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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.persistence.dao.hibernate.taxon;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.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.log4j.Logger;
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import org.apache.lucene.queryParser.ParseException;
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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.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.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.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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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.OriginalSourceBase;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
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import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.TaxonNameComparator;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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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.SynonymRelationship;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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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.view.AuditEvent;
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import eu.etaxonomy.cdm.persistence.dao.QueryParseException;
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import eu.etaxonomy.cdm.persistence.dao.hibernate.AlternativeSpellingSuggestionParser;
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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.fetch.CdmFetch;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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import eu.etaxonomy.cdm.persistence.query.OrderHint.SortOrder;
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/**
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* @author a.mueller
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* @created 24.11.2008
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* @version 1.0
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*/
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@Repository
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@Qualifier("taxonDaoHibernateImpl")
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public class TaxonDaoHibernateImpl extends IdentifiableDaoBase<TaxonBase> 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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@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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference)
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*/
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public List<Taxon> getRootTaxa(Reference sec) {
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return getRootTaxa(sec, CdmFetch.FETCH_CHILDTAXA(), true, false);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.name.Rank, eu.etaxonomy.cdm.model.reference.Reference, eu.etaxonomy.cdm.persistence.fetch.CdmFetch, java.lang.Boolean, java.lang.Boolean)
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*/
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public List<Taxon> getRootTaxa(Rank rank, Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications, List<String> propertyPaths) {
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checkNotInPriorView("TaxonDaoHibernateImpl.getRootTaxa(Rank rank, Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications)");
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if (onlyWithChildren == null){
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onlyWithChildren = true;
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}
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if (withMisapplications == null){
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withMisapplications = true;
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}
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if (cdmFetch == null){
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cdmFetch = CdmFetch.NO_FETCH();
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}
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Criteria crit = getSession().createCriteria(Taxon.class);
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crit.setFetchMode("name", FetchMode.JOIN);
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crit.createAlias("name", "name");
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if (rank != null) {
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crit.add(Restrictions.eq("name.rank", rank));
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}else{
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crit.add(Restrictions.isNull("taxonomicParentCache"));
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}
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if (sec != null){
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crit.add(Restrictions.eq("sec", sec) );
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}
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if (! cdmFetch.includes(CdmFetch.FETCH_CHILDTAXA())){
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logger.info("Not fetching child taxa");
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//TODO overwrite LAZY (SELECT) does not work (bug in hibernate?)
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crit.setFetchMode("relationsToThisTaxon.fromTaxon", FetchMode.LAZY);
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}
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List<Taxon> results = new ArrayList<Taxon>();
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List<Taxon> taxa = crit.list();
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for(Taxon taxon : taxa){
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//childTaxa
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//TODO create restriction instead
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// (a) not using cache fields
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/*Hibernate.initialize(taxon.getRelationsFromThisTaxon());
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if (onlyWithChildren == false || taxon.getRelationsFromThisTaxon().size() > 0){
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if (withMisapplications == true || ! taxon.isMisappliedName()){
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defaultBeanInitializer.initialize(taxon, propertyPaths);
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results.add(taxon);
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}
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}*/
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// (b) using cache fields
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if (onlyWithChildren == false || taxon.hasTaxonomicChildren()){
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if (withMisapplications == true || ! taxon.isMisapplication()){
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defaultBeanInitializer.initialize(taxon, propertyPaths);
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results.add(taxon);
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}
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}
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}
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return results;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference, eu.etaxonomy.cdm.persistence.fetch.CdmFetch, java.lang.Boolean, java.lang.Boolean)
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*/
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public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications) {
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return getRootTaxa(null, sec, cdmFetch, onlyWithChildren, withMisapplications, null);
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}
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/*
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)
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*/
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public List<TaxonBase> getTaxaByName(String queryString, Reference sec) {
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return getTaxaByName(queryString, true, sec);
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}
