TaxonBase> result = criteria.list();
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return result;
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}
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//TODO needed? Currently only used by tests.
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public List<TaxonBase> getTaxaByName(boolean doTaxa, boolean doSynonyms, boolean includeUnpublished,
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String queryString, MatchMode matchMode, Integer pageSize, Integer pageNumber) {
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return getTaxaByName(doTaxa, doSynonyms, false, false, false,
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queryString, null, null, matchMode, null, includeUnpublished, null, pageSize, pageNumber, null);
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}
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@Override
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public List<TaxonBase> getTaxaByName(String queryString, MatchMode matchMode,
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Boolean accepted, boolean includeUnpublished, Integer pageSize, Integer pageNumber) {
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boolean doTaxa = true;
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boolean doSynonyms = true;
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if (accepted == true) {
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doSynonyms = false;
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} else {
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doTaxa = false;
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}
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return getTaxaByName(doTaxa, doSynonyms, includeUnpublished, queryString, matchMode, pageSize, pageNumber);
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}
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@Override
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public List<TaxonBase> getTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, boolean doCommonNames,
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boolean includeAuthors,
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String queryString, Classification classification, TaxonNode subtree,
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MatchMode matchMode, Set<NamedArea> namedAreas, boolean includeUnpublished, NameSearchOrder order,
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Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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boolean doCount = false;
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String searchField = includeAuthors ? "titleCache" : "nameCache";
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Query<TaxonBase> query = prepareTaxaByName(doTaxa, doSynonyms, doMisappliedNames, doCommonNames, includeUnpublished,
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searchField, queryString, classification, subtree, matchMode, namedAreas, order, pageSize, pageNumber, doCount,
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TaxonBase.class);
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if (query != null){
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@SuppressWarnings("rawtypes")
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List<TaxonBase> results = query.list();
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defaultBeanInitializer.initializeAll(results, propertyPaths);
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//Collections.sort(results, comp);
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return results;
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}else{
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return new ArrayList<>();
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}
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}
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//new search for the editor, for performance issues the return values are only uuid and titleCache, to avoid the initialisation of all objects
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@Override
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@SuppressWarnings("unchecked")
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public List<UuidAndTitleCache<? extends IdentifiableEntity>> getTaxaByNameForEditor(boolean doTaxa, boolean doSynonyms, boolean doNamesWithoutTaxa,
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boolean doMisappliedNames, boolean doCommonNames, boolean includeUnpublished, boolean includeAuthors, String queryString, Classification classification, TaxonNode subtree,
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MatchMode matchMode, Set<NamedArea> namedAreas, NameSearchOrder order) {
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if (order == null){
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order = NameSearchOrder.ALPHA; //TODO add to signature
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}
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boolean doCount = false;
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@SuppressWarnings("rawtypes")
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List<UuidAndTitleCache<? extends IdentifiableEntity>> resultObjects = new ArrayList<>();
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if (doNamesWithoutTaxa){
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List<TaxonName> nameResult = taxonNameDao.findByName(
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includeAuthors, queryString, matchMode, null, null, null, null);
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for (TaxonName name: nameResult){
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if (name.getTaxonBases().size() == 0){
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resultObjects.add(new UuidAndTitleCache<>(TaxonName.class, name.getUuid(),
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name.getId(), name.getTitleCache()));
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}
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}
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if (!doSynonyms && !doTaxa && !doCommonNames){
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return resultObjects;
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}
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}
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String searchField = includeAuthors ? "titleCache" : "nameCache";
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Query<Object[]> query = prepareTaxaByNameForEditor(doTaxa, doSynonyms, doMisappliedNames, doCommonNames, includeUnpublished,
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searchField, queryString, classification, subtree, matchMode, namedAreas, doCount, order, Object[].class);
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if (query != null){
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List<Object[]> results = query.list();
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Object[] result;
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for(int i = 0; i<results.size();i++){
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result = results.get(i);
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//differentiate taxa and synonyms
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// new Boolean(result[3].toString()) is due to the fact that result[3] could be a Boolean ora String
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// see FIXME in 'prepareQuery' for more details
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if (doTaxa || doSynonyms || doCommonNames){
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if (result[3].equals("synonym")) {
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resultObjects.add( new UuidAndTitleCache<>(Synonym.class, (UUID) result[0], (Integer) result[1], (String)result[2], new Boolean(result[4].toString()), null));
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}
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else {
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resultObjects.add( new UuidAndTitleCache<>(Taxon.class, (UUID) result[0], (Integer) result[1], (String)result[2], new Boolean(result[4].toString()), null));
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}
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}else if (doSynonyms){
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resultObjects.add( new UuidAndTitleCache<>(Synonym.class, (UUID) result[0], (Integer) result[1], (String)result[2], new Boolean(result[4].toString()), null));
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}
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}
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}
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return resultObjects;
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}
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@Override
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public List<Taxon> getTaxaByCommonName(String queryString, Classification classification,
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MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize,
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Integer pageNumber, List<String> propertyPaths) {
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boolean doCount = false;
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Query<Taxon> query = prepareTaxaByCommonName(queryString, classification, matchMode, namedAreas, pageSize, pageNumber, doCount, false, Taxon.class);
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if (query != null){
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List<Taxon> results = query.list();
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defaultBeanInitializer.initializeAll(results, propertyPaths);
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return results;
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}else{
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return new ArrayList<>();
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}
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}
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/**
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* @param clazz
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* @param searchField the field in TaxonName to be searched through usually either <code>nameCache</code> or <code>titleCache</code>
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* @param queryString
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* @param classification TODO
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* @param matchMode
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* @param namedAreas
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* @param pageSize
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* @param pageNumber
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* @param doCount
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* @return
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*/
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private <R extends Object> Query<R> prepareTaxaByNameForEditor(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, boolean doCommonNames,
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boolean includeUnpublished, String searchField, String queryString, Classification classification, TaxonNode subtree,
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MatchMode matchMode, Set<NamedArea> namedAreas, boolean doCount, NameSearchOrder order, Class<R> returnedClass) {
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return prepareByNameQuery(doTaxa, doSynonyms, doMisappliedNames, doCommonNames, includeUnpublished,
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searchField, queryString,
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|
338
|
classification, subtree, matchMode, namedAreas, order, doCount, true, returnedClass);
|
|
339
|
}
|
|
340
|
|
|
341
|
/**
|
|
342
|
* @param doTaxa
|
|
343
|
* @param doSynonyms
|
|
344
|
* @param doIncludeMisappliedNames
|
|
345
|
* @param doCommonNames
|
|
346
|
* @param includeUnpublished
|
|
347
|
* @param searchField
|
|
348
|
* @param queryString
|
|
349
|
* @param classification
|
|
350
|
* @param matchMode
|
|
351
|
* @param namedAreas
|
|
352
|
* @param order
|
|
353
|
* @param doCount
|
|
354
|
* @param returnIdAndTitle
|
|
355
|
* If set true the seach method will not return synonym and taxon
|
|
356
|
* entities but an array containing the uuid, titleCache, and the
|
|
357
|
* DTYPE in lowercase letters.
|
|
358
|
* @return
|
|
359
|
*/
|
|
360
|
private <R extends Object> Query<R> prepareByNameQuery(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames,
|
|
361
|
boolean doCommonNames, boolean includeUnpublished, String searchField, String queryString,
|
|
362
|
Classification classification, TaxonNode subtree, MatchMode matchMode, Set<NamedArea> namedAreas,
|
|
363
|
NameSearchOrder order, boolean doCount, boolean returnIdAndTitle, Class<R> returnedClass){
|
|
364
|
|
|
365
|
