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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.HashSet;
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import java.util.Iterator;
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import java.util.List;
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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 org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.hibernate.Criteria;
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import org.hibernate.FetchMode;
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import org.hibernate.Hibernate;
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import org.hibernate.Query;
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import org.hibernate.Session;
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import org.hibernate.criterion.Criterion;
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import org.hibernate.criterion.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.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.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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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.name.TaxonNameComparator;
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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.taxon.UuidAndTitleCacheTaxonComparator;
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import eu.etaxonomy.cdm.model.view.AuditEvent;
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import eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase;
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import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
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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 = Logger.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 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.add(Restrictions.eq("sec", 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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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, 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,
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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 query = prepareTaxaByName(doTaxa, doSynonyms, doMisappliedNames, doCommonNames, includeUnpublished, searchField, queryString, classification, matchMode, namedAreas, order, pageSize, pageNumber, doCount);
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if (query != null){
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@SuppressWarnings({ "unchecked", "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, String queryString, Classification classification,
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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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boolean includeAuthors = 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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Query query = prepareTaxaByNameForEditor(doTaxa, doSynonyms, doMisappliedNames, doCommonNames, includeUnpublished,
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"nameCache", queryString, classification, matchMode, namedAreas, doCount, order);
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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 query = prepareTaxaByCommonName(queryString, classification, matchMode, namedAreas, pageSize, pageNumber, doCount, false);
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if (query != null){
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@SuppressWarnings("unchecked")
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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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*
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*/
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private Query prepareTaxaByNameForEditor(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, boolean doCommonNames,
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boolean includeUnpublished, String searchField, String queryString, Classification classification,
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MatchMode matchMode, Set<NamedArea> namedAreas, boolean doCount, NameSearchOrder order) {
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return prepareByNameQuery(doTaxa, doSynonyms, doMisappliedNames, doCommonNames, includeUnpublished,
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searchField, queryString,
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classification, matchMode, namedAreas, order, doCount, true);
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}
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/**
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* @param doTaxa
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* @param doSynonyms
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* @param doIncludeMisappliedNames
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* @param doCommonNames
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* @param includeUnpublished
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* @param searchField
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* @param queryString
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* @param classification
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* @param matchMode
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* @param namedAreas
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* @param order
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* @param doCount
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* @param returnIdAndTitle
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* If set true the seach method will not return synonym and taxon
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* entities but an array containing the uuid, titleCache, and the
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* DTYPE in lowercase letters.
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* @return
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*/
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private Query prepareByNameQuery(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames,
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boolean doCommonNames, boolean includeUnpublished, String searchField, String queryString,
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Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas,
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NameSearchOrder order, boolean doCount, boolean returnIdAndTitle){
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boolean doProParteSynonyms = doSynonyms; //we may distinguish in future
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boolean doConceptRelations = doMisappliedNames || doProParteSynonyms;
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if (order == null){
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order = NameSearchOrder.DEFAULT();
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}
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String hqlQueryString = matchMode.queryStringFrom(queryString);
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String selectWhat;
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if (returnIdAndTitle){
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selectWhat = "t.uuid, t.id, t.titleCache ";
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}else {
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selectWhat = (doCount ? "count(t)": "t");
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}
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//area filter
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//TODO share code with taxon node filter
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String hql = "";
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Set<NamedArea> areasExpanded = new HashSet<>();
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344
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if(namedAreas != null && namedAreas.size() > 0){
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345
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// expand areas and restrict by distribution area
|
|
346
|
Query areaQuery = getSession().createQuery("SELECT childArea "
|
|
347
|
+ " FROM NamedArea AS childArea LEFT JOIN childArea.partOf as parentArea "
|
|
348
|
+ " WHERE parentArea = :area");
|
|
349
|
expandNamedAreas(namedAreas, areasExpanded, areaQuery);
|
|
350
|
}
|
|
351
|
boolean doAreaRestriction = areasExpanded.size() > 0;
|
|
352
|
|
|
353
|
Set<UUID> namedAreasUuids = new HashSet<>();
|
|
354
|
for (NamedArea area:areasExpanded){
|
|
355
|
namedAreasUuids.add(area.getUuid());
|
|
356
|
}
|
|
357
|
|
|
358
|
Subselects subSelects = createByNameHQLString(doConceptRelations,
|
|
359
|
includeUnpublished, classification, areasExpanded, matchMode, searchField);
|
|
360
|
String taxonSubselect = subSelects.taxonSubselect;
|
|
361
|
String synonymSubselect = subSelects.synonymSubselect;
|
|
362
|
String conceptSelect = subSelects.conceptSelect;
|
|
363
|
String commonNameSubSelect = subSelects.commonNameSubselect;
|
|
364
|
|
|
365
|
|
|
366
|
if (logger.isDebugEnabled()) {
|
|
367
|
logger.debug("taxonSubselect: " + (taxonSubselect != null ? taxonSubselect: "NULL"));
|
|
368
|
logger.debug("synonymSubselect: " + (synonymSubselect != null ? synonymSubselect: "NULL"));
|
|
369
|
}
|
|
370
|
|
|
371
|
List<Integer> taxonIDs = new ArrayList<>();
|
|
372
|
List<Integer> synonymIDs = new ArrayList<>();
|
|
373
|
|
|
374
|
if(doTaxa){
|
|
375
|
// find Taxa
|
|
376
|
Query subTaxon = getSearchQueryString(hqlQueryString, taxonSubselect);
|
|
377
|
|
|
378
|
addRestrictions(doAreaRestriction, classification, includeUnpublished,
|
|
379
|
namedAreasUuids, subTaxon);
|
|
380
|
taxonIDs = subTaxon.list();
|
|
381
|
}
|
|
382
|
|
|
383
|
if(doSynonyms){
|
|
384
|
// find synonyms
|
|
385
|
Query subSynonym = getSearchQueryString(hqlQueryString, synonymSubselect);
|
|
386
|
addRestrictions(doAreaRestriction, classification, includeUnpublished, namedAreasUuids,subSynonym);
|
|
387
|
synonymIDs = subSynonym.list();
|
|
388
|
}
|
|
389
|
if (doConceptRelations ){
|
|