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/*
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByName(java.lang.String, java.lang.Boolean, eu.etaxonomy.cdm.model.reference.Reference)
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*/
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public List<TaxonBase> getTaxaByName(String queryString, Boolean accepted, 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 (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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return (List<TaxonBase>)criteria.list();
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}
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public List<TaxonBase> getTaxaByName(Class<? extends TaxonBase> clazz, String queryString, MatchMode matchMode,
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Integer pageSize, Integer pageNumber) {
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return getTaxaByName(clazz, queryString, null, matchMode, null, pageSize, pageNumber, null);
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}
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/*
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, java.lang.Boolean, java.lang.Integer, java.lang.Integer)
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*/
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public List<TaxonBase> getTaxaByName(String queryString, MatchMode matchMode,
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Boolean accepted, Integer pageSize, Integer pageNumber) {
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if (accepted == true) {
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return getTaxaByName(Taxon.class, queryString, matchMode, pageSize, pageNumber);
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} else {
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return getTaxaByName(Synonym.class, queryString, matchMode, pageSize, pageNumber);
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}
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}
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/*
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByName(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.Set, java.lang.Integer, java.lang.Integer, java.util.List)
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*/
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public List<TaxonBase> getTaxaByName(Class<? extends TaxonBase> clazz, 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 = prepareTaxaByName(clazz, "nameCache", queryString, classification, matchMode, namedAreas, pageSize, pageNumber, doCount);
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if (query != null){
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List<TaxonBase> results = query.list();
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defaultBeanInitializer.initializeAll(results, propertyPaths);
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//TaxonComparatorSearch comp = new TaxonComparatorSearch();
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//Collections.sort(results, comp);
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return results;
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}
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return new ArrayList<TaxonBase>();
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}
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/*
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByName(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.Set, java.lang.Integer, java.lang.Integer, java.util.List)
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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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@SuppressWarnings("unchecked")
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public List<UuidAndTitleCache<TaxonBase>> getTaxaByNameForEditor(Class<? extends TaxonBase> clazz, String queryString, Classification classification,
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MatchMode matchMode, Set<NamedArea> namedAreas) {
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long zstVorher;
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long zstNachher;
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boolean doCount = false;
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Query query = prepareTaxaByNameForEditor(clazz, "nameCache", queryString, classification, matchMode, namedAreas, doCount);
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if (query != null){
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List<Object[]> results = query.list();
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List<UuidAndTitleCache<TaxonBase>> resultObjects = new ArrayList<UuidAndTitleCache<TaxonBase>>();
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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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//unterscheiden von taxa und synonymen
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if (clazz.equals(Taxon.class)){
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resultObjects.add( new UuidAndTitleCache(Taxon.class, (UUID) result[0], (String)result[1]));
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}else if (clazz.equals(Synonym.class)){
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resultObjects.add( new UuidAndTitleCache(Synonym.class, (UUID) result[0], (String)result[1]));
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} else{
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if (result[2].equals("synonym")) {
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resultObjects.add( new UuidAndTitleCache(Synonym.class, (UUID) result[0], (String)result[1]));
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}
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else {
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resultObjects.add( new UuidAndTitleCache(Taxon.class, (UUID) result[0], (String)result[1]));
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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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return new ArrayList<UuidAndTitleCache<TaxonBase>>();
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}
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/*
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByCommonName(java.lang.String, eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.Set, java.lang.Integer, java.lang.Integer, java.util.List)
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*/
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public List<TaxonBase> 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);
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if (query != null){
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List<TaxonBase> results = query.list();
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321
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
322
|
return results;
|
|
323
|
}
|
|
324
|
return new ArrayList<TaxonBase>();
|
|
325
|
|
|
326
|
}
|
|
327
|
|
|
328
|
/**
|
|
329
|
* @param clazz
|
|
330
|
* @param searchField the field in TaxonNameBase to be searched through usually either <code>nameCache</code> or <code>titleCache</code>
|
|
331
|
* @param queryString
|
|
332
|
* @param classification TODO
|
|
333
|
* @param matchMode
|
|
334
|
* @param namedAreas
|
|
335
|
* @param pageSize
|
|
336
|
* @param pageNumber
|
|
337
|
* @param doCount
|
|
338
|
* @return
|
|
339
|
*
|
|
340
|
*
|
|
341
|
*/
|
|
342
|
private Query prepareTaxaByNameForEditor(Class<? extends TaxonBase> clazz, String searchField, String queryString, Classification classification,
|
|
343
|
MatchMode matchMode, Set<NamedArea> namedAreas, boolean doCount) {
|
|
344
|
return prepareQuery(clazz, searchField, queryString, classification,
|
|
345
|
matchMode, namedAreas, doCount, true);
|
|
346
|
}
|
|
347
|
|
|
348
|
/**
|
|
349
|
* @param clazz
|
|
350
|
* @param searchField
|
|
351
|
* @param queryString
|
|
352
|
* @param classification
|
|
353
|
* @param matchMode
|
|
354
|
* @param namedAreas
|
|
355
|
* @param doCount
|
|
356
|
* @param doNotReturnFullEntities
|
|
357
|
* if set true the seach method will not return synonym and taxon
|
|
358
|
* entities but an array containing the uuid, titleCache, and the
|
|
359
|
* DTYPE in lowercase letters.