boolean doProParteSynonyms = doSynonyms; //we may distinguish in future
|
|
366
|
boolean doConceptRelations = doMisappliedNames || doProParteSynonyms;
|
|
367
|
|
|
368
|
if (order == null){
|
|
369
|
order = NameSearchOrder.DEFAULT();
|
|
370
|
}
|
|
371
|
String hqlQueryString = matchMode.queryStringFrom(queryString);
|
|
372
|
String selectWhat;
|
|
373
|
if (returnIdAndTitle){
|
|
374
|
selectWhat = "t.uuid, t.id, t.titleCache ";
|
|
375
|
}else {
|
|
376
|
selectWhat = (doCount ? "count(t)": "t");
|
|
377
|
}
|
|
378
|
|
|
379
|
//area filter
|
|
380
|
//TODO share code with taxon node filter
|
|
381
|
String hql = "";
|
|
382
|
Set<NamedArea> areasExpanded = new HashSet<>();
|
|
383
|
if(namedAreas != null && namedAreas.size() > 0){
|
|
384
|
// expand areas and restrict by distribution area
|
|
385
|
Query<NamedArea> areaQuery = getSession().createQuery("SELECT childArea "
|
|
386
|
+ " FROM NamedArea AS childArea LEFT JOIN childArea.partOf as parentArea "
|
|
387
|
+ " WHERE parentArea = :area", NamedArea.class);
|
|
388
|
expandNamedAreas(namedAreas, areasExpanded, areaQuery);
|
|
389
|
}
|
|
390
|
boolean doAreaRestriction = areasExpanded.size() > 0;
|
|
391
|
|
|
392
|
Set<UUID> namedAreasUuids = new HashSet<>();
|
|
393
|
for (NamedArea area:areasExpanded){
|
|
394
|
namedAreasUuids.add(area.getUuid());
|
|
395
|
}
|
|
396
|
|
|
397
|
Subselects subSelects = createByNameHQLString(doConceptRelations,
|
|
398
|
includeUnpublished, classification, subtree, areasExpanded, matchMode, searchField);
|
|
399
|
String taxonSubselect = subSelects.taxonSubselect;
|
|
400
|
String synonymSubselect = subSelects.synonymSubselect;
|
|
401
|
String conceptSelect = subSelects.conceptSelect;
|
|
402
|
String commonNameSubSelect = subSelects.commonNameSubselect;
|
|
403
|
|
|
404
|
if (logger.isDebugEnabled()) {
|
|
405
|
logger.debug("taxonSubselect: " + (taxonSubselect != null ? taxonSubselect: "NULL"));
|
|
406
|
logger.debug("synonymSubselect: " + (synonymSubselect != null ? synonymSubselect: "NULL"));
|
|
407
|
}
|
|
408
|
|
|
409
|
List<Integer> taxonIDs = new ArrayList<>();
|
|
410
|
List<Integer> synonymIDs = new ArrayList<>();
|
|
411
|
|
|
412
|
if(doTaxa){
|
|
413
|
// find Taxa
|
|
414
|
Query<Integer> subTaxon = getSearchQueryString(hqlQueryString, taxonSubselect, true);
|
|
415
|
|
|
416
|
addRestrictions(doAreaRestriction, classification, subtree, includeUnpublished,
|
|
417
|
namedAreasUuids, subTaxon);
|
|
418
|
taxonIDs = subTaxon.list();
|
|
419
|
}
|
|
420
|
|
|
421
|
if(doSynonyms){
|
|
422
|
// find synonyms
|
|
423
|
Query<Integer> subSynonym = getSearchQueryString(hqlQueryString, synonymSubselect, true);
|
|
424
|
addRestrictions(doAreaRestriction, classification, subtree, includeUnpublished, namedAreasUuids,subSynonym);
|
|
425
|
synonymIDs = subSynonym.list();
|
|
426
|
}
|
|
427
|
if (doConceptRelations ){
|
|
428
|
Query<Integer> subMisappliedNames = getSearchQueryString(hqlQueryString, conceptSelect, true);
|
|
429
|
Set<TaxonRelationshipType> relTypeSet = new HashSet<>();
|
|
430
|
if (doMisappliedNames){
|
|
431
|
relTypeSet.addAll(TaxonRelationshipType.allMisappliedNameTypes());
|
|
432
|
}
|
|
433
|
if (doProParteSynonyms){
|
|
434
|
relTypeSet.addAll(TaxonRelationshipType.allSynonymTypes());
|
|
435
|
}
|
|
436
|
subMisappliedNames.setParameterList("rTypeSet", relTypeSet);
|
|
437
|
addRestrictions(doAreaRestriction, classification, subtree, includeUnpublished, namedAreasUuids, subMisappliedNames);
|
|
438
|
taxonIDs.addAll(subMisappliedNames.list());
|
|
439
|
}
|
|
440
|
|
|
441
|
if(doCommonNames){
|
|
442
|
// find Taxa
|
|
443
|
Query<Integer> subCommonNames = getSearchQueryString(hqlQueryString, commonNameSubSelect, false);
|
|
444
|
addRestrictions(doAreaRestriction, classification, subtree, includeUnpublished, namedAreasUuids, subCommonNames);
|
|
445
|
taxonIDs.addAll(subCommonNames.list());
|
|
446
|
}
|
|
447
|
|
|
448
|
|
|
449
|
if(synonymIDs.size()>0 && taxonIDs.size()>0){
|
|
450
|
hql = "SELECT " + selectWhat;
|
|
451
|
// in doNotReturnFullEntities mode it is nesscary to also return the type of the matching entities:
|
|
452
|
// also return the computed isOrphaned flag
|
|
453
|
if (returnIdAndTitle && !doCount ){
|
|
454
|
hql += ", CASE WHEN t.id in (:taxa) THEN 'taxon' ELSE 'synonym' END, " +
|
|
455
|
" CASE WHEN t.id in (:taxa) "
|
|
456
|
+ " AND t.taxonNodes IS EMPTY "
|
|
457
|
+ " AND t.relationsFromThisTaxon IS EMPTY "
|
|
458
|
+ " AND t.relationsToThisTaxon IS EMPTY "
|
|
459
|
+ " THEN true ELSE false END ";
|
|
460
|
}
|
|
461
|
hql += " FROM %s t " +
|
|
462
|
" WHERE (t.id in (:taxa) OR t.id IN (:synonyms)) ";
|
|
463
|
}else if (synonymIDs.size()>0 ){
|
|
464
|
hql = "SELECT " + selectWhat;
|
|
465
|
// in doNotReturnFullEntities mode it is nesscary to also return the type of the matching entities:
|
|
466
|
// also return the computed isOrphaned flag
|
|
467
|
if (returnIdAndTitle && !doCount ){
|
|
468
|
hql += ", 'synonym', 'false' ";
|
|
469
|
|
|
470
|
}
|
|
471
|
hql += " FROM %s t " +
|
|
472
|
" WHERE t.id in (:synonyms) ";
|
|
473
|
|
|
474
|
} else if (taxonIDs.size()>0 ){
|
|
475
|
hql = "SELECT " + selectWhat;
|
|
476
|
// in doNotReturnFullEntities mode it is nesscary to also return the type of the matching entities:
|
|
477
|
// also return the computed isOrphaned flag
|
|
478
|
if (returnIdAndTitle && !doCount ){
|
|
479
|
hql += ", 'taxon', " +
|
|
480
|
" CASE WHEN t.taxonNodes is empty "
|
|
481
|
+ " AND t.relationsFromThisTaxon is empty "
|
|
482
|
+ " AND t.relationsToThisTaxon is empty "
|
|
483
|
+ "THEN true ELSE false END ";
|
|
484
|
}
|
|
485
|
hql += " FROM %s t " +
|
|
486
|
" WHERE t.id in (:taxa) ";
|
|
487
|
} else if (StringUtils.isBlank(queryString)){
|
|
488
|
hql = "SELECT " + selectWhat + " FROM %s t";
|
|
489
|
} else{
|
|
490
|
return null;
|
|
491
|
}
|
|
492
|
|
|
493
|
String classString;
|
|
494
|
if ((doTaxa || doCommonNames || doConceptRelations) && doSynonyms){
|
|
495
|
classString = "TaxonBase";
|
|
496
|
} else if (doTaxa || doCommonNames){
|
|
497
|
classString = "Taxon";
|
|
498
|
} else if (doSynonyms && !(doCommonNames|| doTaxa || doConceptRelations)){
|
|
499
|
classString = "Synonym"; // as long as doProParteSynonyms = doSynonyms this case should not happen
|
|
500
|
} else{//only misappliedNames
|
|
501
|
classString = "Taxon";
|
|
502
|
}
|
|
503
|
|
|
504
|
hql = String.format(hql, classString);
|
|
505
|
|
|
506
|
if (hql.isEmpty()) {
|
|
507
|
return null;
|
|
508
|
}
|
|
509
|
if(!doCount){
|
|
510
|
String orderBy = " ORDER BY ";
|
|
511
|
String alphabeticBase = " t.name.genusOrUninomial, case when t.name.specificEpithet like '\"%\"' then 1 else 0 end, t.name.specificEpithet, t.name.rank desc, t.name.nameCache";
|
|
512
|
|
|
513
|
if (order == NameSearchOrder.LENGTH_ALPHA_NAME){
|
|
514
|
orderBy += " length(t.name.nameCache), " + alphabeticBase;
|
|
515
|
}else if (order == NameSearchOrder.LENGTH_ALPHA_TITLE){
|
|
516
|
orderBy += " length(t.name.titleCache), " + alphabeticBase;
|
|
517
|
}else {
|
|
518
|
orderBy += alphabeticBase;
|
|
519
|
}
|
|
520
|
|
|
521
|
hql += orderBy;
|
|
522
|
}
|
|
523
|
|
|
524
|
if(logger.isDebugEnabled()){ logger.debug("hql: " + hql);}
|
|
525
|
Query<R> query = getSession().createQuery(hql, returnedClass);
|
|
526
|
|
|
527
|
// find taxa and synonyms
|
|
528
|
if (taxonIDs.size()>0){
|
|
529
|
query.setParameterList("taxa", taxonIDs);
|
|
530
|
}
|
|
531
|
if (synonymIDs.size()>0){
|
|
532
|
query.setParameterList("synonyms",synonymIDs);
|
|
533
|
}
|
|
534
|
if (taxonIDs.size()== 0 && synonymIDs.size() == 0){
|
|
535
|
return null;
|
|
536
|
}
|
|
537
|
|
|
538
|
return query;
|
|
539
|
}
|
|
540
|
|
|
541
|
protected Query<Integer> getSearchQueryString(String hqlQueryString, String subselect, boolean includeProtectedTitle) {
|
|
542
|
Query<Integer> result = getSession().createQuery(subselect, Integer.class);
|
|
543
|
result.setParameter("queryString", hqlQueryString);
|
|
544
|
if (includeProtectedTitle){
|
|
545
|
result.setParameter("protectedTitleQueryString", hqlQueryString + "%");
|
|
546
|
}
|
|
547
|
return result;
|
|
548
|
}
|
|
549
|
|
|
550
|
protected void addRestrictions(boolean doAreaRestriction, Classification classification, TaxonNode subtree, boolean includeUnpublished,
|
|
551
|
Set<UUID> namedAreasUuids, Query<Integer> query) {
|
|
552
|
if(doAreaRestriction){
|
|
553
|
query.setParameterList("namedAreasUuids", namedAreasUuids);
|
|
554
|
}
|
|
555
|
if(classification != null){
|
|
556
|
query.setParameter("classification", classification);
|
|
557
|
}
|
|
558
|
if(subtree != null){
|
|
559
|
query.setParameter("treeIndexLike", subtree.treeIndex() + "%");
|
|
560
|
}
|
|
561
|
if(!includeUnpublished){
|
|
562
|
query.setParameter("publish", true);
|
|
563
|
}
|
|
564
|
}
|
|
565
|
|
|
566
|
|
|
567
|
/**
|
|
568
|
* @param searchField the field in TaxonName to be searched through usually either <code>nameCache</code> or <code>titleCache</code>
|
|
569
|
* @param queryString
|
|
570
|
* @param classification TODO
|
|
571
|
* @param matchMode
|
|
572
|
* @param namedAreas
|
|
573
|
* @param pageSize
|
|
574
|
* @param pageNumber
|
|
575
|
* @param doCount
|
|
576
|
* @param clazz
|
|
577
|
* @return
|
|
578
|
*
|
|
579
|
* FIXME implement classification restriction & implement test: see {@link TaxonDaoHibernateImplTest#testCountTaxaByName()}
|
|
580
|
*/
|
|
581
|
private <R extends Object> Query<R> prepareTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames,
|
|
582
|
boolean doCommonNames, boolean includeUnpublished, String searchField, String queryString,
|
|
583
|
Classification classification, TaxonNode subtree, MatchMode matchMode, Set<NamedArea> namedAreas, NameSearchOrder order,
|
|
584
|
Integer pageSize, Integer pageNumber, boolean doCount, Class<R> returnClass) {
|
|
585
|
|
|
586
|
Query<R> query = prepareByNameQuery(doTaxa, doSynonyms, doMisappliedNames, doCommonNames, includeUnpublished,
|
|
587
|
searchField, queryString, classification, subtree, matchMode, namedAreas, order, doCount, false, returnClass);
|
|
588
|
|
|
589
|
if(!doCount && query != null) {
|
|
590
|
this.addPageSizeAndNumber(query, pageSize, pageNumber);
|
|
591
|
}
|
|
592
|
|
|
593
|
return query;
|
|
594
|
}
|
|
595
|
|
|
596
|
private <R extends Object> Query<R> prepareTaxaByCommonName(String queryString, Classification classification,
|
|
597
|
MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber,
|
|
598
|
boolean doCount, boolean returnIdAndTitle, Class<R> returnClass){
|
|
599
|
|
|
600
|
String what = "SELECT DISTINCT";
|
|
601
|
if (returnIdAndTitle){
|
|
602
|
what += " t.uuid, t.id, t.titleCache, \'taxon\', CASE WHEN t.taxonNodes IS EMPTY AND t.relationsFromThisTaxon IS EMPTY AND t.relationsToThisTaxon IS EMPTY THEN true ELSE false END ";
|
|
603
|
}else {
|
|
604
|
what += (doCount ? " count(t)": " t");
|
|
605
|
}
|
|
606
|
String hql= what + " from Taxon t " +
|
|
607
|
"join t.descriptions d "+
|
|
608
|
"join d.descriptionElements e " +
|
|
609
|
// "join e.feature f " +
|
|
610
|
"where e.class = 'CommonTaxonName' and e.name "+matchMode.getMatchOperator()+" :queryString";//and ls.text like 'common%'";
|
|
611
|
|
|
612
|
Query<R> query = getSession().createQuery(hql, returnClass);
|
|
613
|
|
|
614
|
query.setParameter("queryString", matchMode.queryStringFrom(queryString));
|
|
615
|
if(!doCount) {
|
|
616
|
this.addPageSizeAndNumber(query, pageSize, pageNumber);
|
|
617
|
}
|
|
618
|
return query;
|
|
619
|
}
|
|
620
|
|
|
621
|
@Override
|
|
622
|
public long countTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, boolean doCommonNames,
|
|
623
|
boolean doIncludeAuthors, String queryString, Classification classification, TaxonNode subtree,
|
|
624
|
MatchMode matchMode, Set<NamedArea> namedAreas, boolean includeUnpublished) {
|
|
625
|
|
|
626
|
boolean doCount = true;
|
|
627
|
String searchField = doIncludeAuthors ? "titleCache": "nameCache";
|
|
628
|
|
|
629
|
Query<Long> query = prepareTaxaByName(doTaxa, doSynonyms, doMisappliedNames, doCommonNames, includeUnpublished,
|
|
630
|
searchField, queryString, classification, subtree, matchMode, namedAreas, null, null, null, doCount, Long.class);
|
|
631
|
if (query != null) {
|
|
632
|
return query.uniqueResult();
|
|
633
|
}else{
|
|
634
|
return 0;
|
|
635
|
}
|
|
636
|
}
|
|
637
|
|
|
638
|
private void expandNamedAreas(Collection<NamedArea> namedAreas, Set<NamedArea> areasExpanded, Query<NamedArea> areaQuery) {
|
|
639
|
for(NamedArea a : namedAreas){
|
|
640
|
areasExpanded.add(a);
|
|
641
|
areaQuery.setParameter("area", a);
|
|
642
|
List<NamedArea> childAreas = areaQuery.list();
|
|
643
|
if(childAreas.size() > 0){
|
|
644
|
areasExpanded.addAll(childAreas);
|
|
645
|
expandNamedAreas(childAreas, areasExpanded, areaQuery);
|
|
646
|
}
|
|
647
|
}
|
|
648
|
}
|
|
649
|
|
|
650
|
@Override
|
|
651
|
public UUID delete(TaxonBase taxonBase) throws DataAccessException{
|
|
652
|
if (taxonBase == null){
|
|
653
|
logger.warn("TaxonBase was 'null'");
|
|
654
|
return null;
|
|
655
|
}
|
|
656
|
|
|
657
|
// Merge the object in if it is detached
|
|
658
|
//
|
|
659
|
// I think this is preferable to catching lazy initialization errors
|
|
660
|
// as that solution only swallows and hides the exception, but doesn't
|
|
661
|
// actually solve it.