390
|
Query subMisappliedNames = getSearchQueryString(hqlQueryString, conceptSelect);
|
|
391
|
Set<TaxonRelationshipType> relTypeSet = new HashSet<>();
|
|
392
|
if (doMisappliedNames){
|
|
393
|
relTypeSet.addAll(TaxonRelationshipType.allMisappliedNameTypes());
|
|
394
|
}
|
|
395
|
if (doProParteSynonyms){
|
|
396
|
relTypeSet.addAll(TaxonRelationshipType.allSynonymTypes());
|
|
397
|
}
|
|
398
|
subMisappliedNames.setParameterList("rTypeSet", relTypeSet);
|
|
399
|
addRestrictions(doAreaRestriction, classification, includeUnpublished, namedAreasUuids, subMisappliedNames);
|
|
400
|
taxonIDs.addAll(subMisappliedNames.list());
|
|
401
|
}
|
|
402
|
|
|
403
|
if(doCommonNames){
|
|
404
|
// find Taxa
|
|
405
|
Query subCommonNames = getSearchQueryString(hqlQueryString, commonNameSubSelect);
|
|
406
|
addRestrictions(doAreaRestriction, classification, includeUnpublished, namedAreasUuids, subCommonNames);
|
|
407
|
taxonIDs.addAll(subCommonNames.list());
|
|
408
|
}
|
|
409
|
|
|
410
|
|
|
411
|
if(synonymIDs.size()>0 && taxonIDs.size()>0){
|
|
412
|
hql = "SELECT " + selectWhat;
|
|
413
|
// in doNotReturnFullEntities mode it is nesscary to also return the type of the matching entities:
|
|
414
|
// also return the computed isOrphaned flag
|
|
415
|
if (returnIdAndTitle && !doCount ){
|
|
416
|
hql += ", CASE WHEN t.id in (:taxa) THEN 'taxon' ELSE 'synonym' END, " +
|
|
417
|
" CASE WHEN t.id in (:taxa) "
|
|
418
|
+ " AND t.taxonNodes IS EMPTY "
|
|
419
|
+ " AND t.relationsFromThisTaxon IS EMPTY "
|
|
420
|
+ " AND t.relationsToThisTaxon IS EMPTY "
|
|
421
|
+ " THEN true ELSE false END ";
|
|
422
|
}
|
|
423
|
hql += " FROM %s t " +
|
|
424
|
" WHERE (t.id in (:taxa) OR t.id IN (:synonyms)) ";
|
|
425
|
}else if (synonymIDs.size()>0 ){
|
|
426
|
hql = "SELECT " + selectWhat;
|
|
427
|
// in doNotReturnFullEntities mode it is nesscary to also return the type of the matching entities:
|
|
428
|
// also return the computed isOrphaned flag
|
|
429
|
if (returnIdAndTitle && !doCount ){
|
|
430
|
hql += ", 'synonym', 'false' ";
|
|
431
|
|
|
432
|
}
|
|
433
|
hql += " FROM %s t " +
|
|
434
|
" WHERE t.id in (:synonyms) ";
|
|
435
|
|
|
436
|
} else if (taxonIDs.size()>0 ){
|
|
437
|
hql = "SELECT " + selectWhat;
|
|
438
|
// in doNotReturnFullEntities mode it is nesscary to also return the type of the matching entities:
|
|
439
|
// also return the computed isOrphaned flag
|
|
440
|
if (returnIdAndTitle && !doCount ){
|
|
441
|
hql += ", 'taxon', " +
|
|
442
|
" CASE WHEN t.taxonNodes is empty "
|
|
443
|
+ " AND t.relationsFromThisTaxon is empty "
|
|
444
|
+ " AND t.relationsToThisTaxon is empty "
|
|
445
|
+ "THEN true ELSE false END ";
|
|
446
|
}
|
|
447
|
hql += " FROM %s t " +
|
|
448
|
" WHERE t.id in (:taxa) ";
|
|
449
|
} else if (StringUtils.isBlank(queryString)){
|
|
450
|
hql = "SELECT " + selectWhat + " FROM %s t";
|
|
451
|
} else{
|
|
452
|
return null;
|
|
453
|
}
|
|
454
|
|
|
455
|
String classString;
|
|
456
|
if ((doTaxa || doCommonNames || doConceptRelations) && doSynonyms){
|
|
457
|
classString = "TaxonBase";
|
|
458
|
} else if (doTaxa || doCommonNames){
|
|
459
|
classString = "Taxon";
|
|
460
|
} else if (doSynonyms && !(doCommonNames|| doTaxa || doConceptRelations)){
|
|
461
|
classString = "Synonym"; // as long as doProParteSynonyms = doSynonyms this case should not happen
|
|
462
|
} else{//only misappliedNames
|
|
463
|
classString = "Taxon";
|
|
464
|
}
|
|
465
|
|
|
466
|
hql = String.format(hql, classString);
|
|
467
|
|
|
468
|
if (hql == "") {
|
|
469
|
return null;
|
|
470
|
}
|
|
471
|
if(!doCount){
|
|
472
|
String orderBy = " ORDER BY ";
|
|
473
|
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";
|
|
474
|
|
|
475
|
if (order == NameSearchOrder.LENGTH_ALPHA_NAME){
|
|
476
|
orderBy += " length(t.name.nameCache), " + alphabeticBase;
|
|
477
|
}else if (order == NameSearchOrder.LENGTH_ALPHA_TITLE){
|
|
478
|
orderBy += " length(t.name.titleCache), " + alphabeticBase;
|
|
479
|
}else {
|
|
480
|
orderBy += alphabeticBase;
|
|
481
|
}
|
|
482
|
|
|
483
|
hql += orderBy;
|
|
484
|
}
|
|
485
|
|
|
486
|
if(logger.isDebugEnabled()){ logger.debug("hql: " + hql);}
|
|
487
|
Query query = getSession().createQuery(hql);
|
|
488
|
|
|
489
|
// find taxa and synonyms
|
|
490
|
if (taxonIDs.size()>0){
|
|
491
|
query.setParameterList("taxa", taxonIDs);
|
|
492
|
}
|
|
493
|
if (synonymIDs.size()>0){
|
|
494
|
query.setParameterList("synonyms",synonymIDs);
|
|
495
|
}
|
|
496
|
if (taxonIDs.size()== 0 && synonymIDs.size() == 0){
|
|
497
|
return null;
|
|
498
|
}
|
|
499
|
|
|
500
|
return query;
|
|
501
|
}
|
|
502
|
|
|
503
|
/**
|
|
504
|
* @param hqlQueryString
|
|
505
|
* @param synonymSubselect
|
|
506
|
* @return
|
|
507
|
*/
|
|
508
|
protected Query getSearchQueryString(String hqlQueryString, String synonymSubselect) {
|
|
509
|
return getSession().createQuery(synonymSubselect).setParameter("queryString", hqlQueryString);
|
|
510
|
}
|
|
511
|
|
|
512
|
/**
|
|
513
|
* @param includeUnpublished
|
|
514
|
* @param classification
|
|
515
|
* @param doAreaRestriction
|
|
516
|
* @param namedAreasUuids
|
|
517
|
* @param subTaxon
|
|
518
|
*/
|
|
519
|
protected void addRestrictions(boolean doAreaRestriction, Classification classification, boolean includeUnpublished,
|
|
520
|
Set<UUID> namedAreasUuids, Query query) {
|
|
521
|
if(doAreaRestriction){
|
|
522
|
query.setParameterList("namedAreasUuids", namedAreasUuids);
|
|
523
|
}
|
|
524
|
if(classification != null){
|
|
525
|
query.setParameter("classification", classification);
|
|
526
|
}
|
|
527
|
if(!includeUnpublished){
|
|
528
|
query.setBoolean("publish", true);
|
|
529
|
}
|
|
530
|
}
|
|
531
|
|
|
532
|
|
|
533
|
/**
|
|
534
|
* @param searchField the field in TaxonName to be searched through usually either <code>nameCache</code> or <code>titleCache</code>
|
|
535
|
* @param queryString
|
|
536
|
* @param classification TODO
|
|
537
|
* @param matchMode
|
|
538
|
* @param namedAreas
|
|
539
|
* @param pageSize
|
|
540
|
* @param pageNumber
|
|
541
|
* @param doCount
|
|
542
|
* @param clazz
|
|
543
|
* @return
|
|
544
|
*
|
|
545
|
* FIXME implement classification restriction & implement test: see {@link TaxonDaoHibernateImplTest#testCountTaxaByName()}
|
|
546
|
*/
|
|
547
|
private Query prepareTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames,
|
|
548
|
boolean doCommonNames, boolean includeUnpublished, String searchField, String queryString,
|
|
549
|
Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas, NameSearchOrder order, Integer pageSize, Integer pageNumber, boolean doCount) {
|
|
550
|
|
|
551
|
Query query = prepareByNameQuery(doTaxa, doSynonyms, doMisappliedNames, doCommonNames, includeUnpublished,
|
|
552
|
searchField, queryString, classification, matchMode, namedAreas, order, doCount, false);
|
|
553
|
|
|
554
|
if(pageSize != null && !doCount && query != null) {
|
|
555
|
query.setMaxResults(pageSize);
|
|
556
|
if(pageNumber != null) {
|
|
557
|
query.setFirstResult(pageNumber * pageSize);
|
|
558
|
}
|
|
559
|
}
|
|
560
|
|
|
561
|
return query;
|
|
562
|
}
|
|
563
|
|
|
564
|
private Query prepareTaxaByCommonName(String queryString, Classification classification,
|
|
565
|
MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber,
|
|
566
|
boolean doCount, boolean returnIdAndTitle){
|
|
567
|
|
|
568
|
String what = "select distinct";
|
|
569
|
if (returnIdAndTitle){
|
|
570
|
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 ";
|
|
571
|
}else {
|
|
572
|
what += (doCount ? " count(t)": " t");
|
|
573
|
}
|
|
574
|
String hql= what + " from Taxon t " +
|
|
575
|
"join t.descriptions d "+
|
|
576
|
"join d.descriptionElements e " +
|
|
577
|
"join e.feature f " +
|
|
578
|
"where f.supportsCommonTaxonName = true and e.name "+matchMode.getMatchOperator()+" :queryString";//and ls.text like 'common%'";
|
|
579
|
|
|
580
|
Query query = getSession().createQuery(hql);
|
|
581
|
|
|
582
|
query.setParameter("queryString", matchMode.queryStringFrom(queryString));
|
|
583
|
|
|
584
|
if(pageSize != null && !doCount) {
|
|
585
|
query.setMaxResults(pageSize);
|
|
586
|
if(pageNumber != null) {
|
|
587
|
query.setFirstResult(pageNumber * pageSize);
|
|
588
|
}
|
|
589
|
}
|
|
590
|
return query;
|
|
591
|
}
|
|
592
|
|
|
593
|
@Override
|
|
594
|
public long countTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, boolean doCommonNames,
|
|
595
|
boolean doIncludeAuthors, String queryString, Classification classification,
|
|
596
|
MatchMode matchMode, Set<NamedArea> namedAreas, boolean includeUnpublished) {
|
|
597
|
|
|
598
|
boolean doCount = true;
|
|
599
|
/*
|
|
600
|
boolean doTaxa = true;
|
|
601
|
boolean doSynonyms = true;
|
|
602
|
if (clazz.equals(Taxon.class)){
|
|
603
|
doSynonyms = false;
|
|
604
|
} else if (clazz.equals(Synonym.class)){
|
|
605
|
doTaxa = false;
|
|
606
|
}
|
|
607
|
*/
|
|
608
|
String searchField = doIncludeAuthors ? "titleCache": "nameCache";
|
|
609
|
|
|
610
|
Query query = prepareTaxaByName(doTaxa, doSynonyms, doMisappliedNames, doCommonNames, includeUnpublished,
|
|
611
|
searchField, queryString, classification, matchMode, namedAreas, null, null, null, doCount);
|
|
612
|
if (query != null) {
|
|
613
|
return (Long)query.uniqueResult();
|
|
614
|
}else{
|
|
615
|
return 0;
|
|
616
|
}
|
|
617
|
}
|
|
618
|
|
|
619
|
/**
|
|
620
|
* @param namedAreas
|
|
621
|
* @param areasExpanded
|
|
622
|
* @param areaQuery
|
|
623
|
*/
|
|
624
|
private void expandNamedAreas(Collection<NamedArea> namedAreas, Set<NamedArea> areasExpanded, Query areaQuery) {
|
|
625
|
List<NamedArea> childAreas;
|
|
626
|
for(NamedArea a : namedAreas){
|
|
627
|
areasExpanded.add(a);
|
|
628
|
areaQuery.setParameter("area", a);
|
|
629
|
childAreas = areaQuery.list();
|
|
630
|
if(childAreas.size() > 0){
|
|
631
|
areasExpanded.addAll(childAreas);
|
|
632
|
expandNamedAreas(childAreas, areasExpanded, areaQuery);
|
|
633
|
}
|
|
634
|
}
|
|
635
|
}
|
|
636
|
|
|
637
|
|
|
638
|
@Override
|
|
639
|
public UUID delete(TaxonBase taxonBase) throws DataAccessException{
|
|
640
|
if (taxonBase == null){
|
|
641
|
logger.warn("TaxonBase was 'null'");
|
|
642
|
return null;
|
|
643
|
}
|
|
644
|
|
|
645
|
// Merge the object in if it is detached
|
|
646
|
//
|
|
647
|
// I think this is preferable to catching lazy initialization errors
|
|
648
|
// as that solution only swallows and hides the exception, but doesn't
|
|
649
|
// actually solve it.