|
|
360
|
* @return
|
|
361
|
*/
|
|
362
|
private Query prepareQuery(Class<? extends TaxonBase> clazz, String searchField, String queryString, Classification classification,
|
|
363
|
MatchMode matchMode, Set<NamedArea> namedAreas, boolean doCount, boolean doNotReturnFullEntities){
|
|
364
|
|
|
365
|
String hqlQueryString = matchMode.queryStringFrom(queryString);
|
|
366
|
String selectWhat;
|
|
367
|
if (doNotReturnFullEntities){
|
|
368
|
selectWhat = "t.uuid, t.titleCache ";
|
|
369
|
}else {
|
|
370
|
selectWhat = (doCount ? "count(t)": "t");
|
|
371
|
}
|
|
372
|
|
|
373
|
String hql = "";
|
|
374
|
Set<NamedArea> areasExpanded = new HashSet<NamedArea>();
|
|
375
|
if(namedAreas != null && namedAreas.size() > 0){
|
|
376
|
// expand areas and restrict by distribution area
|
|
377
|
List<NamedArea> childAreas;
|
|
378
|
Query areaQuery = getSession().createQuery("select childArea from NamedArea as childArea left join childArea.partOf as parentArea where parentArea = :area");
|
|
379
|
expandNamedAreas(namedAreas, areasExpanded, areaQuery);
|
|
380
|
}
|
|
381
|
boolean doAreaRestriction = areasExpanded.size() > 0;
|
|
382
|
|
|
383
|
Set<UUID> namedAreasUuids = new HashSet<UUID>();
|
|
384
|
for (NamedArea area:areasExpanded){
|
|
385
|
namedAreasUuids.add(area.getUuid());
|
|
386
|
}
|
|
387
|
|
|
388
|
String taxonSubselect = null;
|
|
389
|
String synonymSubselect = null;
|
|
390
|
|
|
391
|
if(classification != null){
|
|
392
|
|
|
393
|
if(doAreaRestriction){
|
|
394
|
|
|
395
|
taxonSubselect = "select t.id from" +
|
|
396
|
" Distribution e" +
|
|
397
|
" join e.inDescription d" +
|
|
398
|
" join d.taxon t" +
|
|
399
|
" join t.name n " +
|
|
400
|
" join t.taxonNodes as tn "+
|
|
401
|
" where" +
|
|
402
|
" e.area.uuid in (:namedAreasUuids) AND" +
|
|
403
|
" tn.classification = :classification" +
|
|
404
|
" AND n." + searchField + " " + matchMode.getMatchOperator() + " :queryString";
|
|
405
|
|
|
406
|
|
|
407
|
synonymSubselect = "select s.id from" +
|
|
408
|
" Distribution e" +
|
|
409
|
" join e.inDescription d" +
|
|
410
|
" join d.taxon t" + // the taxa
|
|
411
|
" join t.taxonNodes as tn "+
|
|
412
|
" join t.synonymRelations sr" +
|
|
413
|
" join sr.relatedFrom s" + // the synonyms
|
|
414
|
" join s.name sn"+
|
|
415
|
" where" +
|
|
416
|
" e.area.uuid in (:namedAreasUuids) AND" +
|
|
417
|
" tn.classification = :classification" +
|
|
418
|
" AND sn." + searchField + " " + matchMode.getMatchOperator() + " :queryString";
|
|
419
|
|
|
420
|
} else {
|
|
421
|
|
|
422
|
taxonSubselect = "select t.id from" +
|
|
423
|
" Taxon t" +
|
|
424
|
" join t.name n " +
|
|
425
|
" join t.taxonNodes as tn "+
|
|
426
|
" where" +
|
|
427
|
" tn.classification = :classification" +
|
|
428
|
" AND n." + searchField + " " + matchMode.getMatchOperator() + " :queryString";
|
|
429
|
|
|
430
|
synonymSubselect = "select s.id from" +
|
|
431
|
" Taxon t" + // the taxa
|
|
432
|
" join t.taxonNodes as tn "+
|
|
433
|
" join t.synonymRelations sr" +
|
|
434
|
" join sr.relatedFrom s" + // the synonyms
|
|
435
|
" join s.name sn"+
|
|
436
|
" where" +
|
|
437
|
" tn.classification = :classification" +
|
|
438
|
" AND sn." + searchField + " " + matchMode.getMatchOperator() + " :queryString";
|
|
439
|
}
|
|
440
|
} else {