|
|
662
|
taxonBase = (TaxonBase)getSession().merge(taxonBase);
|
|
663
|
|
|
664
|
taxonBase.removeSources();
|
|
665
|
|
|
666
|
if (taxonBase instanceof Taxon){ // is Taxon
|
|
667
|
Taxon taxon = ((Taxon)taxonBase);
|
|
668
|
Set<Synonym> syns = new HashSet<>(taxon.getSynonyms());
|
|
669
|
for (Synonym syn: syns){
|
|
670
|
taxon.removeSynonym(syn);
|
|
671
|
}
|
|
672
|
}
|
|
673
|
|
|
674
|
return super.delete(taxonBase);
|
|
675
|
|
|
676
|
}
|
|
677
|
|
|
678
|
@Override
|
|
679
|
public List<TaxonBase> findByNameTitleCache(boolean doTaxa, boolean doSynonyms, boolean includeUnpublished, String queryString, Classification classification, TaxonNode subtree, MatchMode matchMode, Set<NamedArea> namedAreas, NameSearchOrder order, Integer pageNumber, Integer pageSize, List<String> propertyPaths) {
|
|
680
|
|
|
681
|
boolean doCount = false;
|
|
682
|
Query<TaxonBase> query = prepareTaxaByName(doTaxa, doSynonyms, false, false, includeUnpublished, "titleCache", queryString, classification, subtree, matchMode, namedAreas, order, pageSize, pageNumber, doCount, TaxonBase.class);
|
|
683
|
if (query != null){
|
|
684
|
@SuppressWarnings({ "unchecked", "rawtypes" })
|
|
685
|
List<TaxonBase> results = query.list();
|
|
686
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
687
|
return results;
|
|
688
|
}
|
|
689
|
return new ArrayList<>();
|
|
690
|
|
|
691
|
}
|
|
692
|
|
|
693
|
@Override
|
|
694
|
public TaxonBase findByUuid(UUID uuid, List<Criterion> criteria, List<String> propertyPaths) {
|
|
695
|
|
|
696
|
Criteria crit = getSession().createCriteria(type);
|
|
697
|
|
|
698
|
if (uuid != null) {
|
|
699
|
crit.add(Restrictions.eq("uuid", uuid));
|
|
700
|
} else {
|
|
701
|
logger.warn("UUID is NULL");
|
|
702
|
return null;
|
|
703
|
}
|
|
704
|
if(criteria != null){
|
|
705
|
for (Criterion criterion : criteria) {
|
|
706
|
crit.add(criterion);
|
|
707
|
}
|
|
708
|
}
|
|
709
|
crit.addOrder(Order.asc("uuid"));
|
|
710
|
|
|
711
|
@SuppressWarnings({ "unchecked", "rawtypes" })
|
|
712
|
List<? extends TaxonBase> results = crit.list();
|
|
713
|
if (results.size() == 1) {
|
|
714
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
715
|
TaxonBase<?> taxon = results.iterator().next();
|
|
716
|
return taxon;
|
|
717
|
} else if (results.size() > 1) {
|
|
718
|
logger.error("Multiple results for UUID: " + uuid);
|
|
719
|
} else if (results.size() == 0) {
|
|
720
|
logger.info("No results for UUID: " + uuid);
|
|
721
|
}
|
|
722
|
|
|
723
|
return null;
|
|
724
|
}
|
|
725
|
|
|
726
|
@Override
|
|
727
|
public List<? extends TaxonBase> findByUuids(List<UUID> uuids, List<Criterion> criteria, List<String> propertyPaths) {
|
|
728
|
|
|
729
|
Criteria crit = getSession().createCriteria(type);
|
|
730
|
|
|
731
|
if (uuids != null) {
|
|
732
|
crit.add(Restrictions.in("uuid", uuids));
|
|
733
|
} else {
|
|
734
|
logger.warn("List<UUID> uuids is NULL");
|
|
735
|
return null;
|
|
736
|
}
|
|
737
|
if(criteria != null){
|
|
738
|
for (Criterion criterion : criteria) {
|
|
739
|
crit.add(criterion);
|
|
740
|
}
|
|
741
|
}
|
|
742
|
crit.addOrder(Order.asc("uuid"));
|
|
743
|
|
|
744
|
@SuppressWarnings({ "unchecked", "rawtypes" })
|
|
745
|
List<? extends TaxonBase> results = crit.list();
|
|
746
|
|
|
747
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
748
|
return results;
|
|
749
|
}
|
|
750
|
|
|
751
|
@Override
|
|
752
|
public long countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted) {
|
|
753
|
checkNotInPriorView("TaxonDaoHibernateImpl.countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted)");
|
|
754
|
|
|
755
|
Criteria crit = getCriteria(type);
|
|
756
|
crit.add(Restrictions.ilike("titleCache", matchMode.queryStringFrom(queryString)));
|
|
757
|
crit.setProjection(Projections.rowCount());
|
|
758
|
return (Long)crit.uniqueResult();
|
|
759
|
}
|
|
760
|
|
|
761
|
|
|
762
|
@Override
|
|
763
|
public long countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted, List<Criterion> criteria) {
|
|
764
|
checkNotInPriorView("TaxonDaoHibernateImpl.countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted, List<Criterion> criteria)");
|
|
765
|
|
|
766
|
Criteria crit = getCriteria(type);
|
|
767
|
crit.add(Restrictions.ilike("titleCache", matchMode.queryStringFrom(queryString)));
|
|
768
|
if(criteria != null){
|
|
769
|
for (Criterion criterion : criteria) {
|
|
770
|
crit.add(criterion);
|
|
771
|
}
|
|
772
|
}
|
|
773
|
crit.setProjection(Projections.rowCount());
|
|
774
|
return (Long)crit.uniqueResult();
|
|
775
|
}
|
|
776
|
|
|
777
|
|
|
778
|
@Override
|
|
779
|
public long countSynonyms(boolean onlyAttachedToTaxon) {
|
|
780
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
781
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
782
|
String queryStr =
|
|
783
|
" SELECT count(syn) "
|
|
784
|
+ " FROM Synonym syn";
|
|
785
|
if (onlyAttachedToTaxon){
|
|
786
|
queryStr += " WHERE syn.acceptedTaxon IS NOT NULL";
|
|
787
|
}
|
|
788
|
Query<Long> query = getSession().createQuery(queryStr, Long.class);
|
|
789
|
|
|
790
|
return query.uniqueResult();
|
|
791
|
} else {
|
|
792
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(Synonym.class,auditEvent.getRevisionNumber());
|
|
793
|
if (onlyAttachedToTaxon){
|
|
794
|
query.add(new NotNullAuditExpression(null, new EntityPropertyName("acceptedTaxon")));
|
|
795
|
}
|
|
796
|
query.addProjection(AuditEntity.id().count());
|
|
797
|
|
|
798
|
return (Long)query.getSingleResult();
|
|
799
|
}
|
|
800
|
}
|
|
801
|
|
|
802
|
@Override
|
|
803
|
public long countSynonyms(Taxon taxon, SynonymType type) {
|
|
804
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
805
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
806
|
Criteria criteria = getCriteria(Synonym.class);
|
|
807
|
|
|
808
|
criteria.add(Restrictions.eq("acceptedTaxon", taxon));
|
|
809
|
if(type != null) {
|
|
810
|
criteria.add(Restrictions.eq("type", type));
|
|
811
|
}
|
|
812
|
criteria.setProjection(Projections.rowCount());
|
|
813
|
return (Long)criteria.uniqueResult();
|
|
814
|
} else {
|
|
815
|
AuditQuery query = makeAuditQuery(Synonym.class,auditEvent);
|
|
816
|
query.add(AuditEntity.relatedId("acceptedTaxon").eq(taxon.getId()));
|
|
817
|
query.addProjection(AuditEntity.id().count());
|
|
818
|
|
|
819
|
if(type != null) {
|
|
820
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
821
|
}
|
|
822
|
|
|
823
|
return (Long)query.getSingleResult();
|
|
824
|
}
|
|
825
|
}
|
|
826
|
|
|
827
|
@Override
|
|
828
|
public long countSynonyms(Synonym synonym, SynonymType type) {
|
|
829
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
830
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
831
|
Criteria criteria = getCriteria(Synonym.class);
|
|
832
|
|
|
833
|
criteria.add(Restrictions.isNotNull("acceptedTaxon"));
|
|
834
|
if(type != null) {
|
|
835
|
criteria.add(Restrictions.eq("type", type));
|
|
836
|
}
|
|
837
|
|
|
838
|
criteria.setProjection(Projections.rowCount());
|
|
839
|
return (Long)criteria.uniqueResult();
|
|
840
|
} else {
|
|
841
|
AuditQuery query = makeAuditQuery(Synonym.class,auditEvent);
|
|
842
|
query.add(new NotNullAuditExpression(null, new EntityPropertyName("acceptedTaxon")));
|
|
843
|
query.addProjection(AuditEntity.id().count());
|
|
844
|
|
|
845
|
if(type != null) {
|
|
846
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
847
|
}
|
|
848
|
|
|
849
|
return (Long)query.getSingleResult();
|
|
850
|
}
|
|
851
|
}
|
|
852
|
|
|
853
|
@Override
|
|
854
|
public long countTaxaByName(Class<? extends TaxonBase> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet,
|
|
855
|
String infraSpecificEpithet, String authorshipCache, Rank rank) {
|
|
856
|
checkNotInPriorView("TaxonDaoHibernateImpl.countTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, String authorshipCache, Rank rank)");
|
|
857
|
Criteria criteria = null;
|
|
858
|
|
|
859
|
criteria = getCriteria(clazz);
|
|
860
|
|
|
861
|
criteria.setFetchMode( "name", FetchMode.JOIN );
|
|
862
|
criteria.createAlias("name", "name");
|
|
863
|
|
|
864
|
if(genusOrUninomial == null) {
|
|
865
|
criteria.add(Restrictions.isNull("name.genusOrUninomial"));
|
|
866
|
} else if(!genusOrUninomial.equals("*")) {
|
|
867
|
criteria.add(Restrictions.eq("name.genusOrUninomial", genusOrUninomial));
|
|
868
|
}
|
|
869
|
|
|
870
|
if(infraGenericEpithet == null) {
|
|
871
|
criteria.add(Restrictions.isNull("name.infraGenericEpithet"));
|
|
872
|
} else if(!infraGenericEpithet.equals("*")) {
|
|
873
|
criteria.add(Restrictions.eq("name.infraGenericEpithet", infraGenericEpithet));
|
|
874
|
}
|
|
875
|
|
|
876
|
if(specificEpithet == null) {
|
|
877
|
criteria.add(Restrictions.isNull("name.specificEpithet"));
|
|
878
|
} else if(!specificEpithet.equals("*")) {
|
|
879
|
criteria.add(Restrictions.eq("name.specificEpithet", specificEpithet));
|
|
880
|
|
|
881
|
}
|
|
882
|
|
|
883
|
if(infraSpecificEpithet == null) {
|
|
884
|
criteria.add(Restrictions.isNull("name.infraSpecificEpithet"));
|
|
885
|
} else if(!infraSpecificEpithet.equals("*")) {
|
|
886
|
criteria.add(Restrictions.eq("name.infraSpecificEpithet", infraSpecificEpithet));
|
|
887
|
}
|
|
888
|
|
|
889
|