|
|
650
|
taxonBase = (TaxonBase)getSession().merge(taxonBase);
|
|
651
|
|
|
652
|
taxonBase.removeSources();
|
|
653
|
|
|
654
|
|
|
655
|
if (taxonBase instanceof Taxon){ // is Taxon
|
|
656
|
Taxon taxon = ((Taxon)taxonBase);
|
|
657
|
Set<Synonym> syns = new HashSet<>(taxon.getSynonyms());
|
|
658
|
for (Synonym syn: syns){
|
|
659
|
taxon.removeSynonym(syn);
|
|
660
|
}
|
|
661
|
}
|
|
662
|
|
|
663
|
return super.delete(taxonBase);
|
|
664
|
|
|
665
|
}
|
|
666
|
|
|
667
|
@Override
|
|
668
|
public List<TaxonBase> findByNameTitleCache(boolean doTaxa, boolean doSynonyms, boolean includeUnpublished, String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas, NameSearchOrder order, Integer pageNumber, Integer pageSize, List<String> propertyPaths) {
|
|
669
|
|
|
670
|
boolean doCount = false;
|
|
671
|
Query query = prepareTaxaByName(doTaxa, doSynonyms, false, false, includeUnpublished, "titleCache", queryString, classification, matchMode, namedAreas, order, pageSize, pageNumber, doCount);
|
|
672
|
if (query != null){
|
|
673
|
@SuppressWarnings({ "unchecked", "rawtypes" })
|
|
674
|
List<TaxonBase> results = query.list();
|
|
675
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
676
|
return results;
|
|
677
|
}
|
|
678
|
return new ArrayList<>();
|
|
679
|
|
|
680
|
}
|
|
681
|
|
|
682
|
@Override
|
|
683
|
public TaxonBase findByUuid(UUID uuid, List<Criterion> criteria, List<String> propertyPaths) {
|
|
684
|
|
|
685
|
Criteria crit = getSession().createCriteria(type);
|
|
686
|
|
|
687
|
if (uuid != null) {
|
|
688
|
crit.add(Restrictions.eq("uuid", uuid));
|
|
689
|
} else {
|
|
690
|
logger.warn("UUID is NULL");
|
|
691
|
return null;
|
|
692
|
}
|
|
693
|
if(criteria != null){
|
|
694
|
for (Criterion criterion : criteria) {
|
|
695
|
crit.add(criterion);
|
|
696
|
}
|
|
697
|
}
|
|
698
|
crit.addOrder(Order.asc("uuid"));
|
|
699
|
|
|
700
|
@SuppressWarnings({ "unchecked", "rawtypes" })
|
|
701
|
List<? extends TaxonBase> results = crit.list();
|
|
702
|
if (results.size() == 1) {
|
|
703
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
704
|
TaxonBase<?> taxon = results.iterator().next();
|
|
705
|
return taxon;
|
|
706
|
} else if (results.size() > 1) {
|
|
707
|
logger.error("Multiple results for UUID: " + uuid);
|
|
708
|
} else if (results.size() == 0) {
|
|
709
|
logger.info("No results for UUID: " + uuid);
|
|
710
|
}
|
|
711
|
|
|
712
|
return null;
|
|
713
|
}
|
|
714
|
|
|
715
|
@Override
|
|
716
|
public List<? extends TaxonBase> findByUuids(List<UUID> uuids, List<Criterion> criteria, List<String> propertyPaths) {
|
|
717
|
|
|
718
|
Criteria crit = getSession().createCriteria(type);
|
|
719
|
|
|
720
|
if (uuids != null) {
|
|
721
|
crit.add(Restrictions.in("uuid", uuids));
|
|
722
|
} else {
|
|
723
|
logger.warn("List<UUID> uuids is NULL");
|
|
724
|
return null;
|
|
725
|
}
|
|
726
|
if(criteria != null){
|
|
727
|
for (Criterion criterion : criteria) {
|
|
728
|
crit.add(criterion);
|
|
729
|
}
|
|
730
|
}
|
|
731
|
crit.addOrder(Order.asc("uuid"));
|
|
732
|
|
|
733
|
@SuppressWarnings({ "unchecked", "rawtypes" })
|
|
734
|
List<? extends TaxonBase> results = crit.list();
|
|
735
|
|
|
736
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
737
|
return results;
|
|
738
|
}
|
|
739
|
|
|
740
|
@Override
|
|
741
|
public long countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted) {
|
|
742
|
checkNotInPriorView("TaxonDaoHibernateImpl.countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted)");
|
|
743
|
|
|
744
|
Criteria crit = getCriteria(type);
|
|
745
|
crit.add(Restrictions.ilike("titleCache", matchMode.queryStringFrom(queryString)));
|
|
746
|
crit.setProjection(Projections.rowCount());
|
|
747
|
return (Long)crit.uniqueResult();
|
|
748
|
}
|
|
749
|
|
|
750
|
|
|
751
|
@Override
|
|
752
|
public long countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted, List<Criterion> criteria) {
|
|
753
|
checkNotInPriorView("TaxonDaoHibernateImpl.countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted, List<Criterion> criteria)");
|
|
754
|
|
|
755
|
Criteria crit = getCriteria(type);
|
|
756
|
crit.add(Restrictions.ilike("titleCache", matchMode.queryStringFrom(queryString)));
|
|
757
|
if(criteria != null){
|
|
758
|
for (Criterion criterion : criteria) {
|
|
759
|
crit.add(criterion);
|
|
760
|
}
|
|
761
|
}
|
|
762
|
crit.setProjection(Projections.rowCount());
|
|
763
|
return (Long)crit.uniqueResult();
|
|
764
|
}
|
|
765
|
|
|
766
|
|
|
767
|
@Override
|
|
768
|
public long countSynonyms(boolean onlyAttachedToTaxon) {
|
|
769
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
770
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
771
|
Query query = null;
|
|
772
|
|
|
773
|
String queryStr =
|
|
774
|
" SELECT count(syn) "
|
|
775
|
+ " FROM Synonym syn";
|
|
776
|
if (onlyAttachedToTaxon){
|
|
777
|
queryStr += " WHERE syn.acceptedTaxon IS NOT NULL";
|
|
778
|
}
|
|
779
|
query = getSession().createQuery(queryStr);
|
|
780
|
|
|
781
|
return (Long)query.uniqueResult();
|
|
782
|
} else {
|
|
783
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(Synonym.class,auditEvent.getRevisionNumber());
|
|
784
|
if (onlyAttachedToTaxon){
|
|
785
|
query.add(new NotNullAuditExpression(new EntityPropertyName("acceptedTaxon")));
|
|
786
|
}
|
|
787
|
query.addProjection(AuditEntity.id().count());
|
|
788
|
|
|
789
|
return (Long)query.getSingleResult();
|
|
790
|
}
|
|
791
|
}
|
|
792
|
|
|
793
|
@Override
|
|
794
|
public long countSynonyms(Taxon taxon, SynonymType type) {
|
|
795
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
796
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
797
|
Criteria criteria = getCriteria(Synonym.class);
|
|
798
|
|
|
799
|
criteria.add(Restrictions.eq("acceptedTaxon", taxon));
|
|
800
|
if(type != null) {
|
|
801
|
criteria.add(Restrictions.eq("type", type));
|
|
802
|
}
|
|
803
|
criteria.setProjection(Projections.rowCount());
|
|
804
|
return (Long)criteria.uniqueResult();
|
|
805
|
} else {
|
|
806
|
AuditQuery query = makeAuditQuery(Synonym.class,auditEvent);
|
|
807
|
query.add(AuditEntity.relatedId("acceptedTaxon").eq(taxon.getId()));
|
|
808
|
query.addProjection(AuditEntity.id().count());
|
|
809
|
|
|
810
|
if(type != null) {
|
|
811
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
812
|
}
|
|
813
|
|
|
814
|
return (Long)query.getSingleResult();
|
|
815
|
}
|
|
816
|
}
|
|
817
|
|
|
818
|
@Override
|
|
819
|
public long countSynonyms(Synonym synonym, SynonymType type) {
|
|
820
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
821
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
822
|
Criteria criteria = getCriteria(Synonym.class);
|
|
823
|
|
|
824
|
criteria.add(Restrictions.isNotNull("acceptedTaxon"));
|
|
825
|
if(type != null) {
|
|
826
|
criteria.add(Restrictions.eq("type", type));
|
|
827
|
}
|
|
828
|
|
|
829
|
criteria.setProjection(Projections.rowCount());
|
|
830
|
return (Long)criteria.uniqueResult();
|
|
831
|
} else {
|
|
832
|
AuditQuery query = makeAuditQuery(Synonym.class,auditEvent);
|
|
833
|
query.add(new NotNullAuditExpression(new EntityPropertyName("acceptedTaxon")));
|
|
834
|
query.addProjection(AuditEntity.id().count());
|
|
835
|
|
|
836
|
if(type != null) {
|
|
837
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
838
|
}
|
|
839
|
|
|
840
|
return (Long)query.getSingleResult();
|
|
841
|
}
|
|
842
|
}
|
|
843
|
|
|
844
|
@Override
|
|
845
|
public long countTaxaByName(Class<? extends TaxonBase> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank) {
|
|
846
|
checkNotInPriorView("TaxonDaoHibernateImpl.countTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank)");
|
|
847
|
Criteria criteria = null;
|
|
848
|
|
|
849
|
criteria = getCriteria(clazz);
|
|
850
|
|
|
851
|
criteria.setFetchMode( "name", FetchMode.JOIN );
|
|
852
|
criteria.createAlias("name", "name");
|
|
853
|
|
|
854
|
if(genusOrUninomial == null) {
|
|
855
|
criteria.add(Restrictions.isNull("name.genusOrUninomial"));
|
|
856
|
} else if(!genusOrUninomial.equals("*")) {
|
|
857
|
criteria.add(Restrictions.eq("name.genusOrUninomial", genusOrUninomial));
|
|
858
|
}
|
|
859
|
|
|
860
|
if(infraGenericEpithet == null) {
|
|
861
|
criteria.add(Restrictions.isNull("name.infraGenericEpithet"));
|
|
862
|
} else if(!infraGenericEpithet.equals("*")) {
|
|
863
|
criteria.add(Restrictions.eq("name.infraGenericEpithet", infraGenericEpithet));
|
|
864
|
}
|
|
865
|
|
|
866
|
if(specificEpithet == null) {
|
|
867
|
criteria.add(Restrictions.isNull("name.specificEpithet"));
|
|
868
|
} else if(!specificEpithet.equals("*")) {
|
|
869
|
criteria.add(Restrictions.eq("name.specificEpithet", specificEpithet));
|
|
870
|
|
|
871
|
}
|
|
872
|
|
|
873
|
if(infraSpecificEpithet == null) {
|
|
874
|
criteria.add(Restrictions.isNull("name.infraSpecificEpithet"));
|
|
875
|
} else if(!infraSpecificEpithet.equals("*")) {
|
|
876
|
criteria.add(Restrictions.eq("name.infraSpecificEpithet", infraSpecificEpithet));
|
|
877
|
}
|
|
878
|
|
|
879
|
if(rank != null) {
|
|
880
|
criteria.add(Restrictions.eq("name.rank", rank));
|
|
881
|
}
|
|
882
|
|
|
883
|
criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));
|
|