|
|
441
|
|
|
442
|
if(doAreaRestriction){
|
|
443
|
|
|
444
|
taxonSubselect = "select t.id from " +
|
|
445
|
" Distribution e" +
|
|
446
|
" join e.inDescription d" +
|
|
447
|
" join d.taxon t" +
|
|
448
|
" join t.name n "+
|
|
449
|
" where" +
|
|
450
|
(doAreaRestriction ? " e.area.uuid in (:namedAreasUuids) AND" : "") +
|
|
451
|
" n." + searchField + " " + matchMode.getMatchOperator() + " :queryString";
|
|
452
|
|
|
453
|
synonymSubselect = "select s.id from" +
|
|
454
|
" Distribution e" +
|
|
455
|
" join e.inDescription d" +
|
|
456
|
" join d.taxon t" + // the taxa
|
|
457
|
" join t.synonymRelations sr" +
|
|
458
|
" join sr.relatedFrom s" + // the synonyms
|
|
459
|
" join s.name sn"+
|
|
460
|
" where" +
|
|
461
|
(doAreaRestriction ? " e.area.uuid in (:namedAreasUuids) AND" : "") +
|
|
462
|
" sn." + searchField + " " + matchMode.getMatchOperator() + " :queryString";
|
|
463
|
|
|
464
|
} else {
|
|
465
|
|
|
466
|
taxonSubselect = "select t.id from " +
|
|
467
|
" Taxon t" +
|
|
468
|
" join t.name n "+
|
|
469
|
" where" +
|
|
470
|
" n." + searchField + " " + matchMode.getMatchOperator() + " :queryString";
|
|
471
|
|
|
472
|
synonymSubselect = "select s.id from" +
|
|
473
|
" Taxon t" + // the taxa
|
|
474
|
" join t.synonymRelations sr" +
|
|
475
|
" join sr.relatedFrom s" + // the synonyms
|
|
476
|
" join s.name sn"+
|
|
477
|
" where" +
|
|
478
|
" sn." + searchField + " " + matchMode.getMatchOperator() + " :queryString";
|
|
479
|
}
|
|
480
|
|
|
481
|
}
|
|
482
|
|
|
483
|
Query subTaxon = null;
|
|
484
|
Query subSynonym = null;
|
|
485
|
if(clazz.equals(Taxon.class)){
|
|
486
|
// find Taxa
|
|
487
|
subTaxon = getSession().createQuery(taxonSubselect).setParameter("queryString", hqlQueryString);
|
|
488
|
//subTaxon = getSession().createQuery(taxonSubselect);
|
|
489
|
|
|
490
|
if(doAreaRestriction){
|
|
491
|
subTaxon.setParameterList("namedAreasUuids", namedAreasUuids);
|
|
492
|
}
|
|
493
|
if(classification != null){
|
|
494
|
subTaxon.setParameter("classification", classification);
|
|
495
|
}
|
|
496
|
} else if(clazz.equals(Synonym.class)){
|
|
497
|
// find synonyms
|
|
498
|
subSynonym = getSession().createQuery(synonymSubselect).setParameter("queryString", hqlQueryString);
|
|
499
|
|
|
500
|
if(doAreaRestriction){
|
|
501
|
subSynonym.setParameterList("namedAreasUuids", namedAreasUuids);
|
|
502
|
}
|
|
503
|
if(classification != null){
|
|
504
|
subSynonym.setParameter("classification", classification);
|
|
505
|
}
|
|
506
|
} else {
|
|
507
|
// find taxa and synonyms
|
|
508
|
subSynonym = getSession().createQuery(synonymSubselect).setParameter("queryString", hqlQueryString);
|
|
509
|
subTaxon = getSession().createQuery(taxonSubselect).setParameter("queryString", hqlQueryString);
|
|
510
|
if(doAreaRestriction){
|
|
511
|
subTaxon.setParameterList("namedAreasUuids", namedAreasUuids);
|
|
512
|
subSynonym.setParameterList("namedAreasUuids", namedAreasUuids);
|
|
513
|
}
|
|
514
|
if(classification != null){
|
|
515
|
subTaxon.setParameter("classification", classification);
|
|
516
|
subSynonym.setParameter("classification", classification);
|
|
517
|
}
|
|
518
|
}
|
|
519
|
|
|
520
|
List<Integer> taxa = new ArrayList<Integer>();
|
|
521
|
List<Integer> synonyms = new ArrayList<Integer>();