if(authorshipCache == null) {
|
|
890
|
criteria.add(Restrictions.eq("name.authorshipCache", ""));
|
|
891
|
} else if(!authorshipCache.equals("*")) {
|
|
892
|
criteria.add(Restrictions.eq("name.authorshipCache", authorshipCache));
|
|
893
|
}
|
|
894
|
|
|
895
|
if(rank != null) {
|
|
896
|
criteria.add(Restrictions.eq("name.rank", rank));
|
|
897
|
}
|
|
898
|
|
|
899
|
criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));
|
|
900
|
|
|
901
|
return (Long)criteria.uniqueResult();
|
|
902
|
}
|
|
903
|
|
|
904
|
@Override
|
|
905
|
public <T extends TaxonBase> List<T> findTaxaByName(Class<T> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet,
|
|
906
|
String infraSpecificEpithet, String authorship, Rank rank, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
|
|
907
|
checkNotInPriorView("TaxonDaoHibernateImpl.findTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, String authorship, Rank rank, Integer pageSize,Integer pageNumber, List<String> propertyPaths)");
|
|
908
|
Criteria criteria = getCriteria(clazz);
|
|
909
|
|
|
910
|
criteria.setFetchMode( "name", FetchMode.JOIN );
|
|
911
|
criteria.createAlias("name", "name");
|
|
912
|
|
|
913
|
if(genusOrUninomial == null) {
|
|
914
|
criteria.add(Restrictions.isNull("name.genusOrUninomial"));
|
|
915
|
} else if(!genusOrUninomial.equals("*")) {
|
|
916
|
criteria.add(Restrictions.eq("name.genusOrUninomial", genusOrUninomial));
|
|
917
|
}
|
|
918
|
|
|
919
|
if(infraGenericEpithet == null) {
|
|
920
|
criteria.add(Restrictions.isNull("name.infraGenericEpithet"));
|
|
921
|
} else if(!infraGenericEpithet.equals("*")) {
|
|
922
|
criteria.add(Restrictions.eq("name.infraGenericEpithet", infraGenericEpithet));
|
|
923
|
}
|
|
924
|
|
|
925
|
if(specificEpithet == null) {
|
|
926
|
criteria.add(Restrictions.isNull("name.specificEpithet"));
|
|
927
|
} else if(!specificEpithet.equals("*")) {
|
|
928
|
criteria.add(Restrictions.eq("name.specificEpithet", specificEpithet));
|
|
929
|
}
|
|
930
|
|
|
931
|
if(infraSpecificEpithet == null) {
|
|
932
|
criteria.add(Restrictions.isNull("name.infraSpecificEpithet"));
|
|
933
|
} else if(!infraSpecificEpithet.equals("*")) {
|
|
934
|
criteria.add(Restrictions.eq("name.infraSpecificEpithet", infraSpecificEpithet));
|
|
935
|
}
|
|
936
|
|
|
937
|
if(authorship == null) {
|
|
938
|
criteria.add(Restrictions.eq("name.authorshipCache", ""));
|
|
939
|
} else if(!authorship.equals("*")) {
|
|
940
|
criteria.add(Restrictions.eq("name.authorshipCache", authorship));
|
|
941
|
}
|
|
942
|
|
|
943
|
if(rank != null) {
|
|
944
|
criteria.add(Restrictions.eq("name.rank", rank));
|
|
945
|
}
|
|
946
|
|
|
947
|
if(pageSize != null) {
|
|
948
|
criteria.setMaxResults(pageSize);
|
|
949
|
if(pageNumber != null) {
|
|
950
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
951
|
} else {
|
|
952
|
criteria.setFirstResult(0);
|
|
953
|
}
|
|
954
|
}
|
|
955
|
|
|
956
|
@SuppressWarnings({ "unchecked"})
|
|
957
|
List<T> result = criteria.list();
|
|
958
|
|
|
959
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
960
|
return result;
|
|
961
|
}
|
|
962
|
|
|
963
|
@Override
|
|
964
|
public long countTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
|
|
965
|
boolean includeUnpublished, Direction direction) {
|
|
966
|
Set<TaxonRelationshipType> types = null;
|
|
967
|
if (type != null){
|
|
968
|
types = new HashSet<>();
|
|
969
|
types.add(type);
|
|
970
|
}
|
|
971
|
return countTaxonRelationships(taxon, types, includeUnpublished, direction);
|
|
972
|
}
|
|
973
|
|
|
974
|
@Override
|
|
975
|
public long countTaxonRelationships(Taxon taxon, Set<TaxonRelationshipType> types,
|
|
976
|
boolean includeUnpublished, Direction direction) {
|
|
977
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
978
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
979
|
|
|
980
|
String queryString = prepareTaxonRelationshipQuery(types, includeUnpublished, direction, true);
|
|
981
|
Query<Long> query = getSession().createQuery(queryString, Long.class);
|
|
982
|
query.setParameter("relatedTaxon", taxon);
|
|
983
|
if(types != null) {
|
|
984
|
query.setParameterList("types",types);
|
|
985
|
}
|
|
986
|
if(! includeUnpublished) {
|
|
987
|
query.setParameter("publish",Boolean.TRUE);
|
|
988
|
}
|
|
989
|
return query.uniqueResult();
|
|
990
|
} else {
|
|
991
|
//TODO unpublished
|
|
992
|
|
|
993
|
AuditQuery query = makeAuditQuery(TaxonRelationship.class, auditEvent);
|
|
994
|
query.add(AuditEntity.relatedId(direction.toString()).eq(taxon.getId()));
|
|
995
|
query.addProjection(AuditEntity.id().count());
|
|
996
|
|
|
997
|
if(types != null) {
|
|
998
|
//TODO adapt to new Set semantic, was single type before
|
|
999
|
// query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
1000
|
}
|
|
1001
|
|
|
1002
|
return (Long)query.getSingleResult();
|
|
1003
|
}
|
|
1004
|
}
|
|
1005
|
|
|
1006
|
|
|
1007
|
/**
|
|
1008
|
* @param type
|
|
1009
|
* @param includeUnpublished
|
|
1010
|
* @param direction
|
|
1011
|
* @param b
|
|
1012
|
* @return
|
|
1013
|
*/
|
|
1014
|
private String prepareTaxonRelationshipQuery(Set<TaxonRelationshipType> types, boolean includeUnpublished,
|
|
1015
|
Direction direction, boolean isCount) {
|
|
1016
|
String selectStr = isCount? " count(rel) as n ":" rel ";
|
|
1017
|
String result = "SELECT " + selectStr + " FROM TaxonRelationship rel ";
|
|
1018
|
if(direction != null){
|
|
1019
|
result += " WHERE rel."+direction+" = :relatedTaxon";
|
|
1020
|
} else {
|
|
1021
|
result += " WHERE (rel.relatedFrom = :relatedTaxon OR rel.relatedTo = :relatedTaxon )";
|
|
1022
|
}
|
|
1023
|
if (types != null){
|
|
1024
|
result += " AND rel.type IN (:types) ";
|
|
1025
|
}
|
|
1026
|
if(! includeUnpublished) {
|
|
1027
|
result += " AND rel."+direction.invers()+".publish = :publish";
|
|
1028
|
}
|
|
1029
|
return result;
|
|
1030
|
}
|
|
1031
|
|
|
1032
|
@Override
|
|
1033
|
public List<TaxonRelationship> getTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
|
|
1034
|
boolean includeUnpublished, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
|
1035
|
List<String> propertyPaths, Direction direction) {
|
|
1036
|
Set<TaxonRelationshipType> types = null;
|
|
1037
|
if (type != null){
|
|
1038
|
types = new HashSet<>();
|
|
1039
|
types.add(type);
|
|
1040
|
}
|
|
1041
|
return getTaxonRelationships(taxon, types, includeUnpublished, pageSize, pageNumber, orderHints, propertyPaths, direction);
|
|
1042
|
}
|
|
1043
|
|
|
1044
|
@Override
|
|
1045
|
public List<TaxonRelationship> getTaxonRelationships(Taxon taxon, Set<TaxonRelationshipType> types,
|
|
1046
|
boolean includeUnpublished, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
|
1047
|
List<String> propertyPaths, Direction direction) {
|
|
1048
|
|
|
1049
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
1050
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
1051
|
|
|
1052
|
String queryString = prepareTaxonRelationshipQuery(types, includeUnpublished, direction, false);
|
|
1053
|
|
|
1054
|
queryString += orderByClause("rel", orderHints);
|
|
1055
|
|
|
1056
|
Query<TaxonRelationship> query = getSession().createQuery(queryString, TaxonRelationship.class);
|
|
1057
|
query.setParameter("relatedTaxon", taxon);
|
|
1058
|
if(types != null) {
|
|
1059
|
query.setParameterList("types",types);
|
|
1060
|
}
|
|
1061
|
if(! includeUnpublished) {
|
|
1062
|
query.setParameter("publish",Boolean.TRUE);
|
|
1063
|
}
|
|
1064
|
addPageSizeAndNumber(query, pageSize, pageNumber);
|
|
1065
|
|
|
1066
|
List<TaxonRelationship> result = query.list();
|
|
1067
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1068
|
|
|
1069
|
return result;
|
|
1070
|
} else {
|
|
1071
|
//TODO unpublished
|
|
1072
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonRelationship.class,auditEvent.getRevisionNumber());
|
|
1073
|
query.add(AuditEntity.relatedId("relatedTo").eq(taxon.getId()));
|
|
1074
|
|
|
1075
|
if(types != null) {
|
|
1076
|
//FIXME adapt to Set (was single type before)
|
|
1077
|
// query.add(AuditEntity.relatedId("type").eq(types.getId()));
|
|
1078
|
}
|
|
1079
|
|
|
1080
|
if(pageSize != null) {
|
|
1081
|
query.setMaxResults(pageSize);
|
|
1082
|
if(pageNumber != null) {
|
|
1083
|
query.setFirstResult(pageNumber * pageSize);
|
|
1084
|
} else {
|
|
1085
|
query.setFirstResult(0);
|
|
1086
|
}
|
|
1087
|
}
|
|
1088
|
|
|
1089
|
@SuppressWarnings("unchecked")
|
|
1090
|
List<TaxonRelationship> result = query.getResultList();
|
|
1091
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1092
|
|
|
1093
|
// Ugly, but for now, there is no way to sort on a related entity property in Envers,
|
|
1094
|
// and we can't live without this functionality in CATE as it screws up the whole
|
|
1095
|
// taxon tree thing
|
|
1096
|
if(orderHints != null && !orderHints.isEmpty()) {
|
|
1097
|
SortedSet<TaxonRelationship> sortedList = new TreeSet<>(new TaxonRelationshipFromTaxonComparator());
|
|
1098
|
sortedList.addAll(result);
|
|
1099
|
return new ArrayList<>(sortedList);
|
|
1100
|
}
|
|
1101
|
|
|
1102
|
return result;
|
|
1103
|
}
|
|
1104
|
}
|
|
1105
|
|
|
1106
|
class TaxonRelationshipFromTaxonComparator implements Comparator<TaxonRelationship> {
|