884
|
|
|
885
|
return (Long)criteria.uniqueResult();
|
|
886
|
}
|
|
887
|
|
|
888
|
@Override
|
|
889
|
public List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber) {
|
|
890
|
checkNotInPriorView("TaxonDaoHibernateImpl.findTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber)");
|
|
891
|
Criteria criteria = getCriteria(clazz);
|
|
892
|
|
|
893
|
criteria.setFetchMode( "name", FetchMode.JOIN );
|
|
894
|
criteria.createAlias("name", "name");
|
|
895
|
|
|
896
|
if(genusOrUninomial == null) {
|
|
897
|
criteria.add(Restrictions.isNull("name.genusOrUninomial"));
|
|
898
|
} else if(!genusOrUninomial.equals("*")) {
|
|
899
|
criteria.add(Restrictions.eq("name.genusOrUninomial", genusOrUninomial));
|
|
900
|
}
|
|
901
|
|
|
902
|
if(infraGenericEpithet == null) {
|
|
903
|
criteria.add(Restrictions.isNull("name.infraGenericEpithet"));
|
|
904
|
} else if(!infraGenericEpithet.equals("*")) {
|
|
905
|
criteria.add(Restrictions.eq("name.infraGenericEpithet", infraGenericEpithet));
|
|
906
|
}
|
|
907
|
|
|
908
|
if(specificEpithet == null) {
|
|
909
|
criteria.add(Restrictions.isNull("name.specificEpithet"));
|
|
910
|
} else if(!specificEpithet.equals("*")) {
|
|
911
|
criteria.add(Restrictions.eq("name.specificEpithet", specificEpithet));
|
|
912
|
|
|
913
|
}
|
|
914
|
|
|
915
|
if(infraSpecificEpithet == null) {
|
|
916
|
criteria.add(Restrictions.isNull("name.infraSpecificEpithet"));
|
|
917
|
} else if(!infraSpecificEpithet.equals("*")) {
|
|
918
|
criteria.add(Restrictions.eq("name.infraSpecificEpithet", infraSpecificEpithet));
|
|
919
|
}
|
|
920
|
|
|
921
|
if(authorship == null) {
|
|
922
|
criteria.add(Restrictions.eq("name.authorshipCache", ""));
|
|
923
|
} else if(!authorship.equals("*")) {
|
|
924
|
criteria.add(Restrictions.eq("name.authorshipCache", authorship));
|
|
925
|
}
|
|
926
|
|
|
927
|
if(rank != null) {
|
|
928
|
criteria.add(Restrictions.eq("name.rank", rank));
|
|
929
|
}
|
|
930
|
|
|
931
|
if(pageSize != null) {
|
|
932
|
criteria.setMaxResults(pageSize);
|
|
933
|
if(pageNumber != null) {
|
|
934
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
935
|
} else {
|
|
936
|
criteria.setFirstResult(0);
|
|
937
|
}
|
|
938
|
}
|
|
939
|
|
|
940
|
@SuppressWarnings({ "unchecked", "rawtypes" })
|
|
941
|
List<TaxonBase> result = criteria.list();
|
|
942
|
return result;
|
|
943
|
}
|
|
944
|
|
|
945
|
|
|
946
|
@Override
|
|
947
|
public long countTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
|
|
948
|
boolean includeUnpublished, Direction direction) {
|
|
949
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
950
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
951
|
|
|
952
|
String queryString = prepareTaxonRelationshipQuery(type, includeUnpublished, direction, true);
|
|
953
|
Query query = getSession().createQuery(queryString);
|
|
954
|
query.setParameter("relatedTaxon", taxon);
|
|
955
|
if(type != null) {
|
|
956
|
query.setParameter("type",type);
|
|
957
|
}
|
|
958
|
if(! includeUnpublished) {
|
|
959
|
query.setBoolean("publish",Boolean.TRUE);
|
|
960
|
}
|
|
961
|
|
|
962
|
|
|
963
|
// if(type == null) {
|
|
964
|
// query = getSession().createQuery(
|
|
965
|
// "select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship."+direction+" = :relatedTaxon");
|
|
966
|
// } else {
|
|
967
|
// query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship."+direction+" = :relatedTaxon and taxonRelationship.type = :type");
|
|
968
|
// query.setParameter("type",type);
|
|
969
|
// }
|
|
970
|
// query.setParameter("relatedTaxon", taxon);
|
|
971
|
|
|
972
|
return (Long)query.uniqueResult();
|
|
973
|
} else {
|
|
974
|
//TODO unpublished
|
|
975
|
|
|
976
|
AuditQuery query = makeAuditQuery(TaxonRelationship.class, auditEvent);
|
|
977
|
query.add(AuditEntity.relatedId(direction.toString()).eq(taxon.getId()));
|
|
978
|
query.addProjection(AuditEntity.id().count());
|
|
979
|
|
|
980
|
if(type != null) {
|
|
981
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
982
|
}
|
|
983
|
|
|
984
|
return (Long)query.getSingleResult();
|
|
985
|
}
|
|
986
|
}
|
|
987
|
|
|
988
|
|
|
989
|
/**
|
|
990
|
* @param type
|
|
991
|
* @param includeUnpublished
|
|
992
|
* @param direction
|
|
993
|
* @param b
|
|
994
|
* @return
|
|
995
|
*/
|
|
996
|
private String prepareTaxonRelationshipQuery(TaxonRelationshipType type, boolean includeUnpublished,
|
|
997
|
Direction direction, boolean isCount) {
|
|
998
|
String selectStr = isCount? " count(rel) as n ":" rel ";
|
|
999
|
String result = "SELECT " + selectStr +
|
|
1000
|
" FROM TaxonRelationship rel " +
|
|
1001
|
" WHERE rel."+direction+" = :relatedTaxon";
|
|
1002
|
if (type != null){
|
|
1003
|
result += " AND rel.type = :type ";
|
|
1004
|
}
|
|
1005
|
if(! includeUnpublished) {
|
|
1006
|
result += " AND rel."+direction.invers()+".publish = :publish";
|
|
1007
|
}
|
|
1008
|
return result;
|
|
1009
|
}
|
|
1010
|
|
|
1011
|
@Override
|
|
1012
|
public List<TaxonRelationship> getTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
|
|
1013
|
boolean includeUnpublished, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
|
1014
|
List<String> propertyPaths, Direction direction) {
|
|
1015
|
|
|
1016
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
1017
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
1018
|
|
|
1019
|
String queryString = prepareTaxonRelationshipQuery(type, includeUnpublished, direction, false);
|
|
1020
|
|
|
1021
|
queryString += orderByClause("rel", orderHints);
|
|
1022
|
|
|
1023
|
Query query = getSession().createQuery(queryString);
|
|
1024
|
query.setParameter("relatedTaxon", taxon);
|
|
1025
|
if(type != null) {
|
|
1026
|
query.setParameter("type",type);
|
|
1027
|
}
|
|
1028
|
if(! includeUnpublished) {
|
|
1029
|
query.setBoolean("publish",Boolean.TRUE);
|
|
1030
|
}
|
|
1031
|
setPagingParameter(query, pageSize, pageNumber);
|
|
1032
|
|
|
1033
|
// Criteria criteria = getSession().createCriteria(TaxonRelationship.class);
|
|
1034
|
//
|
|
1035
|
// if(direction != null) {
|
|
1036
|
// criteria.add(Restrictions.eq(direction.name(), taxon));
|
|
1037
|
// } else {
|
|
1038
|
// criteria.add(Restrictions.or(
|
|
1039
|
// Restrictions.eq(Direction.relatedFrom.name(), taxon),
|
|
1040
|
// Restrictions.eq(Direction.relatedTo.name(), taxon))
|
|
1041
|
// );
|
|
1042
|
// }
|
|
1043
|
//
|
|
1044
|
// if(type != null) {
|
|
1045
|
// criteria.add(Restrictions.eq("type", type));
|
|
1046
|
// }
|
|
1047
|
//
|
|
1048
|
// addOrder(criteria,orderHints);
|
|
1049
|
//
|
|
1050
|
// if(pageSize != null) {
|
|
1051
|
// criteria.setMaxResults(pageSize);
|
|
1052
|
// if(pageNumber != null) {
|
|
1053
|
// criteria.setFirstResult(pageNumber * pageSize);
|
|
1054
|
// } else {
|
|
1055
|
// criteria.setFirstResult(0);
|
|
1056
|
// }
|
|
1057
|
// }
|
|
1058
|
|
|
1059
|
@SuppressWarnings("unchecked")
|
|
1060
|
List<TaxonRelationship> result = query.list();
|
|
1061
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1062
|
|
|
1063
|
return result;
|
|
1064
|
} else {
|
|
1065
|
//TODO unpublished
|
|
1066
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonRelationship.class,auditEvent.getRevisionNumber());
|
|
1067
|
query.add(AuditEntity.relatedId("relatedTo").eq(taxon.getId()));
|
|
1068
|
|
|
1069
|
if(type != null) {
|
|
1070
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
1071
|
}
|
|
1072
|
|
|
1073
|
if(pageSize != null) {
|
|
1074
|
query.setMaxResults(pageSize);
|
|
1075
|
if(pageNumber != null) {
|
|
1076
|
query.setFirstResult(pageNumber * pageSize);
|
|
1077
|
} else {
|
|
1078
|
query.setFirstResult(0);
|
|
1079
|
}
|
|
1080
|
}
|
|
1081
|
|
|
1082
|
@SuppressWarnings("unchecked")
|
|
1083
|
List<TaxonRelationship> result = query.getResultList();
|
|
1084
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1085
|
|
|
1086
|
// Ugly, but for now, there is no way to sort on a related entity property in Envers,
|
|
1087
|
// and we can't live without this functionality in CATE as it screws up the whole
|
|
1088
|
// taxon tree thing
|
|
1089
|
if(orderHints != null && !orderHints.isEmpty()) {
|
|
1090
|
SortedSet<TaxonRelationship> sortedList = new TreeSet<>(new TaxonRelationshipFromTaxonComparator());
|
|
1091
|
sortedList.addAll(result);
|
|
1092
|
return new ArrayList<>(sortedList);
|
|
1093
|
}
|
|
1094
|
|
|
1095
|
return result;
|
|
1096
|
}
|
|
1097
|
}
|
|
1098
|
|
|
1099
|
class TaxonRelationshipFromTaxonComparator implements Comparator<TaxonRelationship> {
|
|
1100
|
|
|
1101
|
@Override
|
|
1102
|
public int compare(TaxonRelationship o1, TaxonRelationship o2) {
|
|
1103
|
if (o1.equals(o2)){
|
|
1104
|
return 0;
|
|
1105
|
}
|
|
1106
|
int result = o1.getFromTaxon().getTitleCache().compareTo(o2.getFromTaxon().getTitleCache());
|
|
1107
|
if (result == 0 ){
|
|
1108
|
result = o1.getUuid().compareTo(o2.getUuid());
|
|
1109
|
}
|
|
1110
|
return result;
|
|
1111
|
}
|
|
1112
|
|
|
1113
|
}
|
|
1114
|
|
|
1115
|
@Override
|
|
1116
|
public List<Synonym> getSynonyms(Taxon taxon, SynonymType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1117
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
1118
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