|
|
522
|
if(clazz.equals(Taxon.class)){
|
|
523
|
taxa = subTaxon.list();
|
|
524
|
|
|
525
|
}else if (clazz.equals(Synonym.class)){
|
|
526
|
synonyms = subSynonym.list();
|
|
527
|
}else {
|
|
528
|
taxa = subTaxon.list();
|
|
529
|
synonyms = subSynonym.list();
|
|
530
|
}
|
|
531
|
if(clazz.equals(Taxon.class)){
|
|
532
|
if (taxa.size()>0){
|
|
533
|
if (doNotReturnFullEntities){
|
|
534
|
hql = "select " + selectWhat + ", 'taxon' from " + clazz.getSimpleName() + " t" + " where t.id in (:taxa)";
|
|
535
|
}else{
|
|
536
|
hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t" + " where t.id in (:taxa)";
|
|
537
|
}
|
|
538
|
}else{
|
|
539
|
hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t";
|
|
540
|
}
|
|
541
|
} else if(clazz.equals(Synonym.class) ){
|
|
542
|
if (synonyms.size()>0){
|
|
543
|
if (doNotReturnFullEntities){
|
|
544
|
hql = "select " + selectWhat + ", 'synonym' from " + clazz.getSimpleName() + " t" + " where t.id in (:synonyms)";
|
|
545
|
}else{
|
|
546
|
hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t" + " where t.id in (:synonyms)";
|
|
547
|
}
|
|
548
|
}else{
|
|
549
|
hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t";
|
|
550
|
}
|
|
551
|
} else {
|
|
552
|
|
|
553
|
if(synonyms.size()>0 && taxa.size()>0){
|
|
554
|
if (doNotReturnFullEntities && !doCount ){
|
|
555
|
// in doNotReturnFullEntities mode it is nesscary to also return the type of the matching entities:
|
|
556
|
hql = "select " + selectWhat + ", case when t.id in (:taxa) then 'taxon' else 'synonym' end" + " from " + clazz.getSimpleName() + " t" + " where t.id in (:taxa) OR t.id in (:synonyms)";
|
|
557
|
}else{
|
|
558
|
hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t" + " where t.id in (:taxa) OR t.id in (:synonyms)";
|
|
559
|
}
|
|
560
|
}else if (synonyms.size()>0 ){
|
|
561
|
if (doNotReturnFullEntities && !doCount ){
|
|
562
|
// in doNotReturnFullEntities mode it is nesscary to also return the type of the matching entities:
|
|
563
|
hql = "select " + selectWhat + ", 'synonym' from " + clazz.getSimpleName() + " t" + " where t.id in (:synonyms)";
|
|
564
|
} else {
|
|
565
|
hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t" + " where t.id in (:synonyms)";
|
|
566
|
}
|
|
567
|
} else if (taxa.size()>0 ){
|
|
568
|
if (doNotReturnFullEntities && !doCount ){
|
|
569
|
// in doNotReturnFullEntities mode it is nesscary to also return the type of the matching entities:
|
|
570
|
hql = "select " + selectWhat + ", 'taxon' from " + clazz.getSimpleName() + " t" + " where t.id in (:taxa) ";
|
|
571
|
} else {
|
|
572
|
hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t" + " where t.id in (:taxa) ";
|
|
573
|
}
|
|
574
|
} else{
|
|
575
|
hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t";
|
|
576
|
}
|
|
577
|
}
|
|
578
|
|
|
579
|
if (hql == "") return null;
|
|
580
|
if(!doCount){
|
|
581
|
hql += " order by t.name.genusOrUninomial, case when t.name.specificEpithet like '\"%\"' then 1 else 0 end, t.name.specificEpithet, t.name.rank desc, t.name.nameCache";
|
|
582
|
}
|
|
583
|
|
|
584
|
Query query = getSession().createQuery(hql);
|
|
585
|
|
|
586
|
if(clazz.equals(Taxon.class) && taxa.size()>0){
|
|
587
|
//find taxa
|
|
588
|
query.setParameterList("taxa", taxa );
|
|
589
|