|
1107
|
|
|
1108
|
@Override
|
|
1109
|
public int compare(TaxonRelationship o1, TaxonRelationship o2) {
|
|
1110
|
if (o1.equals(o2)){
|
|
1111
|
return 0;
|
|
1112
|
}
|
|
1113
|
int result = o1.getFromTaxon().getTitleCache().compareTo(o2.getFromTaxon().getTitleCache());
|
|
1114
|
if (result == 0 ){
|
|
1115
|
result = o1.getUuid().compareTo(o2.getUuid());
|
|
1116
|
}
|
|
1117
|
return result;
|
|
1118
|
}
|
|
1119
|
|
|
1120
|
}
|
|
1121
|
|
|
1122
|
@Override
|
|
1123
|
public List<Synonym> getSynonyms(Taxon taxon, SynonymType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1124
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
1125
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
1126
|
Criteria criteria = getSession().createCriteria(Synonym.class);
|
|
1127
|
|
|
1128
|
criteria.add(Restrictions.eq("acceptedTaxon", taxon));
|
|
1129
|
if(type != null) {
|
|
1130
|
criteria.add(Restrictions.eq("type", type));
|
|
1131
|
}
|
|
1132
|
|
|
1133
|
addOrder(criteria,orderHints);
|
|
1134
|
|
|
1135
|
if(pageSize != null) {
|
|
1136
|
criteria.setMaxResults(pageSize);
|
|
1137
|
if(pageNumber != null) {
|
|
1138
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
1139
|
} else {
|
|
1140
|
criteria.setFirstResult(0);
|
|
1141
|
}
|
|
1142
|
}
|
|
1143
|
|
|
1144
|
@SuppressWarnings("unchecked")
|
|
1145
|
List<Synonym> result = criteria.list();
|
|
1146
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1147
|
|
|
1148
|
return result;
|
|
1149
|
} else {
|
|
1150
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(Synonym.class,auditEvent.getRevisionNumber());
|
|
1151
|
query.add(AuditEntity.relatedId("acceptedTaxon").eq(taxon.getId()));
|
|
1152
|
|
|
1153
|
if(type != null) {
|
|
1154
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
1155
|
}
|
|
1156
|
|
|
1157
|
if(pageSize != null) {
|
|
1158
|
query.setMaxResults(pageSize);
|
|
1159
|
if(pageNumber != null) {
|
|
1160
|
query.setFirstResult(pageNumber * pageSize);
|
|
1161
|
} else {
|
|
1162
|
query.setFirstResult(0);
|
|
1163
|
}
|
|
1164
|
}
|
|
1165
|
|
|
1166
|
@SuppressWarnings("unchecked")
|
|
1167
|
List<Synonym> result = query.getResultList();
|
|
1168
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1169
|
|
|
1170
|
return result;
|
|
1171
|
}
|
|
1172
|
}
|
|
1173
|
|
|
1174
|
@Override
|
|
1175
|
public void rebuildIndex() {
|
|
1176
|
FullTextSession fullTextSession = Search.getFullTextSession(getSession());
|
|
1177
|
|
|
1178
|
for(TaxonBase<?> taxonBase : list(null,null)) { // re-index all taxon base
|
|
1179
|
Hibernate.initialize(taxonBase.getName());
|
|
1180
|
fullTextSession.index(taxonBase);
|
|
1181
|
}
|
|
1182
|
fullTextSession.flushToIndexes();
|
|
1183
|
}
|
|
1184
|
|
|
1185
|
@Override
|
|
1186
|
public String suggestQuery(String queryString) {
|
|
1187
|
throw new RuntimeException("Query suggestion currently not implemented in TaxonDaoHibernateImpl");
|
|
1188
|
// checkNotInPriorView("TaxonDaoHibernateImpl.suggestQuery(String queryString)");
|
|
1189
|
// String alternativeQueryString = null;
|
|
1190
|
// if (alternativeSpellingSuggestionParser != null) {
|
|
1191
|
// try {
|
|
1192
|
//
|
|
1193
|
// alternativeSpellingSuggestionParser.parse(queryString);
|
|
1194
|
// org.apache.lucene.search.Query alternativeQuery = alternativeSpellingSuggestionParser.suggest(queryString);
|
|
1195
|
// if (alternativeQuery != null) {
|
|
1196
|
// alternativeQueryString = alternativeQuery
|
|
1197
|
// .toString("name.titleCache");
|
|
1198
|
// }
|
|
1199
|
//
|
|
1200
|
// } catch (ParseException e) {
|
|
1201
|
// throw new QueryParseException(e, queryString);
|
|
1202
|
// }
|
|
1203
|
// }
|
|
1204
|
// return alternativeQueryString;
|
|
1205
|
}
|
|
1206
|
|
|
1207
|
@Override
|
|
1208
|
public Taxon acceptedTaxonFor(Synonym synonym, Classification classificationFilter, List<String> propertyPaths){
|
|
1209
|
|
|
1210
|
String hql = prepareListAcceptedTaxaFor(classificationFilter, false);
|
|
1211
|
|
|
1212
|
Query<Taxon> query = getSession().createQuery(hql, Taxon.class);
|
|
1213
|
query.setParameter("synonym", synonym);
|
|
1214
|
if(classificationFilter != null){
|
|
1215
|
query.setParameter("classificationFilter", classificationFilter);
|
|
1216
|
}
|
|
1217
|
|
|
1218
|
List<Taxon> result = query.list();
|
|
1219
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1220
|
return result.isEmpty()? null: result.get(0);
|
|
1221
|
}
|
|
1222
|
|
|
1223
|
@Override
|
|
1224
|
public long countAcceptedTaxonFor(Synonym synonym, Classification classificationFilter){
|
|
1225
|
|
|
1226
|
String hql = prepareListAcceptedTaxaFor(classificationFilter, true);
|
|
1227
|
|
|
1228
|
Query<Long> query = getSession().createQuery(hql, Long.class);
|
|
1229
|
query.setParameter("synonym", synonym);
|
|
1230
|
if(classificationFilter != null){
|
|
1231
|
query.setParameter("classificationFilter", classificationFilter);
|
|
1232
|
}
|
|
1233
|
|
|
1234
|
Long count = query.uniqueResult();
|
|
1235
|
return count;
|
|
1236
|
}
|
|
1237
|
|
|
1238
|
private String prepareListAcceptedTaxaFor(Classification classificationFilter, boolean doCount) {
|
|
1239
|
|
|
1240
|
String hql;
|
|
1241
|
String hqlSelect = "SELECT " + (doCount? "COUNT(taxon)" : "taxon") +
|
|
1242
|
" FROM Synonym as syn "
|
|
1243
|
+ " JOIN syn.acceptedTaxon as taxon ";
|
|
1244
|
String hqlWhere = " WHERE syn = :synonym";
|
|
1245
|
|
|
1246
|
if(classificationFilter != null){
|
|
1247
|
hqlSelect += " JOIN taxon.taxonNodes AS taxonNode";
|
|
1248
|
hqlWhere += " AND taxonNode.classification = :classificationFilter";
|
|
1249
|
}
|
|
1250
|
hql = hqlSelect + hqlWhere;
|
|
1251
|
return hql;
|
|
1252
|
}
|
|
1253
|
|
|
1254
|
@Override
|
|
1255
|
public TaxonBase find(LSID lsid) {
|
|
1256
|
TaxonBase<?> taxonBase = super.find(lsid);
|
|
1257
|
if(taxonBase != null) {
|
|
1258
|
List<String> propertyPaths = new ArrayList<>();
|
|
1259
|
propertyPaths.add("createdBy");
|
|
1260
|
propertyPaths.add("updatedBy");
|
|
1261
|
propertyPaths.add("name");
|
|
1262
|
propertyPaths.add("secSource.citation");
|
|
1263
|
propertyPaths.add("relationsToThisTaxon");
|
|
1264
|
propertyPaths.add("relationsToThisTaxon.fromTaxon");
|
|
1265
|
propertyPaths.add("relationsToThisTaxon.toTaxon");
|
|
1266
|
propertyPaths.add("relationsFromThisTaxon");
|
|
1267
|
propertyPaths.add("relationsFromThisTaxon.toTaxon");
|
|
1268
|
propertyPaths.add("relationsToThisTaxon.type");
|
|
1269
|
propertyPaths.add("synonyms");
|
|
1270
|
propertyPaths.add("synonyms.type");
|
|
1271
|
propertyPaths.add("descriptions");
|
|
1272
|
|
|
1273
|
defaultBeanInitializer.initialize(taxonBase, propertyPaths);
|
|
1274
|
}
|
|
1275
|
return taxonBase;
|
|
1276
|
}
|
|
1277
|
|
|
1278
|
@Override
|
|
1279
|
public List<String> taxaByNameNotInDB(List<String> taxonNames){
|
|
1280
|
//get all taxa, already in db
|
|
1281
|
Query<TaxonName> query = getSession().createQuery(
|
|
1282
|
" FROM TaxonName t "
|
|
1283
|
+" WHERE t.nameCache IN (:taxonList)",
|
|
1284
|
TaxonName.class);
|
|
1285
|
query.setParameterList("taxonList", taxonNames);
|
|
1286
|
List<TaxonName> taxaInDB = query.list();
|
|
1287
|
//compare the original list with the result of the query
|
|
1288
|
for (TaxonName taxonName: taxaInDB){
|
|
1289
|
String nameCache = taxonName.getNameCache();
|
|
1290
|
if (taxonNames.contains(nameCache)){
|
|
1291
|
taxonNames.remove(nameCache);
|
|
1292
|
}
|
|
1293
|
}
|
|
1294
|
|
|
1295
|
return taxonNames;
|
|
1296
|
}
|
|
1297
|
|
|
1298
|
@Override
|
|
1299
|
public Map<String, Map<UUID,Set<TaxonName>>> findIdenticalNames(List<UUID> sourceRefUuids, List<String> propertyPaths){
|
|
1300
|
Set<String> nameCacheCandidates = new HashSet<>();
|
|
1301
|
try {
|
|
1302
|
for (int i = 0; i<sourceRefUuids.size()-1;i++){
|
|
1303
|
UUID sourceUuid1 = sourceRefUuids.get(i);
|
|
1304
|
for (int j = i+1; j<sourceRefUuids.size();j++){
|
|
1305
|
UUID sourceUuid2 = sourceRefUuids.get(j);
|
|
1306
|
if (sourceUuid1.equals(sourceUuid2)){
|
|
1307
|
continue; //just in case we have duplicates in the list
|
|
1308
|
}
|
|
1309
|
|
|
1310
|
Query<String> query = getSession().createQuery(
|
|
1311
|
" SELECT DISTINCT n1.nameCache "
|
|
1312
|
+ " FROM TaxonBase t1 JOIN t1.name n1 JOIN t1.sources s1 JOIN s1.citation ref1 "
|
|
1313
|
+ " , TaxonBase t2 JOIN t2.name n2 JOIN t2.sources s2 JOIN s2.citation ref2 "
|
|
1314
|
+ " WHERE ref1.uuid = (:sourceUuid1) "
|
|
1315
|
+ " AND n1.id <> n2.id "
|
|
1316
|
+ " AND ref2.uuid IN (:sourceUuid2)"
|
|
1317
|
+ " AND ref1.uuid <> ref2.uuid "
|
|
1318
|
+ " AND n1.nameCache = n2.nameCache) "
|
|
1319
|
+ " AND t1.publish = 1 AND t2.publish = 1) "
|
|
1320
|
+ " ORDER BY n1.nameCache ",
|
|
1321
|
String.class);
|
|
1322
|
query.setParameter("sourceUuid1", sourceUuid1);
|
|
1323
|
query.setParameter("sourceUuid2", sourceUuid2);
|
|
1324
|
|
|
1325
|
@SuppressWarnings("unchecked")
|
|
1326
|
List<String> queryNameCacheCandidates = query.list();
|
|
1327
|
nameCacheCandidates.addAll(queryNameCacheCandidates);
|
|
1328
|
}
|
|
1329
|
}
|
|
1330
|
|
|
1331
|
Map<UUID, List<TaxonName>> duplicates = new HashMap<>();
|
|
1332
|
for (UUID sourceUuid : sourceRefUuids){
|
|
1333
|