1119
|
Criteria criteria = getSession().createCriteria(Synonym.class);
|
|
1120
|
|
|
1121
|
criteria.add(Restrictions.eq("acceptedTaxon", taxon));
|
|
1122
|
if(type != null) {
|
|
1123
|
criteria.add(Restrictions.eq("type", type));
|
|
1124
|
}
|
|
1125
|
|
|
1126
|
addOrder(criteria,orderHints);
|
|
1127
|
|
|
1128
|
if(pageSize != null) {
|
|
1129
|
criteria.setMaxResults(pageSize);
|
|
1130
|
if(pageNumber != null) {
|
|
1131
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
1132
|
} else {
|
|
1133
|
criteria.setFirstResult(0);
|
|
1134
|
}
|
|
1135
|
}
|
|
1136
|
|
|
1137
|
@SuppressWarnings("unchecked")
|
|
1138
|
List<Synonym> result = criteria.list();
|
|
1139
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1140
|
|
|
1141
|
return result;
|
|
1142
|
} else {
|
|
1143
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(Synonym.class,auditEvent.getRevisionNumber());
|
|
1144
|
query.add(AuditEntity.relatedId("acceptedTaxon").eq(taxon.getId()));
|
|
1145
|
|
|
1146
|
if(type != null) {
|
|
1147
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
1148
|
}
|
|
1149
|
|
|
1150
|
if(pageSize != null) {
|
|
1151
|
query.setMaxResults(pageSize);
|
|
1152
|
if(pageNumber != null) {
|
|
1153
|
query.setFirstResult(pageNumber * pageSize);
|
|
1154
|
} else {
|
|
1155
|
query.setFirstResult(0);
|
|
1156
|
}
|
|
1157
|
}
|
|
1158
|
|
|
1159
|
@SuppressWarnings("unchecked")
|
|
1160
|
List<Synonym> result = query.getResultList();
|
|
1161
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1162
|
|
|
1163
|
return result;
|
|
1164
|
}
|
|
1165
|
}
|
|
1166
|
|
|
1167
|
@Override
|
|
1168
|
public void rebuildIndex() {
|
|
1169
|
FullTextSession fullTextSession = Search.getFullTextSession(getSession());
|
|
1170
|
|
|
1171
|
for(TaxonBase<?> taxonBase : list(null,null)) { // re-index all taxon base
|
|
1172
|
Hibernate.initialize(taxonBase.getName());
|
|
1173
|
fullTextSession.index(taxonBase);
|
|
1174
|
}
|
|
1175
|
fullTextSession.flushToIndexes();
|
|
1176
|
}
|
|
1177
|
|
|
1178
|
@Override
|
|
1179
|
public String suggestQuery(String queryString) {
|
|
1180
|
throw new RuntimeException("Query suggestion currently not implemented in TaxonDaoHibernateImpl");
|
|
1181
|
// checkNotInPriorView("TaxonDaoHibernateImpl.suggestQuery(String queryString)");
|
|
1182
|
// String alternativeQueryString = null;
|
|
1183
|
// if (alternativeSpellingSuggestionParser != null) {
|
|
1184
|
// try {
|
|
1185
|
//
|
|
1186
|
// alternativeSpellingSuggestionParser.parse(queryString);
|
|
1187
|
// org.apache.lucene.search.Query alternativeQuery = alternativeSpellingSuggestionParser.suggest(queryString);
|
|
1188
|
// if (alternativeQuery != null) {
|
|
1189
|
// alternativeQueryString = alternativeQuery
|
|
1190
|
// .toString("name.titleCache");
|
|
1191
|
// }
|
|
1192
|
//
|
|
1193
|
// } catch (ParseException e) {
|
|
1194
|
// throw new QueryParseException(e, queryString);
|
|
1195
|
// }
|
|
1196
|
// }
|
|
1197
|
// return alternativeQueryString;
|
|
1198
|
}
|
|
1199
|
|
|
1200
|
@Override
|
|
1201
|
public Taxon acceptedTaxonFor(Synonym synonym, Classification classificationFilter, List<String> propertyPaths){
|
|
1202
|
|
|
1203
|
String hql = prepareListAcceptedTaxaFor(classificationFilter, false);
|
|
1204
|
|
|
1205
|
Query query = getSession().createQuery(hql);
|
|
1206
|
query.setParameter("synonym", synonym);
|
|
1207
|
if(classificationFilter != null){
|
|
1208
|
query.setParameter("classificationFilter", classificationFilter);
|
|
1209
|
}
|
|
1210
|
|
|
1211
|
@SuppressWarnings("unchecked")
|
|
1212
|
List<Taxon> result = query.list();
|
|
1213
|
|
|
1214
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1215
|
|
|
1216
|
return result.isEmpty()? null: result.get(0);
|
|
1217
|
}
|
|
1218
|
|
|
1219
|
@Override
|
|
1220
|
public long countAcceptedTaxonFor(Synonym synonym, Classification classificationFilter){
|
|
1221
|
|
|
1222
|
String hql = prepareListAcceptedTaxaFor(classificationFilter, true);
|
|
1223
|
|
|
1224
|
Query query = getSession().createQuery(hql);
|
|
1225
|
query.setParameter("synonym", synonym);
|
|
1226
|
if(classificationFilter != null){
|
|
1227
|
query.setParameter("classificationFilter", classificationFilter);
|
|
1228
|
}
|
|
1229
|
|
|
1230
|
Long count = Long.parseLong(query.uniqueResult().toString());
|
|
1231
|
return count;
|
|
1232
|
|
|
1233
|
}
|
|
1234
|
|
|
1235
|
|
|
1236
|
/**
|
|
1237
|
* @param classificationFilter
|
|
1238
|
* @param orderHints
|
|
1239
|
* @return
|
|
1240
|
*/
|
|
1241
|
private String prepareListAcceptedTaxaFor(Classification classificationFilter, boolean doCount) {
|
|
1242
|
|
|
1243
|
String hql;
|
|
1244
|
String hqlSelect = "SELECT " + (doCount? "COUNT(taxon)" : "taxon") +
|
|
1245
|
" FROM Synonym as syn "
|
|
1246
|
+ " JOIN syn.acceptedTaxon as taxon ";
|
|
1247
|
String hqlWhere = " WHERE syn = :synonym";
|
|
1248
|
|
|
1249
|
if(classificationFilter != null){
|
|
1250
|
hqlSelect += " JOIN taxon.taxonNodes AS taxonNode";
|
|
1251
|
hqlWhere += " AND taxonNode.classification = :classificationFilter";
|
|
1252
|
}
|
|
1253
|
hql = hqlSelect + hqlWhere;
|
|
1254
|
return hql;
|
|
1255
|
}
|
|
1256
|
|
|
1257
|
@Override
|
|
1258
|
public TaxonBase find(LSID lsid) {
|
|
1259
|
TaxonBase<?> taxonBase = super.find(lsid);
|
|
1260
|
if(taxonBase != null) {
|
|
1261
|
List<String> propertyPaths = new ArrayList<>();
|
|
1262
|
propertyPaths.add("createdBy");
|
|
1263
|
propertyPaths.add("updatedBy");
|
|
1264
|
propertyPaths.add("name");
|
|
1265
|
propertyPaths.add("sec");
|
|
1266
|
propertyPaths.add("relationsToThisTaxon");
|
|
1267
|
propertyPaths.add("relationsToThisTaxon.fromTaxon");
|
|
1268
|
propertyPaths.add("relationsToThisTaxon.toTaxon");
|
|
1269
|
propertyPaths.add("relationsFromThisTaxon");
|
|
1270
|
propertyPaths.add("relationsFromThisTaxon.toTaxon");
|
|
1271
|
propertyPaths.add("relationsToThisTaxon.type");
|
|
1272
|
propertyPaths.add("synonyms");
|
|
1273
|
propertyPaths.add("synonyms.type");
|
|
1274
|
propertyPaths.add("descriptions");
|
|
1275
|
|
|
1276
|
defaultBeanInitializer.initialize(taxonBase, propertyPaths);
|
|
1277
|
}
|
|
1278
|
return taxonBase;
|
|
1279
|
}
|
|
1280
|
|
|
1281
|
@Override
|
|
1282
|
public List<String> taxaByNameNotInDB(List<String> taxonNames){
|
|
1283
|
//get all taxa, already in db
|
|
1284
|
Query query = getSession().createQuery(
|
|
1285
|
" FROM TaxonName t "
|
|
1286
|
+" WHERE t.nameCache IN (:taxonList)");
|
|
1287
|
query.setParameterList("taxonList", taxonNames);
|
|
1288
|
@SuppressWarnings("unchecked")
|
|
1289
|
List<TaxonName> taxaInDB = query.list();
|
|
1290
|
//compare the original list with the result of the query
|
|
1291
|
for (TaxonName taxonName: taxaInDB){
|
|
1292
|
String nameCache = taxonName.getNameCache();
|
|
1293
|
if (taxonNames.contains(nameCache)){
|
|
1294
|
taxonNames.remove(nameCache);
|
|
1295
|
}
|
|
1296
|
}
|
|
1297
|
|
|
1298
|
return taxonNames;
|
|
1299
|
}
|
|
1300
|
|
|
1301
|
//TODO: mal nur mit UUID probieren (ohne fetch all properties), vielleicht geht das schneller?
|
|
1302
|
@Override
|
|
1303
|
public List<UUID> findIdenticalTaxonNameIds(List<String> propertyPaths){
|
|
1304
|
Query query=getSession().createQuery(
|
|
1305
|
"SELECT tmb2 "
|
|
1306
|
+ " FROM ZoologicalName tmb, ZoologicalName tmb2 FETCH ALL properties "
|
|
1307
|
+ " WHERE tmb.id != tmb2.id AND tmb.nameCache = tmb2.nameCache");
|
|
1308
|
@SuppressWarnings("unchecked")
|
|
1309
|
List<UUID> zooNames = query.list();
|
|
1310
|
|
|
1311
|
return zooNames;
|
|
1312
|
|
|
1313
|
}
|
|
1314
|
|
|
1315
|
@Override
|
|
1316
|
public List<TaxonName> findIdenticalTaxonNames(List<String> propertyPaths) {
|
|
1317
|
|
|
1318
|
Query query=getSession().createQuery(
|
|
1319
|
" SELECT tmb2 "
|
|
1320
|
+ " FROM ZoologicalName tmb, ZoologicalName tmb2 FETCH ALL properties "
|
|
1321
|
+ " WHERE tmb.id != tmb2.id AND tmb.nameCache = tmb2.nameCache");
|
|
1322
|
|
|
1323
|
@SuppressWarnings("unchecked")
|
|
1324
|
List<TaxonName> zooNames = query.list();
|
|
1325
|
|
|
1326
|
TaxonNameComparator taxComp = new TaxonNameComparator();
|
|
1327
|
Collections.sort(zooNames, taxComp);
|
|
1328
|
|
|
1329
|
for (TaxonName taxonName: zooNames){
|
|
1330
|
defaultBeanInitializer.initialize(taxonName, propertyPaths);
|
|
1331
|
}
|
|
1332
|
|
|
1333
|
return zooNames;
|
|
1334
|
}
|
|
1335
|
|
|
1336
|
@Override
|
|
1337
|
public List<TaxonName> findIdenticalNamesNew(List<String> propertyPaths){
|
|
1338
|
|
|
1339
|
//Hole die beiden Source_ids von "Fauna Europaea" und "Erms" und in sources der names darf jeweils nur das entgegengesetzte auftreten (i member of tmb.taxonBases)
|
|
1340
|
Query query = getSession().createQuery("SELECT id "
|
|
1341
|
+ "FROM Reference "
|
|
1342
|
+ " WHERE titleCache LIKE 'Fauna Europaea database'");
|
|
1343
|
@SuppressWarnings("unchecked")
|
|
1344
|
List<String> secRefFauna = query.list();
|
|
1345
|
query = getSession().createQuery("Select id from Reference where titleCache like 'ERMS'");
|
|
1346
|
@SuppressWarnings("unchecked")
|
|
1347
|
List<String> secRefErms = query.list();
|
|
1348
|