} else if(clazz.equals(Synonym.class) && synonyms.size()>0){
|
|
590
|
// find synonyms
|
|
591
|
query.setParameterList("synonyms", synonyms);
|
|
592
|
|
|
593
|
|
|
594
|
} else {
|
|
595
|
// find taxa and synonyms
|
|
596
|
if (taxa.size()>0){
|
|
597
|
query.setParameterList("taxa", taxa);
|
|
598
|
}
|
|
599
|
if (synonyms.size()>0){
|
|
600
|
query.setParameterList("synonyms",synonyms);
|
|
601
|
}
|
|
602
|
if (taxa.size()== 0 && synonyms.size() == 0){
|
|
603
|
return null;
|
|
604
|
}
|
|
605
|
}
|
|
606
|
return query;
|
|
607
|
|
|
608
|
}
|
|
609
|
|
|
610
|
|
|
611
|
/**
|
|
612
|
* @param clazz
|
|
613
|
* @param searchField the field in TaxonNameBase to be searched through usually either <code>nameCache</code> or <code>titleCache</code>
|
|
614
|
* @param queryString
|
|
615
|
* @param classification TODO
|
|
616
|
* @param matchMode
|
|
617
|
* @param namedAreas
|
|
618
|
* @param pageSize
|
|
619
|
* @param pageNumber
|
|
620
|
* @param doCount
|
|
621
|
* @return
|
|
622
|
*
|
|
623
|
* FIXME implement classification restriction & implement test: see {@link TaxonDaoHibernateImplTest#testCountTaxaByName()}
|
|
624
|
*/
|
|
625
|
private Query prepareTaxaByName(Class<? extends TaxonBase> clazz, String searchField, String queryString, Classification classification,
|
|
626
|
MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber, boolean doCount) {
|
|
627
|
|
|
628
|
Query query = prepareQuery(clazz, searchField, queryString, classification, matchMode, namedAreas, doCount, false);
|
|
629
|
|
|
630
|
if(pageSize != null && !doCount) {
|
|
631
|
query.setMaxResults(pageSize);
|
|
632
|
if(pageNumber != null) {
|
|
633
|
query.setFirstResult(pageNumber * pageSize);
|
|
634
|
}
|
|
635
|
}
|
|
636
|
|
|
637
|
return query;
|
|
638
|
}
|
|
639
|
|
|
640
|
private Query prepareTaxaByCommonName(String queryString, Classification classification,
|
|
641
|
MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber, boolean doCount){
|
|
642
|
|
|
643
|
String hql= "from Taxon t " +
|
|
644
|
"join t.descriptions d "+
|
|
645
|
"join d.descriptionElements e " +
|
|
646
|
"join e.feature f " +
|
|
647
|
"where f.supportsCommonTaxonName = true and e.name "+matchMode.getMatchOperator()+" :queryString";//and ls.text like 'common%'";
|
|
648
|
|
|
649
|
Query query = getSession().createQuery(hql);
|
|
650
|
|
|
651
|
query.setParameter("queryString", queryString);
|
|
652
|
|
|
653
|
if(pageSize != null && !doCount) {
|
|
654
|
query.setMaxResults(pageSize);
|
|
655
|
if(pageNumber != null) {
|
|
656
|
query.setFirstResult(pageNumber * pageSize);
|
|
657
|
}
|
|
658
|
}
|
|
659
|
return query;
|
|
660
|
}
|
|
661
|
|
|
662
|
/* (non-Javadoc)
|
|
663
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countTaxaByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, eu.etaxonomy.cdm.persistence.query.SelectMode, eu.etaxonomy.cdm.model.reference.Reference, java.util.Set)
|
|
664
|
*/
|
|
665
|
public long countTaxaByName(Class<? extends TaxonBase> clazz, String queryString, Classification classification,
|
|
666
|
MatchMode matchMode, Set<NamedArea> namedAreas) {
|
|
667
|
|
|
668
|
boolean doCount = true;
|
|
669
|
Query query = prepareTaxaByName(clazz, "nameCache", queryString, classification, matchMode, namedAreas, null, null, doCount);