Query<TaxonName> query=getSession().createQuery("SELECT n "
|
|
1334
|
+ " FROM TaxonBase t JOIN t.name n JOIN t.sources s JOIN s.citation ref "
|
|
1335
|
+ " WHERE ref.uuid = :sourceUuid AND n.nameCache IN (:nameCacheCandidates) AND t.publish = 1 "
|
|
1336
|
+ " ORDER BY n.nameCache",
|
|
1337
|
TaxonName.class);
|
|
1338
|
query.setParameter("sourceUuid", sourceUuid);
|
|
1339
|
query.setParameterList("nameCacheCandidates", nameCacheCandidates);
|
|
1340
|
List<TaxonName> sourceDuplicates = query.list();
|
|
1341
|
defaultBeanInitializer.initializeAll(sourceDuplicates, propertyPaths);
|
|
1342
|
|
|
1343
|
duplicates.put(sourceUuid, sourceDuplicates);
|
|
1344
|
}
|
|
1345
|
|
|
1346
|
List<String> nameCacheCandidateList = new ArrayList<>(nameCacheCandidates);
|
|
1347
|
Map<String, Map<UUID,Set<TaxonName>>> result = new HashMap<>();
|
|
1348
|
for (String nameCache: nameCacheCandidateList) {
|
|
1349
|
Map<UUID,Set<TaxonName>> uuidNameMap = new HashMap<>();
|
|
1350
|
result.put(nameCache, uuidNameMap);
|
|
1351
|
for(UUID sourceUuid: duplicates.keySet()){
|
|
1352
|
Set<TaxonName> names = duplicates.get(sourceUuid).stream().filter(name->
|
|
1353
|
name.getNameCache().equals(nameCache)).collect(Collectors.toSet());
|
|
1354
|
uuidNameMap.put(sourceUuid, names);
|
|
1355
|
}
|
|
1356
|
}
|
|
1357
|
|
|
1358
|
return result;
|
|
1359
|
} catch (Exception e) {
|
|
1360
|
e.printStackTrace();
|
|
1361
|
throw e;
|
|
1362
|
}
|
|
1363
|
}
|
|
1364
|
|
|
1365
|
@Override
|
|
1366
|
public long countTaxaByCommonName(String searchString,
|
|
1367
|
Classification classification, MatchMode matchMode,
|
|
1368
|
Set<NamedArea> namedAreas) {
|
|
1369
|
boolean doCount = true;
|
|
1370
|
Query<Long> query = prepareTaxaByCommonName(searchString, classification, matchMode, namedAreas, null, null, doCount, false, Long.class);
|
|
1371
|
if (query != null && !query.list().isEmpty()) {
|
|
1372
|
Long o = query.uniqueResult();
|
|
1373
|
if(o != null) {
|
|
1374
|
return o;
|
|
1375
|
}
|
|
1376
|
}
|
|
1377
|
return 0;
|
|
1378
|
}
|
|
1379
|
|
|
1380
|
private Subselects createByNameHQLString(boolean doConceptRelations,
|
|
1381
|
boolean includeUnpublished, Classification classification, TaxonNode subtree,
|
|
1382
|
Set<NamedArea> areasExpanded, MatchMode matchMode, String searchField){
|
|
1383
|
|
|
1384
|
|
|
1385
|
boolean doAreaRestriction = areasExpanded.size() > 0;
|
|
1386
|
boolean hasTaxonNodeFilter = classification != null || subtree != null;
|
|
1387
|
|
|
1388
|
String doAreaRestrictionSubSelect =
|
|
1389
|
" SELECT %s.id "
|
|
1390
|
+ " FROM Distribution e "
|
|
1391
|
+ " JOIN e.inDescription d "
|
|
1392
|
+ " JOIN d.taxon t " +
|
|
1393
|
(hasTaxonNodeFilter ? " JOIN t.taxonNodes AS tn " : " ");
|
|
1394
|
|
|
1395
|
String doAreaRestrictionConceptRelationSubSelect =
|
|
1396
|
"SELECT %s.id "
|
|
1397
|
+ " FROM Distribution e "
|
|
1398
|
+ " JOIN e.inDescription d"
|
|
1399
|
+ " JOIN d.taxon t";
|
|
1400
|
|
|
1401
|
String doTaxonSubSelect =
|
|
1402
|
" SELECT %s.id "
|
|
1403
|
+ " FROM Taxon t " + (hasTaxonNodeFilter ? " "
|
|
1404
|
+ " JOIN t.taxonNodes AS tn " : " ");
|
|
1405
|
|
|
1406
|
String doTaxonMisappliedNameSubSelect =
|
|
1407
|
" SELECT %s.id "
|
|
1408
|
+ " FROM Taxon t ";
|
|
1409
|
|
|
1410
|
String doTaxonNameJoin = " JOIN t.name n ";
|
|
1411
|
|
|
1412
|
String doSynonymSubSelect =
|
|
1413
|
" FROM Synonym s "
|
|
1414
|
+ " JOIN s.name sn "
|
|
1415
|
+ " LEFT JOIN s.acceptedTaxon ";
|
|
1416
|
|
|
1417
|
String doSynonymNameJoin =
|
|
1418
|
" JOIN t.synonyms s "
|
|
1419
|
+ " JOIN s.name sn";
|
|
1420
|
|
|
1421
|
String doConceptRelationJoin =
|
|
1422
|
" LEFT JOIN t.relationsFromThisTaxon AS rft " +
|
|
1423
|
" LEFT JOIN rft.relatedTo AS rt " +
|
|
1424
|
(hasTaxonNodeFilter ? " LEFT JOIN rt.taxonNodes AS tn2 " : " ") +
|
|
1425
|
" LEFT JOIN rt.name AS n2" +
|
|
1426
|
" LEFT JOIN rft.type as rtype";
|
|
1427
|
|
|
1428
|
String doCommonNamesJoin =
|
|
1429
|
" JOIN t.descriptions AS description "+
|
|
1430
|
" LEFT JOIN description.descriptionElements AS com " +
|
|
1431
|
" LEFT JOIN com.feature f ";
|
|
1432
|
|
|
1433
|
|
|
1434
|
String doTreeWhere = classification == null ? "" : " AND tn.classification = :classification";
|
|
1435
|
String doTreeForConceptRelationsWhere = classification == null ? "": " AND tn2.classification = :classification";
|
|
1436
|
|
|
1437
|
String doSubtreeWhere = subtree == null? "":" AND tn.treeIndex like :treeIndexLike";
|
|
1438
|
String doSubtreeForConceptRelationsWhere = subtree == null? "":" AND tn2.treeIndex like :treeIndexLike";
|
|
1439
|
|
|
1440
|
String doAreaRestrictionWhere = " e.area.uuid in (:namedAreasUuids)";
|
|
1441
|
String doCommonNamesRestrictionWhere = " (com.class = 'CommonTaxonName' and com.name "+matchMode.getMatchOperator()+" :queryString )";
|
|
1442
|
|
|
1443
|
String doSearchFieldWhere = " (%s." + searchField + " " + matchMode.getMatchOperator() + " :queryString OR "
|
|
1444
|
+ " %s.protectedTitleCache = TRUE AND %s.titleCache LIKE :protectedTitleQueryString) ";
|
|
1445
|
|
|
1446
|
String doRelationshipTypeComparison = " rtype in (:rTypeSet) ";
|
|
1447
|
|
|
1448
|
String taxonSubselect = null;
|
|
1449
|
String synonymSubselect = null;
|
|
1450
|
String conceptSelect = null;
|
|
1451
|
String commonNameSubselect = null;
|
|
1452
|
|
|
1453
|
if(hasTaxonNodeFilter){
|
|
1454
|
if (!doConceptRelations){
|
|
1455
|
if(doAreaRestriction){
|
|
1456
|
taxonSubselect = String.format(doAreaRestrictionSubSelect, "t") + doTaxonNameJoin +
|
|
1457
|
" WHERE (1=1) AND " + doAreaRestrictionWhere +
|
|
1458
|
doTreeWhere + doSubtreeWhere +
|
|
1459
|
" AND " + String.format(doSearchFieldWhere, "n", "n", "n");
|
|
1460
|
synonymSubselect = String.format(doAreaRestrictionSubSelect, "s") + doSynonymNameJoin +
|
|
1461
|
" WHERE (1=1) AND " + doAreaRestrictionWhere +
|
|
1462
|
doTreeWhere + doSubtreeWhere +
|
|
1463
|
" AND " + String.format(doSearchFieldWhere, "sn", "sn", "sn");
|
|
1464
|
commonNameSubselect = String.format(doAreaRestrictionSubSelect, "t") + doCommonNamesJoin +
|
|
1465
|
" WHERE (1=1) AND " + doAreaRestrictionWhere +
|
|
1466
|
doTreeWhere + doSubtreeWhere +
|
|
1467
|
" AND " + String.format(doSearchFieldWhere, "n", "n", "n") +
|
|
1468
|
" AND " + doCommonNamesRestrictionWhere;
|
|
1469
|
} else {//no area restriction
|
|
1470
|
taxonSubselect = String.format(doTaxonSubSelect, "t" )+ doTaxonNameJoin +
|
|
1471
|
" WHERE (1=1) " + doTreeWhere + doSubtreeWhere +
|
|
1472
|
" AND " + String.format(doSearchFieldWhere, "n", "n", "n");
|
|
1473
|
synonymSubselect = String.format(doTaxonSubSelect, "s" ).replace("FROM Taxon ", doSynonymSubSelect) + //we could also use default synonym handling here as a taxon node filter requires an accepted taxon (#9047)
|
|
1474
|
" WHERE (1=1) " + doTreeWhere + doSubtreeWhere +
|
|
1475
|
" AND " + String.format(doSearchFieldWhere, "sn", "sn", "sn");
|
|
1476
|
commonNameSubselect =String.format(doTaxonSubSelect, "t" )+ doCommonNamesJoin +
|
|
1477
|
" WHERE (1=1) " + doTreeWhere + doSubtreeWhere +
|
|
1478
|
" AND " + doCommonNamesRestrictionWhere;
|
|
1479
|
}
|
|
1480
|
}else{ //concept relations included
|
|
1481
|
if(doAreaRestriction){
|
|
1482
|
conceptSelect = String.format(doAreaRestrictionConceptRelationSubSelect, "t") + doTaxonNameJoin + doConceptRelationJoin +
|
|
1483
|
" WHERE " + doAreaRestrictionWhere +
|
|
1484
|
" AND " + String.format(doSearchFieldWhere, "n", "n", "n") +
|
|
1485
|
doTreeForConceptRelationsWhere + doSubtreeForConceptRelationsWhere +
|
|
1486
|
" AND " + doRelationshipTypeComparison;
|
|
1487
|
taxonSubselect = String.format(doAreaRestrictionSubSelect, "t") + doTaxonNameJoin +
|
|
1488
|
" WHERE " + doAreaRestrictionWhere +
|
|
1489
|
" AND " + String.format(doSearchFieldWhere, "n", "n", "n") +
|
|
1490
|
doTreeWhere + doSubtreeWhere;
|
|
1491
|
synonymSubselect = String.format(doAreaRestrictionSubSelect, "s") + doSynonymNameJoin +
|
|
1492
|
" WHERE " + doAreaRestrictionWhere +
|
|
1493
|
doTreeWhere + doSubtreeWhere +
|
|
1494
|
" AND " + String.format(doSearchFieldWhere, "sn", "sn", "sn");
|
|
1495
|
commonNameSubselect= String.format(doAreaRestrictionSubSelect, "t")+ doCommonNamesJoin +
|
|
1496
|
" WHERE " + doAreaRestrictionWhere +
|
|
1497
|
doTreeWhere + doSubtreeWhere +
|
|
1498
|
" AND " + doCommonNamesRestrictionWhere;
|
|
1499
|
} else {//no area restriction
|
|
1500
|
conceptSelect = String.format(doTaxonMisappliedNameSubSelect, "t" ) + doTaxonNameJoin + doConceptRelationJoin +
|
|
1501
|
" WHERE " + String.format(doSearchFieldWhere, "n", "n", "n") +
|
|
1502
|
doTreeForConceptRelationsWhere + doSubtreeForConceptRelationsWhere +
|
|
1503
|
" AND " + doRelationshipTypeComparison;
|
|
1504
|
taxonSubselect = String.format(doTaxonSubSelect, "t" ) + doTaxonNameJoin +
|
|
1505
|
" WHERE " + String.format(doSearchFieldWhere, "n", "n", "n") +
|
|
1506
|
doTreeWhere + doSubtreeWhere;
|
|
1507
|
synonymSubselect = String.format(doTaxonSubSelect, "s" ).replace("FROM Taxon ", doSynonymSubSelect) + //we could also use default synonym handling here as a taxon node filter requires an accepted taxon (#9047)
|
|
1508
|
" WHERE (1=1) " + doTreeWhere + doSubtreeWhere +