//Query query = getSession().createQuery("select tmb2.nameCache from ZoologicalName tmb, TaxonBase tb1, ZoologicalName tmb2, TaxonBase tb2 where tmb.id != tmb2.id and tb1.name = tmb and tb2.name = tmb2 and tmb.nameCache = tmb2.nameCache and tb1.sec != tb2.sec");
|
|
1349
|
//Get all names of fauna europaea
|
|
1350
|
query = getSession().createQuery("select zn.nameCache from ZoologicalName zn, TaxonBase tb where tb.name = zn and tb.sec.id = :secRefFauna");
|
|
1351
|
query.setParameter("secRefFauna", secRefFauna.get(0));
|
|
1352
|
@SuppressWarnings("unchecked")
|
|
1353
|
List<String> namesFauna= query.list();
|
|
1354
|
|
|
1355
|
//Get all names of erms
|
|
1356
|
|
|
1357
|
query = getSession().createQuery("select zn.nameCache from ZoologicalName zn, TaxonBase tb where tb.name = zn and tb.sec.id = :secRefErms");
|
|
1358
|
query.setParameter("secRefErms", secRefErms.get(0));
|
|
1359
|
|
|
1360
|
@SuppressWarnings("unchecked")
|
|
1361
|
List<String> namesErms = query.list();
|
|
1362
|
/*TaxonNameComparator comp = new TaxonNameComparator();
|
|
1363
|
Collections.sort(namesFauna);
|
|
1364
|
Collections.sort(namesErms);
|
|
1365
|
*/
|
|
1366
|
List <String> identicalNames = new ArrayList<>();
|
|
1367
|
|
|
1368
|
for (String nameFauna: namesFauna){
|
|
1369
|
if (namesErms.contains(nameFauna)){
|
|
1370
|
identicalNames.add(nameFauna);
|
|
1371
|
}
|
|
1372
|
}
|
|
1373
|
|
|
1374
|
query = getSession().createQuery("from ZoologicalName zn where zn.nameCache IN (:identicalNames)");
|
|
1375
|
query.setParameterList("identicalNames", identicalNames);
|
|
1376
|
List<TaxonName> result = query.list();
|
|
1377
|
TaxonName tempName = result.get(0);
|
|
1378
|
|
|
1379
|
Iterator<IdentifiableSource> sources = tempName.getSources().iterator();
|
|
1380
|
|
|
1381
|
TaxonNameComparator taxComp = new TaxonNameComparator();
|
|
1382
|
Collections.sort(result, taxComp);
|
|
1383
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1384
|
return result;
|
|
1385
|
|
|
1386
|
}
|
|
1387
|
|
|
1388
|
//
|
|
1389
|
//
|
|
1390
|
// @Override
|
|
1391
|
// public String getPhylumName(TaxonName name){
|
|
1392
|
// List results = new ArrayList();
|
|
1393
|
// try{
|
|
1394
|
// Query query = getSession().createSQLQuery("select getPhylum("+ name.getId()+");");
|
|
1395
|
// results = query.list();
|
|
1396
|
// }catch(Exception e){
|
|
1397
|
// System.err.println(name.getUuid());
|
|
1398
|
// return null;
|
|
1399
|
// }
|
|
1400
|
// System.err.println("phylum of "+ name.getTitleCache() );
|
|
1401
|
// return (String)results.get(0);
|
|
1402
|
// }
|
|
1403
|
|
|
1404
|
|
|
1405
|
@Override
|
|
1406
|
public long countTaxaByCommonName(String searchString,
|
|
1407
|
Classification classification, MatchMode matchMode,
|
|
1408
|
Set<NamedArea> namedAreas) {
|
|
1409
|
boolean doCount = true;
|
|
1410
|
Query query = prepareTaxaByCommonName(searchString, classification, matchMode, namedAreas, null, null, doCount, false);
|
|
1411
|
if (query != null && !query.list().isEmpty()) {
|
|
1412
|
Object o = query.uniqueResult();
|
|
1413
|
if(o != null) {
|
|
1414
|
return (Long)o;
|
|
1415
|
}
|
|
1416
|
}
|
|
1417
|
return 0;
|
|
1418
|
}
|
|
1419
|
|
|
1420
|
private Subselects createByNameHQLString(boolean doConceptRelations,
|
|
1421
|
boolean includeUnpublished, Classification classification, Set<NamedArea> areasExpanded,
|
|
1422
|
MatchMode matchMode, String searchField){
|
|
1423
|
|
|
1424
|
boolean doAreaRestriction = areasExpanded.size() > 0;
|
|
1425
|
String doAreaRestrictionSubSelect =
|
|
1426
|
" SELECT %s.id "
|
|
1427
|
+ " FROM Distribution e "
|
|
1428
|
+ " JOIN e.inDescription d "
|
|
1429
|
+ " JOIN d.taxon t " +
|
|
1430
|
(classification != null ? " JOIN t.taxonNodes AS tn " : " ");
|
|
1431
|
|
|
1432
|
String doAreaRestrictionConceptRelationSubSelect =
|
|
1433
|
"SELECT %s.id "
|
|
1434
|
+ " FROM Distribution e "
|
|
1435
|
+ " JOIN e.inDescription d"
|
|
1436
|
+ " JOIN d.taxon t";
|
|
1437
|
|
|
1438
|
String doTaxonSubSelect =
|
|
1439
|
" SELECT %s.id "
|
|
1440
|
+ " FROM Taxon t " + (classification != null ? " "
|
|
1441
|
+ " JOIN t.taxonNodes AS tn " : " ");
|
|
1442
|
|
|
1443
|
String doTaxonMisappliedNameSubSelect =
|
|
1444
|
" SELECT %s.id "
|
|
1445
|
+ " FROM Taxon t ";
|
|
1446
|
|
|
1447
|
String doTaxonNameJoin = " JOIN t.name n ";
|
|
1448
|
|
|
1449
|
String doSynonymNameJoin =
|
|
1450
|
" JOIN t.synonyms s "
|
|
1451
|
+ " JOIN s.name sn";
|
|
1452
|
|
|
1453
|
String doConceptRelationJoin =
|
|
1454
|
" LEFT JOIN t.relationsFromThisTaxon AS rft " +
|
|
1455
|
" LEFT JOIN rft.relatedTo AS rt " +
|
|
1456
|
(classification != null ? " LEFT JOIN rt.taxonNodes AS tn2 " : " ") +
|
|
1457
|
" LEFT JOIN rt.name AS n2" +
|
|
1458
|
" LEFT JOIN rft.type as rtype";
|
|
1459
|
|
|
1460
|
String doCommonNamesJoin =
|
|
1461
|
" JOIN t.descriptions AS description "+
|
|
1462
|
" LEFT JOIN description.descriptionElements AS com " +
|
|
1463
|
" LEFT JOIN com.feature f ";
|
|
1464
|
|
|
1465
|
|
|
1466
|
String doClassificationWhere = " tn.classification = :classification";
|
|
1467
|
String doClassificationForConceptRelationsWhere = " tn2.classification = :classification";
|
|
1468
|
|
|
1469
|
String doAreaRestrictionWhere = " e.area.uuid in (:namedAreasUuids)";
|
|
1470
|
String doCommonNamesRestrictionWhere = " (f.supportsCommonTaxonName = true and com.name "+matchMode.getMatchOperator()+" :queryString )";
|
|
1471
|
|
|
1472
|
String doSearchFieldWhere = "%s." + searchField + " " + matchMode.getMatchOperator() + " :queryString";
|
|
1473
|
|
|
1474
|
String doRelationshipTypeComparison = " rtype in (:rTypeSet) ";
|
|
1475
|
|
|
1476
|
String taxonSubselect = null;
|
|
1477
|
String synonymSubselect = null;
|
|
1478
|
String conceptSelect = null;
|
|
1479
|
String commonNameSubselect = null;
|
|
1480
|
|
|
1481
|
if(classification != null ){
|
|
1482
|
if (!doConceptRelations){
|
|
1483
|
if(doAreaRestriction){
|
|
1484
|
taxonSubselect = String.format(doAreaRestrictionSubSelect, "t") + doTaxonNameJoin +
|
|
1485
|
" WHERE " + doAreaRestrictionWhere +
|
|
1486
|
" AND " + doClassificationWhere +
|
|
1487
|
" AND " + String.format(doSearchFieldWhere, "n");
|
|
1488
|
synonymSubselect = String.format(doAreaRestrictionSubSelect, "s") + doSynonymNameJoin +
|
|
1489
|
" WHERE " + doAreaRestrictionWhere +
|
|
1490
|
" AND " + doClassificationWhere +
|
|
1491
|
" AND " + String.format(doSearchFieldWhere, "sn");
|
|
1492
|
commonNameSubselect = String.format(doAreaRestrictionSubSelect, "t") + doCommonNamesJoin +
|
|
1493
|
" WHERE " + doAreaRestrictionWhere +
|
|
1494
|
" AND " + doClassificationWhere +
|
|
1495
|
" AND " + String.format(doSearchFieldWhere, "n") +
|
|
1496
|
" AND " + doCommonNamesRestrictionWhere;
|
|
1497
|
} else {//no area restriction
|
|
1498
|
taxonSubselect = String.format(doTaxonSubSelect, "t" )+ doTaxonNameJoin +
|
|
1499
|
" WHERE " + doClassificationWhere +
|
|
1500
|
" AND " + String.format(doSearchFieldWhere, "n");
|
|
1501
|
synonymSubselect = String.format(doTaxonSubSelect, "s" ) + doSynonymNameJoin +
|
|
1502
|
" WHERE " + doClassificationWhere +
|
|
1503
|
" AND " + String.format(doSearchFieldWhere, "sn");
|
|
1504
|
commonNameSubselect =String.format(doTaxonSubSelect, "t" )+ doCommonNamesJoin +
|
|
1505
|
" WHERE " + doClassificationWhere +
|
|
1506
|
" AND " + doCommonNamesRestrictionWhere;
|
|
1507
|
}
|
|
1508
|
}else{ //concept relations included
|
|
1509
|
if(doAreaRestriction){
|
|
1510
|
conceptSelect = String.format(doAreaRestrictionConceptRelationSubSelect, "t") + doTaxonNameJoin + doConceptRelationJoin +
|
|
1511
|
" WHERE " + doAreaRestrictionWhere +
|
|
1512
|
" AND " + String.format(doSearchFieldWhere, "n") +
|
|
1513
|
" AND " + doClassificationForConceptRelationsWhere +
|
|
1514
|
" AND " + doRelationshipTypeComparison;
|
|
1515
|
taxonSubselect = String.format(doAreaRestrictionSubSelect, "t") + doTaxonNameJoin +
|
|
1516
|
" WHERE " + doAreaRestrictionWhere +
|
|
1517
|
" AND " + String.format(doSearchFieldWhere, "n") +
|
|
1518
|
" AND " + doClassificationWhere;
|
|
1519
|
synonymSubselect = String.format(doAreaRestrictionSubSelect, "s") + doSynonymNameJoin +
|
|
1520
|
" WHERE " + doAreaRestrictionWhere +
|
|
1521
|
" AND " + doClassificationWhere +
|
|
1522
|
" AND " + String.format(doSearchFieldWhere, "sn");
|
|
1523
|
commonNameSubselect= String.format(doAreaRestrictionSubSelect, "t")+ doCommonNamesJoin +
|
|
1524
|
" WHERE " + doAreaRestrictionWhere +
|
|
1525
|
" AND " + doClassificationWhere +
|
|
1526
|
" AND " + doCommonNamesRestrictionWhere;
|
|
1527
|
} else {//no area restriction
|
|
1528
|
conceptSelect = String.format(doTaxonMisappliedNameSubSelect, "t" ) + doTaxonNameJoin + doConceptRelationJoin +
|
|
1529
|
" WHERE " + String.format(doSearchFieldWhere, "n") +
|
|
1530
|
" AND " + doClassificationForConceptRelationsWhere +
|
|
1531
|
" AND " + doRelationshipTypeComparison;
|
|
1532
|
taxonSubselect = String.format(doTaxonSubSelect, "t" ) + doTaxonNameJoin +
|
|
1533
|
" WHERE " + String.format(doSearchFieldWhere, "n") +
|
|
1534
|
" AND "+ doClassificationWhere;
|
|
1535
|
synonymSubselect = String.format(doTaxonSubSelect, "s" ) + doSynonymNameJoin +
|
|
1536
|
" WHERE " + doClassificationWhere +