|
|
670
|
if (query != null) {
|
|
671
|
return (Long)query.uniqueResult();
|
|
672
|
}else{
|
|
673
|
return 0;
|
|
674
|
}
|
|
675
|
}
|
|
676
|
|
|
677
|
/**
|
|
678
|
* @param namedAreas
|
|
679
|
* @param areasExpanded
|
|
680
|
* @param areaQuery
|
|
681
|
*/
|
|
682
|
private void expandNamedAreas(Collection<NamedArea> namedAreas, Set<NamedArea> areasExpanded, Query areaQuery) {
|
|
683
|
List<NamedArea> childAreas;
|
|
684
|
for(NamedArea a : namedAreas){
|
|
685
|
areasExpanded.add(a);
|
|
686
|
areaQuery.setParameter("area", a);
|
|
687
|
childAreas = areaQuery.list();
|
|
688
|
if(childAreas.size() > 0){
|
|
689
|
areasExpanded.addAll(childAreas);
|
|
690
|
expandNamedAreas(childAreas, areasExpanded, areaQuery);
|
|
691
|
}
|
|
692
|
}
|
|
693
|
}
|
|
694
|
|
|
695
|
// /* (non-Javadoc)
|
|
696
|
// * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countTaxaByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, eu.etaxonomy.cdm.persistence.query.SelectMode)
|
|
697
|
// */
|
|
698
|
// public Integer countTaxaByName(String queryString, MatchMode matchMode, SelectMode selectMode) {
|
|
699
|
// return countTaxaByName(queryString, matchMode, selectMode, null);
|
|
700
|
// }
|
|
701
|
|
|
702
|
// /* (non-Javadoc)
|
|
703
|
// * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countTaxaByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, eu.etaxonomy.cdm.persistence.query.SelectMode, eu.etaxonomy.cdm.model.reference.Reference)
|
|
704
|
// */
|
|
705
|
// public Integer countTaxaByName(String queryString,
|
|
706
|
// MatchMode matchMode, SelectMode selectMode, Reference sec) {
|
|
707
|
//
|
|
708
|
// Long count = countTaxaByName(queryString, matchMode, selectMode, sec, null);
|
|
709
|
// return count.intValue();
|
|
710
|
//
|
|
711
|
// }
|
|
712
|
|
|
713
|
// public Integer countTaxaByName(String queryString, MatchMode matchMode, Boolean accepted) {
|
|
714
|
//
|
|
715
|
// SelectMode selectMode = (accepted ? SelectMode.TAXA : SelectMode.SYNONYMS);
|
|
716
|
// Long count = countTaxaByName(queryString, matchMode, selectMode, null, null);
|
|
717
|
// return count.intValue();
|
|
718
|
// }
|
|
719
|
|
|
720
|
public List<TaxonBase> getAllTaxonBases(Integer pagesize, Integer page) {
|
|
721
|
return super.list(pagesize, page);
|
|
722
|
}
|
|
723
|
|
|
724
|
/*
|
|
725
|
* (non-Javadoc)
|
|
726
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getAllSynonyms(java.lang.Integer, java.lang.Integer)
|
|
727
|
*/
|
|
728
|
public List<Synonym> getAllSynonyms(Integer limit, Integer start) {
|
|
729
|
Criteria criteria = getSession().createCriteria(Synonym.class);
|
|
730
|
|
|
731
|
if(limit != null) {
|
|
732
|
criteria.setFirstResult(start);
|
|
733
|
criteria.setMaxResults(limit);
|
|
734
|
}
|
|
735
|
|
|
736
|
return criteria.list();
|
|
737
|
}
|
|
738
|
|
|
739
|
/*
|
|
740
|
* (non-Javadoc)
|
|
741
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getAllTaxa(java.lang.Integer, java.lang.Integer)
|
|
742
|
*/
|
|
743
|
public List<Taxon> getAllTaxa(Integer limit, Integer start) {
|
|
744
|
Criteria criteria = getSession().createCriteria(Taxon.class);
|
|
745
|
|
|
746
|
if(limit != null) {
|
|
747
|
criteria.setFirstResult(start);
|
|
748
|
criteria.setMaxResults(limit);
|
|
749