|
|
1509
|
" AND " + String.format(doSearchFieldWhere, "sn", "sn", "sn");
|
|
1510
|
commonNameSubselect= String.format(doTaxonSubSelect, "t")+ doCommonNamesJoin +
|
|
1511
|
" WHERE (1=1) " + doTreeWhere + doSubtreeWhere +
|
|
1512
|
" AND " + doCommonNamesRestrictionWhere;
|
|
1513
|
}
|
|
1514
|
}
|
|
1515
|
} else { //classification = null && subtree = null
|
|
1516
|
if(doAreaRestriction){
|
|
1517
|
conceptSelect = String.format(doAreaRestrictionConceptRelationSubSelect, "t") + doTaxonNameJoin + doConceptRelationJoin +
|
|
1518
|
" WHERE " + doAreaRestrictionWhere +
|
|
1519
|
" AND " + String.format(doSearchFieldWhere, "n", "n", "n")+
|
|
1520
|
" AND " + doRelationshipTypeComparison;
|
|
1521
|
taxonSubselect = String.format(doAreaRestrictionSubSelect, "t") + doTaxonNameJoin +
|
|
1522
|
" WHERE " + doAreaRestrictionWhere +
|
|
1523
|
" AND " + String.format(doSearchFieldWhere, "n", "n", "n");
|
|
1524
|
synonymSubselect = String.format(doAreaRestrictionSubSelect, "s") + doSynonymNameJoin +
|
|
1525
|
" WHERE " + doAreaRestrictionWhere +
|
|
1526
|
" AND " + String.format(doSearchFieldWhere, "sn", "sn", "sn");
|
|
1527
|
commonNameSubselect = String.format(doAreaRestrictionSubSelect, "t")+ doCommonNamesJoin +
|
|
1528
|
" WHERE " + doAreaRestrictionWhere +
|
|
1529
|
" AND " + doCommonNamesRestrictionWhere;
|
|
1530
|
} else { //no area restriction
|
|
1531
|
conceptSelect = String.format(doTaxonMisappliedNameSubSelect, "t" ) + doTaxonNameJoin + doConceptRelationJoin +
|
|
1532
|
" WHERE " + String.format(doSearchFieldWhere, "n", "n", "n") +
|
|
1533
|
" AND " + doRelationshipTypeComparison;
|
|
1534
|
taxonSubselect = String.format(doTaxonSubSelect, "t" ) + doTaxonNameJoin +
|
|
1535
|
" WHERE " + String.format(doSearchFieldWhere, "n", "n", "n");
|
|
1536
|
synonymSubselect = String.format(doTaxonSubSelect, "s" ).replace("FROM Taxon ", doSynonymSubSelect) +
|
|
1537
|
" WHERE " + String.format(doSearchFieldWhere, "sn", "sn", "sn");
|
|
1538
|
commonNameSubselect = String.format(doTaxonSubSelect, "t" ) +doCommonNamesJoin +
|
|
1539
|
" WHERE "+ doCommonNamesRestrictionWhere;
|
|
1540
|
}
|
|
1541
|
}
|
|
1542
|
|
|
1543
|
if (!includeUnpublished){
|
|
1544
|
taxonSubselect += " AND t.publish = :publish ";
|
|
1545
|
synonymSubselect += " AND s.publish = :publish AND t.publish = :publish ";
|
|
1546
|
commonNameSubselect += " AND t.publish = :publish ";
|
|
1547
|
conceptSelect += " AND t.publish = :publish AND rt.publish = :publish ";
|
|
1548
|
}
|
|
1549
|
|
|
1550
|
Subselects result = new Subselects(taxonSubselect, synonymSubselect, conceptSelect, commonNameSubselect);
|
|
1551
|
return result;
|
|
1552
|
}
|
|
1553
|
|
|
1554
|
private class Subselects{
|
|
1555
|
String taxonSubselect;
|
|
1556
|
String synonymSubselect;
|
|
1557
|
String conceptSelect;
|
|
1558
|
String commonNameSubselect;
|
|
1559
|
private Subselects(String taxonSubselect, String synonymSubselect, String conceptSelect,
|
|
1560
|
String commonNameSubselect) {
|
|
1561
|
this.taxonSubselect = taxonSubselect;
|
|
1562
|
this.synonymSubselect = synonymSubselect;
|
|
1563
|
this.conceptSelect = conceptSelect;
|
|
1564
|
this.commonNameSubselect = commonNameSubselect;
|
|
1565
|
}
|
|
1566
|
}
|
|
1567
|
|
|
1568
|
@Override
|
|
1569
|
public List<UuidAndTitleCache<Taxon>> getTaxaByCommonNameForEditor(
|
|
1570
|
String titleSearchStringSqlized, Classification classification,
|
|
1571
|
MatchMode matchMode, Set<NamedArea> namedAreas) {
|
|
1572
|
|
|
1573
|
Query<Object[]> query = prepareTaxaByCommonName(titleSearchStringSqlized, classification, matchMode, namedAreas, null, null, false, true, Object[].class);
|
|
1574
|
if (query != null){
|
|
1575
|
List<Object[]> resultArray = query.list();
|
|
1576
|
List<UuidAndTitleCache<Taxon>> returnResult = new ArrayList<>() ;
|
|
1577
|
Object[] result;
|
|
1578
|
for(int i = 0; i<resultArray.size();i++){
|
|
1579
|
result = resultArray.get(i);
|
|
1580
|
returnResult.add(new UuidAndTitleCache<>(Taxon.class, (UUID) result[0],(Integer)result[1], (String)result[2], new Boolean(result[4].toString()), null));
|
|
1581
|
}
|
|
1582
|
return returnResult;
|
|
1583
|
}else{
|
|
1584
|
return new ArrayList<>();
|
|
1585
|
}
|
|
1586
|
}
|
|
1587
|
|
|
1588
|
@Override
|
|
1589
|
public <S extends TaxonBase> long countByIdentifier(Class<S> clazz,
|
|
1590
|
String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter, MatchMode matchmode) {
|
|
1591
|
if (subtreeFilter == null){
|
|
1592
|
return countByIdentifier(clazz, identifier, identifierType, matchmode);
|
|
1593
|
}
|
|
1594
|
|
|
1595
|
Class<?> clazzParam = (clazz == null) ? type : clazz;
|
|
1596
|
checkNotInPriorView("TaxonDaoHibernateImpl.countByIdentifier(T clazz, String identifier, DefinedTerm identifierType, TaxonNode subMatchMode matchmode)");
|
|
1597
|
|
|
1598
|
boolean isTaxon = clazzParam == Taxon.class || clazzParam == TaxonBase.class;
|
|
1599
|
boolean isSynonym = clazzParam == Synonym.class || clazzParam == TaxonBase.class;
|
|
1600
|
|
|
1601
|
getSession().update(subtreeFilter); //to avoid LIE when retrieving treeindex
|
|
1602
|
String filterStr = "'" + subtreeFilter.treeIndex() + "%%'";
|
|
1603
|
String accTreeJoin = isTaxon? " LEFT JOIN c.taxonNodes tn " : "";
|
|
1604
|
String synTreeJoin = isSynonym ? " LEFT JOIN c.acceptedTaxon as acc LEFT JOIN acc.taxonNodes synTn " : "";
|
|
1605
|
String accWhere = isTaxon ? "tn.treeIndex like " + filterStr : "(1=0)";
|
|
1606
|
String synWhere = isSynonym ? "synTn.treeIndex like " + filterStr : "(1=0)";
|
|
1607
|
|
|
1608
|
String queryString = "SELECT count(*) FROM %s as c " +
|
|
1609
|
" INNER JOIN c.identifiers as ids " +
|
|
1610
|
accTreeJoin +
|
|
1611
|
synTreeJoin +
|
|
1612
|
" WHERE (1=1) " +
|
|
1613
|
" AND ( " + accWhere + " OR " + synWhere + ")";
|
|
1614
|
queryString = String.format(queryString, clazzParam.getSimpleName());
|
|
1615
|
|
|
1616
|
if (identifier != null){
|
|
1617
|
if (matchmode == null || matchmode == MatchMode.EXACT){
|
|
1618
|
queryString += " AND ids.identifier = '" + identifier + "'";
|
|
1619
|
}else {
|
|
1620
|
queryString += " AND ids.identifier LIKE '" + matchmode.queryStringFrom(identifier) + "'";
|
|
1621
|
}
|
|
1622
|
}
|
|
1623
|
if (identifierType != null){
|
|
1624
|
queryString += " AND ids.type = :type";
|
|
1625
|
}
|
|
1626
|
|
|
1627
|
Query<Long> query = getSession().createQuery(queryString, Long.class);
|
|
1628
|
if (identifierType != null){
|
|
1629
|
query.setParameter("type", identifierType);
|
|
1630
|
}
|
|
1631
|
|
|
1632
|
return query.uniqueResult();
|
|
1633
|
}
|
|
1634
|
|
|
1635
|
@Override
|
|
1636
|
public <S extends TaxonBase> List<Object[]> findByIdentifier(
|
|
1637
|
Class<S> clazz, String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter,
|
|
1638
|
MatchMode matchmode, boolean includeEntity,
|
|
1639
|
Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
|
|
1640
|
|
|
1641
|
checkNotInPriorView("TaxonDaoHibernateImpl.findByIdentifier(T clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)");
|
|
1642
|
Class<?> clazzParam = clazz == null ? type : clazz;
|
|
1643
|
|
|
1644
|
boolean isTaxon = clazzParam == Taxon.class || clazzParam == TaxonBase.class;
|
|
1645
|
boolean isSynonym = clazzParam == Synonym.class || clazzParam == TaxonBase.class;
|
|
1646
|
getSession().update(subtreeFilter); //to avoid LIE when retrieving treeindex
|
|
1647
|
String filterStr = "'" + subtreeFilter.treeIndex() + "%%'";
|
|
1648
|
String accTreeJoin = isTaxon? " LEFT JOIN c.taxonNodes tn " : "";
|
|
1649
|
String synTreeJoin = isSynonym ? " LEFT JOIN c.acceptedTaxon as acc LEFT JOIN acc.taxonNodes synTn " : "";
|
|
1650
|
String accWhere = isTaxon ? "tn.treeIndex like " + filterStr : "(1=0)";
|
|
1651
|
String synWhere = isSynonym ? "synTn.treeIndex like " + filterStr : "(1=0)";
|
|
1652
|
|
|
1653
|
String queryString = " SELECT ids.type, ids.identifier, %s " +
|
|
1654
|
" FROM %s as c " +
|
|
1655
|
" INNER JOIN c.identifiers as ids " +
|
|
1656
|
accTreeJoin +
|
|
1657
|
synTreeJoin +
|
|
1658
|
" WHERE (1=1) " +
|
|
1659
|
" AND ( " + accWhere + " OR " + synWhere + ")";
|
|
1660
|
queryString = String.format(queryString, (includeEntity ? "c":"c.uuid, c.titleCache") , clazzParam.getSimpleName());
|
|
1661
|
|
|
1662
|
//Matchmode and identifier
|
|
1663
|
if (identifier != null){
|
|
1664
|
if (matchmode == null || matchmode == MatchMode.EXACT){
|
|
1665
|
queryString += " AND ids.identifier = '" + identifier + "'";
|
|
1666
|
}else {
|
|
1667
|
queryString += " AND ids.identifier LIKE '" + matchmode.queryStringFrom(identifier) + "'";
|
|
1668
|
}
|
|
1669
|
}
|
|
1670
|
if (identifierType != null){
|
|
1671
|
queryString += " AND ids.type = :type";
|
|
1672
|
}
|
|
1673
|
//order
|
|
1674
|
queryString +=" ORDER BY ids.type.uuid, ids.identifier, c.uuid ";
|
|
1675
|
|
|
1676
|
Query<Object[]> query = getSession().createQuery(queryString, Object[].class);
|
|
1677
|
|
|
1678
|
//parameters
|
|
1679
|
if (identifierType != null){
|
|
1680
|
query.setParameter("type", identifierType);
|
|
1681
|
}
|
|
1682
|
|
|
1683
|
//paging
|
|
1684
|
addPageSizeAndNumber(query, pageSize, pageNumber);
|
|
1685
|
|
|
1686