|
|
1537
|
" AND " + String.format(doSearchFieldWhere, "sn");
|
|
1538
|
commonNameSubselect= String.format(doTaxonSubSelect, "t")+ doCommonNamesJoin +
|
|
1539
|
" WHERE " + doClassificationWhere +
|
|
1540
|
" AND " + doCommonNamesRestrictionWhere;
|
|
1541
|
}
|
|
1542
|
}
|
|
1543
|
} else { //classification = null
|
|
1544
|
if(doAreaRestriction){
|
|
1545
|
conceptSelect = String.format(doAreaRestrictionConceptRelationSubSelect, "t") + doTaxonNameJoin + doConceptRelationJoin +
|
|
1546
|
" WHERE " + doAreaRestrictionWhere +
|
|
1547
|
" AND " + String.format(doSearchFieldWhere, "n")+
|
|
1548
|
" AND " + doRelationshipTypeComparison;
|
|
1549
|
taxonSubselect = String.format(doAreaRestrictionSubSelect, "t") + doTaxonNameJoin +
|
|
1550
|
" WHERE " + doAreaRestrictionWhere +
|
|
1551
|
" AND " + String.format(doSearchFieldWhere, "n");
|
|
1552
|
synonymSubselect = String.format(doAreaRestrictionSubSelect, "s") + doSynonymNameJoin +
|
|
1553
|
" WHERE " + doAreaRestrictionWhere +
|
|
1554
|
" AND " + String.format(doSearchFieldWhere, "sn");
|
|
1555
|
commonNameSubselect = String.format(doAreaRestrictionSubSelect, "t")+ doCommonNamesJoin +
|
|
1556
|
" WHERE " + doAreaRestrictionWhere +
|
|
1557
|
" AND " + doCommonNamesRestrictionWhere;
|
|
1558
|
} else { //no area restriction
|
|
1559
|
conceptSelect = String.format(doTaxonMisappliedNameSubSelect, "t" ) + doTaxonNameJoin + doConceptRelationJoin +
|
|
1560
|
" WHERE " + String.format(doSearchFieldWhere, "n") +
|
|
1561
|
" AND " + doRelationshipTypeComparison;
|
|
1562
|
taxonSubselect = String.format(doTaxonSubSelect, "t" ) + doTaxonNameJoin +
|
|
1563
|
" WHERE " + String.format(doSearchFieldWhere, "n");
|
|
1564
|
synonymSubselect = String.format(doTaxonSubSelect, "s" ) + doSynonymNameJoin +
|
|
1565
|
" WHERE " + String.format(doSearchFieldWhere, "sn");
|
|
1566
|
commonNameSubselect = String.format(doTaxonSubSelect, "t" ) +doCommonNamesJoin +
|
|
1567
|
" WHERE "+ doCommonNamesRestrictionWhere;
|
|
1568
|
}
|
|
1569
|
}
|
|
1570
|
|
|
1571
|
if (!includeUnpublished){
|
|
1572
|
taxonSubselect += " AND t.publish = :publish ";
|
|
1573
|
synonymSubselect += " AND s.publish = :publish AND t.publish = :publish ";
|
|
1574
|
commonNameSubselect += " AND t.publish = :publish ";
|
|
1575
|
conceptSelect += " AND t.publish = :publish AND rt.publish = :publish ";
|
|
1576
|
}
|
|
1577
|
|
|
1578
|
Subselects result = new Subselects(taxonSubselect, synonymSubselect, conceptSelect, commonNameSubselect);
|
|
1579
|
return result;
|
|
1580
|
}
|
|
1581
|
|
|
1582
|
private class Subselects{
|
|
1583
|
String taxonSubselect;
|
|
1584
|
String synonymSubselect;
|
|
1585
|
String conceptSelect;
|
|
1586
|
String commonNameSubselect;
|
|
1587
|
private Subselects(String taxonSubselect, String synonymSubselect, String conceptSelect,
|
|
1588
|
String commonNameSubselect) {
|
|
1589
|
this.taxonSubselect = taxonSubselect;
|
|
1590
|
this.synonymSubselect = synonymSubselect;
|
|
1591
|
this.conceptSelect = conceptSelect;
|
|
1592
|
this.commonNameSubselect = commonNameSubselect;
|
|
1593
|
}
|
|
1594
|
}
|
|
1595
|
|
|
1596
|
@Override
|
|
1597
|
public List<UuidAndTitleCache<Taxon>> getTaxaByCommonNameForEditor(
|
|
1598
|
String titleSearchStringSqlized, Classification classification,
|
|
1599
|
MatchMode matchMode, Set<NamedArea> namedAreas) {
|
|
1600
|
Query query = prepareTaxaByCommonName(titleSearchStringSqlized, classification, matchMode, namedAreas, null, null, false, true);
|
|
1601
|
if (query != null){
|
|
1602
|
@SuppressWarnings("unchecked")
|
|
1603
|
List<Object> resultArray = query.list();
|
|
1604
|
List<UuidAndTitleCache<Taxon>> returnResult = new ArrayList<>() ;
|
|
1605
|
Object[] result;
|
|
1606
|
for(int i = 0; i<resultArray.size();i++){
|
|
1607
|
result = (Object[]) resultArray.get(i);
|
|
1608
|
returnResult.add(new UuidAndTitleCache<Taxon>(Taxon.class, (UUID) result[0],(Integer)result[1], (String)result[2], new Boolean(result[4].toString()), null));
|
|
1609
|
}
|
|
1610
|
return returnResult;
|
|
1611
|
}else{
|
|
1612
|
return new ArrayList<>();
|
|
1613
|
}
|
|
1614
|
}
|
|
1615
|
|
|
1616
|
|
|
1617
|
/**
|
|
1618
|
* @param
|
|
1619
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countByIdentifier(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.model.common.DefinedTerm, eu.etaxonomy.cdm.model.taxon.TaxonNode, eu.etaxonomy.cdm.persistence.query.MatchMode)
|
|
1620
|
*/
|
|
1621
|
@Override
|
|
1622
|
public <S extends TaxonBase> long countByIdentifier(Class<S> clazz,
|
|
1623
|
String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter, MatchMode matchmode) {
|
|
1624
|
if (subtreeFilter == null){
|
|
1625
|
return countByIdentifier(clazz, identifier, identifierType, matchmode);
|
|
1626
|
}
|
|
1627
|
|
|
1628
|
Class<?> clazzParam = (clazz == null) ? type : clazz;
|
|
1629
|
checkNotInPriorView("TaxonDaoHibernateImpl.countByIdentifier(T clazz, String identifier, DefinedTerm identifierType, TaxonNode subMatchMode matchmode)");
|
|
1630
|
|
|
1631
|
boolean isTaxon = clazzParam == Taxon.class || clazzParam == TaxonBase.class;
|
|
1632
|
boolean isSynonym = clazzParam == Synonym.class || clazzParam == TaxonBase.class;
|
|
1633
|
|
|
1634
|
getSession().update(subtreeFilter); //to avoid LIE when retrieving treeindex
|
|
1635
|
String filterStr = "'" + subtreeFilter.treeIndex() + "%%'";
|
|
1636
|
String accTreeJoin = isTaxon? " LEFT JOIN c.taxonNodes tn " : "";
|
|
1637
|
String synTreeJoin = isSynonym ? " LEFT JOIN c.acceptedTaxon as acc LEFT JOIN acc.taxonNodes synTn " : "";
|
|
1638
|
String accWhere = isTaxon ? "tn.treeIndex like " + filterStr : "(1=0)";
|
|
1639
|
String synWhere = isSynonym ? "synTn.treeIndex like " + filterStr : "(1=0)";
|
|
1640
|
|
|
1641
|
String queryString = "SELECT count(*) FROM %s as c " +
|
|
1642
|
" INNER JOIN c.identifiers as ids " +
|
|
1643
|
accTreeJoin +
|
|
1644
|
synTreeJoin +
|
|
1645
|
" WHERE (1=1) " +
|
|
1646
|
" AND ( " + accWhere + " OR " + synWhere + ")";
|
|
1647
|
queryString = String.format(queryString, clazzParam.getSimpleName());
|
|
1648
|
|
|
1649
|
if (identifier != null){
|
|
1650
|
if (matchmode == null || matchmode == MatchMode.EXACT){
|
|
1651
|
queryString += " AND ids.identifier = '" + identifier + "'";
|
|
1652
|
}else {
|
|
1653
|
queryString += " AND ids.identifier LIKE '" + matchmode.queryStringFrom(identifier) + "'";
|
|
1654
|
}
|
|
1655
|
}
|
|
1656
|
if (identifierType != null){
|
|
1657
|
queryString += " AND ids.type = :type";
|
|
1658
|
}
|
|
1659
|
|
|
1660
|
Query query = getSession().createQuery(queryString);
|
|
1661
|
if (identifierType != null){
|
|
1662
|
query.setEntity("type", identifierType);
|
|
1663
|
}
|
|
1664
|
|
|
1665
|
return (Long)query.uniqueResult();
|
|
1666
|
}
|
|
1667
|
|
|
1668
|
@Override
|
|
1669
|
public <S extends TaxonBase> List<Object[]> findByIdentifier(
|
|
1670
|
Class<S> clazz, String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter,
|
|
1671
|
MatchMode matchmode, boolean includeEntity,
|
|
1672
|
Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
|
|
1673
|
|
|
1674
|
checkNotInPriorView("TaxonDaoHibernateImpl.findByIdentifier(T clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)");
|
|
1675
|
Class<?> clazzParam = clazz == null ? type : clazz;
|
|
1676
|
|
|
1677
|
boolean isTaxon = clazzParam == Taxon.class || clazzParam == TaxonBase.class;
|
|
1678
|
boolean isSynonym = clazzParam == Synonym.class || clazzParam == TaxonBase.class;
|
|
1679
|
getSession().update(subtreeFilter); //to avoid LIE when retrieving treeindex
|
|
1680
|
String filterStr = "'" + subtreeFilter.treeIndex() + "%%'";
|
|
1681
|
String accTreeJoin = isTaxon? " LEFT JOIN c.taxonNodes tn " : "";
|
|
1682
|
String synTreeJoin = isSynonym ? " LEFT JOIN c.acceptedTaxon as acc LEFT JOIN acc.taxonNodes synTn " : "";
|
|
1683
|
String accWhere = isTaxon ? "tn.treeIndex like " + filterStr : "(1=0)";
|
|
1684
|
String synWhere = isSynonym ? "synTn.treeIndex like " + filterStr : "(1=0)";
|
|
1685
|
|
|
1686
|
String queryString = " SELECT ids.type, ids.identifier, %s " +
|
|
1687
|
" FROM %s as c " +
|
|
1688
|
" INNER JOIN c.identifiers as ids " +
|
|
1689
|
accTreeJoin +
|
|
1690
|
synTreeJoin +
|
|
1691
|
" WHERE (1=1) " +
|
|
1692
|
" AND ( " + accWhere + " OR " + synWhere + ")";
|
|
1693
|
queryString = String.format(queryString, (includeEntity ? "c":"c.uuid, c.titleCache") , clazzParam.getSimpleName());
|
|
1694
|
|
|
1695
|
//Matchmode and identifier
|
|
1696
|
if (identifier != null){
|
|
1697
|
if (matchmode == null || matchmode == MatchMode.EXACT){
|
|
1698
|
queryString += " AND ids.identifier = '" + identifier + "'";
|
|
1699
|
}else {
|
|
1700
|
queryString += " AND ids.identifier LIKE '" + matchmode.queryStringFrom(identifier) + "'";
|
|
1701
|
}
|
|
1702
|
}
|
|
1703
|
if (identifierType != null){
|
|
1704
|
queryString += " AND ids.type = :type";
|
|
1705
|
}
|
|
1706
|
//order
|
|
1707
|
queryString +=" ORDER BY ids.type.uuid, ids.identifier, c.uuid ";
|
|
1708
|
|
|
1709
|
Query query = getSession().createQuery(queryString);
|
|
1710
|
|
|
1711
|
//parameters
|
|
1712
|
if (identifierType != null){
|
|
1713
|
query.setEntity("type", identifierType);
|
|
1714
|
}
|
|
1715
|
|
|
1716
|
//paging
|
|
1717
|
setPagingParameter(query, pageSize, pageNumber);
|
|
1718
|
|
|
1719
|
List<Object[]> results = query.list();
|
|
1720
|
//initialize
|
|
1721
|
if (includeEntity){
|
|
1722
|
List<S> entities = new ArrayList<S>();
|
|
1723
|
for (Object[] result : results){
|
|
1724
|
entities.add((S)result[2]);
|
|
1725
|
}
|
|
1726
|
defaultBeanInitializer.initializeAll(entities, propertyPaths);
|
|
1727
|
}
|
|
1728
|
return results;
|
|
1729
|
}
|
|
1730
|
|
|
1731
|
/**
|
|
1732
|
* {@inheritDoc}
|
|
1733
|
* @see #countByIdentifier(Class, String, DefinedTerm, TaxonNode, MatchMode)
|
|
1734
|
*/
|
|
1735
|
@Override
|
|
1736
|
public <S extends TaxonBase> long countByMarker(Class<S> clazz, MarkerType markerType,
|
|
1737
|
Boolean markerValue, TaxonNode subtreeFilter) {
|
|
1738
|
if (markerType == null){
|
|
1739
|
return 0;
|
|
1740
|
}
|
|
1741
|
|
|
1742
|
if (subtreeFilter == null){
|
|
1743
|
return countByMarker(clazz, markerType, markerValue);
|
|
1744
|
}
|
|
1745
|
|
|
1746
|
Class<?> clazzParam = clazz == null ? type : clazz;
|
|
1747
|
checkNotInPriorView("TaxonDaoHibernateImpl.countByMarker(Class<S> clazz, DefinedTerm markerType, boolean markerValue, TaxonNode subtreeFilter)");
|
|
1748
|
|
|
1749
|
boolean isTaxon = clazzParam == Taxon.class || clazzParam == TaxonBase.class;
|
|
1750
|
boolean isSynonym = clazzParam == Synonym.class || clazzParam == TaxonBase.class;
|
|
1751
|
|
|
1752
|
getSession().update(subtreeFilter); //to avoid LIE when retrieving treeindex
|
|
1753
|
String filterStr = "'" + subtreeFilter.treeIndex() + "%%'";
|
|
1754
|
String accTreeJoin = isTaxon? " LEFT JOIN c.taxonNodes tn " : "";
|
|
1755
|
String synTreeJoin = isSynonym ? " LEFT JOIN c.acceptedTaxon acc LEFT JOIN acc.taxonNodes synTn " : "";
|
|
1756
|
String accWhere = isTaxon ? "tn.treeIndex like " + filterStr : "(1=0)";
|
|
1757
|
String synWhere = isSynonym ? "synTn.treeIndex like " + filterStr : "(1=0)";
|
|
1758
|
|
|
1759
|
String queryString = "SELECT count(*) FROM %s as c " +
|
|
1760
|
" INNER JOIN c.markers as mks " +
|
|
1761
|
accTreeJoin +
|
|
1762
|
synTreeJoin +
|
|
1763
|
" WHERE (1=1) " +
|
|
1764
|
" AND ( " + accWhere + " OR " + synWhere + ")";
|
|
1765
|
queryString = String.format(queryString, clazzParam.getSimpleName());
|
|
1766
|
|
|
1767
|
if (markerValue != null){
|
|
1768
|
queryString += " AND mks.flag = :flag";
|
|
1769
|
}
|
|
1770
|
if (markerType != null){
|
|
1771
|
queryString += " AND mks.markerType = :type";
|
|
1772
|
}
|
|
1773
|
|
|
1774
|
Query query = getSession().createQuery(queryString);
|
|
1775
|
if (markerType != null){
|
|
1776
|
query.setEntity("type", markerType);
|
|
1777
|
}
|
|
1778
|
if (markerValue != null){
|
|
1779
|
query.setBoolean("flag", markerValue);
|
|
1780
|
}
|
|
1781
|
|
|
1782
|
Long c = (Long)query.uniqueResult();
|
|
1783
|
return c;
|
|
1784
|
}
|
|
1785
|
|
|
1786
|
/**
|
|
1787
|
* {@inheritDoc}
|
|
1788
|
*/
|
|
1789
|
@Override
|
|
1790
|
public <S extends TaxonBase> List<Object[]> findByMarker(Class<S> clazz, MarkerType markerType,
|
|
1791
|
Boolean markerValue, TaxonNode subtreeFilter, boolean includeEntity,
|
|
1792
|
TaxonTitleType titleType, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
|
|
1793
|
checkNotInPriorView("TaxonDaoHibernateImpl.findByMarker(T clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)");
|
|
1794
|
if (markerType == null){
|
|
1795
|
return new ArrayList<Object[]>();
|
|
1796
|
}
|
|
1797
|
if (titleType == null){
|
|
1798
|
titleType = TaxonTitleType.DEFAULT();
|
|
1799
|
}
|
|
1800
|
|
|
1801
|
Class<?> clazzParam = clazz == null ? type : clazz;
|
|
1802
|
|
|
1803
|
boolean isTaxon = clazzParam == Taxon.class || clazzParam == TaxonBase.class;
|
|
1804
|
boolean isSynonym = clazzParam == Synonym.class || clazzParam == TaxonBase.class;
|
|
1805
|
getSession().update(subtreeFilter); //to avoid LIE when retrieving treeindex
|
|
1806
|
String filterStr = "'" + subtreeFilter.treeIndex() + "%%'";
|
|
1807
|
String accTreeJoin = isTaxon? " LEFT JOIN c.taxonNodes tn " : "";
|
|
1808
|
String synTreeJoin = isSynonym ? " LEFT JOIN c.acceptedTaxon as acc LEFT JOIN acc.taxonNodes synTn " : "";
|
|
1809
|
String accWhere = isTaxon ? "tn.treeIndex like " + filterStr : "(1=0)";
|
|
1810
|
String synWhere = isSynonym ? "synTn.treeIndex like " + filterStr : "(1=0)";
|
|
1811
|
String selectParams = includeEntity ? "c" : titleType.hqlReplaceSelect("c.uuid, c.titleCache", "c.titleCache");
|
|
1812
|
String titleTypeJoin = includeEntity ? "" : titleType.hqlJoin();
|
|
1813
|
|
|
1814
|
String queryString = "SELECT mks.markerType, mks.flag, %s " +
|
|
1815
|
" FROM %s as c " +
|
|
1816
|
" INNER JOIN c.markers as mks " +
|
|
1817
|
titleTypeJoin +
|
|
1818
|
accTreeJoin +
|
|
1819
|
synTreeJoin +
|
|
1820
|
" WHERE (1=1) " +
|
|
1821
|
" AND ( " + accWhere + " OR " + synWhere + ")";
|
|
1822
|
queryString = String.format(queryString, selectParams, clazzParam.getSimpleName());
|
|
1823
|
|
|
1824
|
//type and value
|
|
1825
|
if (markerValue != null){
|
|
1826
|
queryString += " AND mks.flag = :flag";
|
|
1827
|
}
|
|
1828
|
queryString += " AND mks.markerType = :type";
|
|
1829
|
//order
|
|
1830
|
queryString +=" ORDER BY mks.markerType.uuid, mks.flag, c.uuid ";
|
|
1831
|
|
|
1832
|
Query query = getSession().createQuery(queryString);
|
|
1833
|
|
|
1834
|
//parameters
|
|
1835
|
query.setEntity("type", markerType);
|
|
1836
|
if (markerValue != null){
|
|
1837
|
query.setBoolean("flag", markerValue);
|
|
1838
|
}
|
|
1839
|
|
|
1840
|
//paging
|
|
1841
|
setPagingParameter(query, pageSize, pageNumber);
|
|
1842
|
|
|
1843
|
List<Object[]> results = query.list();
|
|
1844
|
//initialize
|
|
1845
|
if (includeEntity){
|
|
1846
|
List<S> entities = new ArrayList<S>();
|
|
1847
|
for (Object[] result : results){
|
|
1848
|
entities.add((S)result[2]);
|
|
1849
|
}
|
|
1850
|
defaultBeanInitializer.initializeAll(entities, propertyPaths);
|
|
1851
|
}
|
|
1852
|
return results;
|
|
1853
|
}
|
|
1854
|
|
|
1855
|
@Override
|
|
1856
|
public long countTaxonRelationships(Set<TaxonRelationshipType> types) {
|
|
1857
|
Criteria criteria = getSession().createCriteria(TaxonRelationship.class);
|
|
1858
|
|
|
1859
|
if (types != null) {
|
|
1860
|
if (types.isEmpty()){
|
|
1861
|
return 0l;
|
|
1862
|
}else{
|
|
1863
|
criteria.add(Restrictions.in("type", types) );
|
|
1864
|
}
|
|
1865
|
}
|
|
1866
|
//count
|
|
1867
|
criteria.setProjection(Projections.rowCount());
|
|
1868
|
long result = (Long)criteria.uniqueResult();
|
|
1869
|
|
|
1870
|
return result;
|
|
1871
|
}
|
|
1872
|
|
|
1873
|
@Override
|
|
1874
|
public List<TaxonRelationship> getTaxonRelationships(Set<TaxonRelationshipType> types,
|
|
1875
|
Integer pageSize, Integer pageNumber,
|
|
1876
|
List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1877
|
Criteria criteria = getCriteria(TaxonRelationship.class);
|
|
1878
|
|
|
1879
|
if (types != null) {
|
|
1880
|
if (types.isEmpty()){
|
|
1881
|
return new ArrayList<>();
|
|
1882
|
}else{
|
|
1883
|
criteria.add(Restrictions.in("type", types) );
|
|
1884
|
}
|
|
1885
|
}
|
|
1886
|
addOrder(criteria,orderHints);
|
|
1887
|
addPageSizeAndNumber(criteria, pageSize, pageNumber);
|
|
1888
|
|
|
1889
|
@SuppressWarnings("unchecked")
|
|
1890
|
List<TaxonRelationship> results = criteria.list();
|
|
1891
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
1892
|
|
|
1893
|
return results;
|
|
1894
|
}
|
|
1895
|
|
|
1896
|
@Override
|
|
1897
|
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCache(Integer limit, String pattern){
|
|
1898
|
Session session = getSession();
|
|
1899
|
Query query = null;
|
|
1900
|
if (pattern != null){
|
|
1901
|
query = session.createQuery(
|
|
1902
|
" SELECT tb.uuid, tb.id, tb.titleCache, tb.name.rank "
|
|
1903
|
+ " FROM TaxonBase as tb "
|
|
1904
|
+ " WHERE tb.titleCache LIKE :pattern");
|
|
1905
|
pattern = pattern.replace("*", "%");
|
|
1906
|
pattern = pattern.replace("?", "_");
|
|
1907
|
pattern = pattern + "%";
|
|
1908
|
query.setParameter("pattern", pattern);
|
|
1909
|
} else {
|
|
1910
|
query = session.createQuery(
|
|
1911
|
" SELECT tb.uuid, taxonBase.id, tb.titleCache, tb.name.rank "
|
|
1912
|
+ " FROM TaxonBase AS tb");
|
|
1913
|
}
|
|
1914
|
if (limit != null){
|
|
1915
|
query.setMaxResults(limit);
|
|
1916
|
}
|
|
1917
|
|
|
1918
|
return getUuidAndTitleCache(query);
|
|
1919
|
}
|
|
1920
|
|
|
1921
|
@Override
|
|
1922
|
protected List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCache(Query query){
|
|
1923
|
List<UuidAndTitleCache<TaxonBase>> list = new ArrayList<>();
|
|
1924
|
|
|
1925
|
@SuppressWarnings("unchecked")
|
|
1926
|
List<Object[]> result = query.list();
|
|
1927
|
if (!result.isEmpty()){
|
|
1928
|
if (result.iterator().next().length == 4){
|
|
1929
|
Collections.sort(result, new UuidAndTitleCacheTaxonComparator());
|
|
1930
|
}
|
|
1931
|
}
|
|
1932
|
|
|
1933
|
for(Object[] object : result){
|
|
1934
|
list.add(new UuidAndTitleCache<TaxonBase>((UUID) object[0],(Integer) object[1], (String) object[2]));
|
|
1935
|
}
|
|
1936
|
return list;
|
|
1937
|
}
|
|
1938
|
|
|
1939
|
|
|
1940
|
}
|