|
List<Object[]> results = query.list();
|
|
1687
|
//initialize
|
|
1688
|
if (includeEntity){
|
|
1689
|
List<S> entities = new ArrayList<>();
|
|
1690
|
for (Object[] result : results){
|
|
1691
|
entities.add((S)result[2]);
|
|
1692
|
}
|
|
1693
|
defaultBeanInitializer.initializeAll(entities, propertyPaths);
|
|
1694
|
}
|
|
1695
|
return results;
|
|
1696
|
}
|
|
1697
|
|
|
1698
|
/**
|
|
1699
|
* {@inheritDoc}
|
|
1700
|
*
|
|
1701
|
* @see #countByIdentifier(Class, String, DefinedTerm, TaxonNode, MatchMode)
|
|
1702
|
*/
|
|
1703
|
@Override
|
|
1704
|
public <S extends TaxonBase> long countByMarker(Class<S> clazz, MarkerType markerType,
|
|
1705
|
Boolean markerValue, TaxonNode subtreeFilter) {
|
|
1706
|
if (markerType == null){
|
|
1707
|
return 0;
|
|
1708
|
}
|
|
1709
|
|
|
1710
|
if (subtreeFilter == null){
|
|
1711
|
return countByMarker(clazz, markerType, markerValue);
|
|
1712
|
}
|
|
1713
|
|
|
1714
|
Class<?> clazzParam = clazz == null ? type : clazz;
|
|
1715
|
checkNotInPriorView("TaxonDaoHibernateImpl.countByMarker(Class<S> clazz, DefinedTerm markerType, boolean markerValue, TaxonNode subtreeFilter)");
|
|
1716
|
|
|
1717
|
boolean isTaxon = clazzParam == Taxon.class || clazzParam == TaxonBase.class;
|
|
1718
|
boolean isSynonym = clazzParam == Synonym.class || clazzParam == TaxonBase.class;
|
|
1719
|
|
|
1720
|
getSession().update(subtreeFilter); //to avoid LIE when retrieving treeindex
|
|
1721
|
String filterStr = "'" + subtreeFilter.treeIndex() + "%%'";
|
|
1722
|
String accTreeJoin = isTaxon? " LEFT JOIN c.taxonNodes tn " : "";
|
|
1723
|
String synTreeJoin = isSynonym ? " LEFT JOIN c.acceptedTaxon acc LEFT JOIN acc.taxonNodes synTn " : "";
|
|
1724
|
String accWhere = isTaxon ? "tn.treeIndex like " + filterStr : "(1=0)";
|
|
1725
|
String synWhere = isSynonym ? "synTn.treeIndex like " + filterStr : "(1=0)";
|
|
1726
|
|
|
1727
|
String queryString = "SELECT count(*) FROM %s as c " +
|
|
1728
|
" INNER JOIN c.markers as mks " +
|
|
1729
|
accTreeJoin +
|
|
1730
|
synTreeJoin +
|
|
1731
|
" WHERE (1=1) " +
|
|
1732
|
" AND ( " + accWhere + " OR " + synWhere + ")";
|
|
1733
|
queryString = String.format(queryString, clazzParam.getSimpleName());
|
|
1734
|
|
|
1735
|
if (markerValue != null){
|
|
1736
|
queryString += " AND mks.flag = :flag";
|
|
1737
|
}
|
|
1738
|
queryString += " AND mks.markerType = :type";
|
|
1739
|
|
|
1740
|
Query<Long> query = getSession().createQuery(queryString, Long.class);
|
|
1741
|
query.setParameter("type", markerType);
|
|
1742
|
if (markerValue != null){
|
|
1743
|
query.setParameter("flag", markerValue);
|
|
1744
|
}
|
|
1745
|
|
|
1746
|
Long c = query.uniqueResult();
|
|
1747
|
return c;
|
|
1748
|
}
|
|
1749
|
|
|
1750
|
@Override
|
|
1751
|
public <S extends TaxonBase> List<Object[]> findByMarker(Class<S> clazz, MarkerType markerType,
|
|
1752
|
Boolean markerValue, TaxonNode subtreeFilter, boolean includeEntity,
|
|
1753
|
TaxonTitleType titleType, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
|
|
1754
|
checkNotInPriorView("TaxonDaoHibernateImpl.findByMarker(T clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)");
|
|
1755
|
if (markerType == null){
|
|
1756
|
return new ArrayList<Object[]>();
|
|
1757
|
}
|
|
1758
|
if (titleType == null){
|
|
1759
|
titleType = TaxonTitleType.DEFAULT();
|
|
1760
|
}
|
|
1761
|
|
|
1762
|
Class<?> clazzParam = clazz == null ? type : clazz;
|
|
1763
|
|
|
1764
|
boolean isTaxon = clazzParam == Taxon.class || clazzParam == TaxonBase.class;
|
|
1765
|
boolean isSynonym = clazzParam == Synonym.class || clazzParam == TaxonBase.class;
|
|
1766
|
getSession().update(subtreeFilter); //to avoid LIE when retrieving treeindex
|
|
1767
|
String filterStr = "'" + subtreeFilter.treeIndex() + "%%'";
|
|
1768
|
String accTreeJoin = isTaxon? " LEFT JOIN c.taxonNodes tn " : "";
|
|
1769
|
String synTreeJoin = isSynonym ? " LEFT JOIN c.acceptedTaxon as acc LEFT JOIN acc.taxonNodes synTn " : "";
|
|
1770
|
String accWhere = isTaxon ? "tn.treeIndex like " + filterStr : "(1=0)";
|
|
1771
|
String synWhere = isSynonym ? "synTn.treeIndex like " + filterStr : "(1=0)";
|
|
1772
|
String selectParams = includeEntity ? "c" : titleType.hqlReplaceSelect("c.uuid, c.titleCache", "c.titleCache");
|
|
1773
|
String titleTypeJoin = includeEntity ? "" : titleType.hqlJoin();
|
|
1774
|
|
|
1775
|
String queryString = "SELECT mks.markerType, mks.flag, %s " +
|
|
1776
|
" FROM %s as c " +
|
|
1777
|
" INNER JOIN c.markers as mks " +
|
|
1778
|
titleTypeJoin +
|
|
1779
|
accTreeJoin +
|
|
1780
|
synTreeJoin +
|
|
1781
|
" WHERE (1=1) " +
|
|
1782
|
" AND ( " + accWhere + " OR " + synWhere + ")";
|
|
1783
|
queryString = String.format(queryString, selectParams, clazzParam.getSimpleName());
|
|
1784
|
|
|
1785
|
//type and value
|
|
1786
|
if (markerValue != null){
|
|
1787
|
queryString += " AND mks.flag = :flag";
|
|
1788
|
}
|
|
1789
|
queryString += " AND mks.markerType = :type";
|
|
1790
|
//order
|
|
1791
|
queryString +=" ORDER BY mks.markerType.uuid, mks.flag, c.uuid ";
|
|
1792
|
|
|
1793
|
Query<Object[]> query = getSession().createQuery(queryString, Object[].class);
|
|
1794
|
|
|
1795
|
//parameters
|
|
1796
|
query.setParameter("type", markerType);
|
|
1797
|
if (markerValue != null){
|
|
1798
|
query.setParameter("flag", markerValue);
|
|
1799
|
}
|
|
1800
|
|
|
1801
|
//paging
|
|
1802
|
addPageSizeAndNumber(query, pageSize, pageNumber);
|
|
1803
|
|
|
1804
|
List<Object[]> results = query.list();
|
|
1805
|
//initialize
|
|
1806
|
if (includeEntity){
|
|
1807
|
List<S> entities = new ArrayList<S>();
|
|
1808
|
for (Object[] result : results){
|
|
1809
|
entities.add((S)result[2]);
|
|
1810
|
}
|
|
1811
|
defaultBeanInitializer.initializeAll(entities, propertyPaths);
|
|
1812
|
}
|
|
1813
|
return results;
|
|
1814
|
}
|
|
1815
|
|
|
1816
|
@Override
|
|
1817
|
public long countTaxonRelationships(Set<TaxonRelationshipType> types) {
|
|
1818
|
Criteria criteria = getSession().createCriteria(TaxonRelationship.class);
|
|
1819
|
|
|
1820
|
if (types != null) {
|
|
1821
|
if (types.isEmpty()){
|
|
1822
|
return 0l;
|
|
1823
|
}else{
|
|
1824
|
criteria.add(Restrictions.in("type", types) );
|
|
1825
|
}
|
|
1826
|
}
|
|
1827
|
//count
|
|
1828
|
criteria.setProjection(Projections.rowCount());
|
|
1829
|
long result = (Long)criteria.uniqueResult();
|
|
1830
|
|
|
1831
|
return result;
|
|
1832
|
}
|
|
1833
|
|
|
1834
|
@Override
|
|
1835
|
public List<TaxonRelationship> getTaxonRelationships(Set<TaxonRelationshipType> types,
|
|
1836
|
Integer pageSize, Integer pageNumber,
|
|
1837
|
List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1838
|
|
|
1839
|
Criteria criteria = getCriteria(TaxonRelationship.class);
|
|
1840
|
if (types != null) {
|
|
1841
|
if (types.isEmpty()){
|
|
1842
|
return new ArrayList<>();
|
|
1843
|
}else{
|
|
1844
|
criteria.add(Restrictions.in("type", types) );
|
|
1845
|
}
|
|
1846
|
}
|
|
1847
|
addOrder(criteria,orderHints);
|
|
1848
|
addPageSizeAndNumber(criteria, pageSize, pageNumber);
|
|
1849
|
|
|
1850
|
@SuppressWarnings("unchecked")
|
|
1851
|
List<TaxonRelationship> results = criteria.list();
|
|
1852
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
1853
|
|
|
1854
|
return results;
|
|
1855
|
}
|
|
1856
|
|
|
1857
|
@Override
|
|
1858
|
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCache(Integer limit, String pattern){
|
|
1859
|
Session session = getSession();
|
|
1860
|
Query<SortableTaxonNodeQueryResult> query = null;
|
|
1861
|
if (pattern != null){
|
|
1862
|
query = session.createQuery(
|
|
1863
|
"SELECT new " + SortableTaxonNodeQueryResult.class.getName() + "("
|
|
1864
|
+ " tb.uuid, tb.id, tb.titleCache, tb.name.rank "
|
|
1865
|
+ ") "
|
|
1866
|
+ " FROM TaxonBase as tb "
|
|
1867
|
+ " WHERE tb.titleCache LIKE :pattern",
|
|
1868
|
SortableTaxonNodeQueryResult.class);
|
|
1869
|
pattern = pattern.replace("*", "%");
|
|
1870
|
pattern = pattern.replace("?", "_");
|
|
1871
|
pattern = pattern + "%";
|
|
1872
|
query.setParameter("pattern", pattern);
|
|
1873
|
} else {
|
|
1874
|
query = session.createQuery(
|
|
1875
|
" SELECT new " + SortableTaxonNodeQueryResult.class.getName()
|
|
1876
|
+ " (tb.uuid, taxonBase.id, tb.titleCache, tb.name.rank) "
|
|
1877
|
+ " FROM TaxonBase AS tb",
|
|
1878
|
SortableTaxonNodeQueryResult.class);
|
|
1879
|
}
|
|
1880
|
if (limit != null){
|
|
1881
|
query.setMaxResults(limit);
|
|
1882
|
}
|
|
1883
|
|
|
1884
|
return getUuidAndTitleCache(query);
|
|
1885
|
}
|
|
1886
|
|
|
1887
|
@Override
|
|
1888
|
protected List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCache(Query query){
|
|
1889
|
List<UuidAndTitleCache<TaxonBase>> list = new ArrayList<>();
|
|
1890
|
|
|
1891
|
List<SortableTaxonNodeQueryResult> result = query.list();
|
|
1892
|
if (!result.isEmpty()){
|
|
1893
|
Collections.sort(result, new SortableTaxonNodeQueryResultComparator());
|
|
1894
|
}
|
|
1895
|
|
|
1896
|
for(SortableTaxonNodeQueryResult stnqr : result){
|
|
1897
|
list.add(new UuidAndTitleCache<TaxonBase>(stnqr.getTaxonNodeUuid(),stnqr.getTaxonNodeId(), stnqr.getTaxonTitleCache()));
|
|
1898
|
}
|
|
1899
|
return list;
|
|
1900
|
}
|
|
1901
|
|
|
1902
|
|
|
1903
|
}
|