|
}
|
|
750
|
|
|
751
|
return criteria.list();
|
|
752
|
}
|
|
753
|
|
|
754
|
/*
|
|
755
|
* (non-Javadoc)
|
|
756
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getAllRelationships(java.lang.Integer, java.lang.Integer)
|
|
757
|
*/
|
|
758
|
public List<RelationshipBase> getAllRelationships(Integer limit, Integer start) {
|
|
759
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
760
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
761
|
Criteria criteria = getSession().createCriteria(RelationshipBase.class);
|
|
762
|
criteria.setFirstResult(start);
|
|
763
|
criteria.setMaxResults(limit);
|
|
764
|
return (List<RelationshipBase>)criteria.list();
|
|
765
|
} else {
|
|
766
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(RelationshipBase.class,auditEvent.getRevisionNumber());
|
|
767
|
return (List<RelationshipBase>)query.getResultList();
|
|
768
|
}
|
|
769
|
}
|
|
770
|
|
|
771
|
/** Sets the taxonomic parent to null. Does not handle taxonomic relationships. */
|
|
772
|
// private boolean nullifyTaxonomicParent(Taxon taxon) {
|
|
773
|
//
|
|
774
|
// try {
|
|
775
|
// Method nullifyTaxonomicParent = taxon.getClass().getMethod("nullifyTaxonomicParent");
|
|
776
|
// nullifyTaxonomicParent.invoke(taxon);
|
|
777
|
// } catch (NoSuchMethodException ex) {
|
|
778
|
// logger.error("NoSuchMethod: " + ex.getMessage());
|
|
779
|
// return false;
|
|
780
|
// } catch (IllegalArgumentException ex) {
|
|
781
|
// logger.error("IllegalArgumentException: " + ex.getMessage());
|
|
782
|
// return false;
|
|
783
|
// } catch (IllegalAccessException ex) {
|
|
784
|
// logger.error("IllegalAccessException: " + ex.getMessage());
|
|
785
|
// return false;
|
|
786
|
// } catch (InvocationTargetException ex) {
|
|
787
|
// logger.error("IllegalAccessException: " + ex.getMessage());
|
|
788
|
// return false;
|
|
789
|
// }
|
|
790
|
// return true;
|
|
791
|
// }
|
|
792
|
|
|
793
|
@Override
|
|
794
|
public UUID delete(TaxonBase taxonBase) throws DataAccessException{
|
|
795
|
if (taxonBase == null){
|
|
796
|
logger.warn("TaxonBase was 'null'");
|
|
797
|
return null;
|
|
798
|
}
|
|
799
|
|
|
800
|
// Merge the object in if it is detached
|
|
801
|
//
|
|
802
|
// I think this is preferable to catching lazy initialization errors
|
|
803
|
// as that solution only swallows and hides the exception, but doesn't
|
|
804
|
// actually solve it.
|
|
805
|
getSession().merge(taxonBase);
|
|
806
|
|
|
807
|
if (taxonBase instanceof Taxon){ // is Taxon
|
|
808
|
for (Iterator<TaxonRelationship> iterator = ((Taxon)taxonBase).getRelationsFromThisTaxon().iterator(); iterator.hasNext();){
|
|
809
|
TaxonRelationship relationFromThisTaxon = iterator.next();
|
|
810
|
|
|
811
|
// decrease children count of taxonomic parent by one
|
|
812
|
if (relationFromThisTaxon.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())) {
|
|
813
|
Taxon toTaxon = relationFromThisTaxon.getToTaxon(); // parent
|
|
814
|
if (toTaxon != null) {
|
|
815
|
toTaxon.setTaxonomicChildrenCount(toTaxon.getTaxonomicChildrenCount() - 1);
|
|
816
|
}
|
|
817
|
}
|
|
818
|
}
|
|
819
|
}
|
|
820
|
|
|
821
|
return super.delete(taxonBase);
|
|
822
|
}
|
|
823
|
|
|
824
|
|
|
825
|
/* (non-Javadoc)
|
|
826
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#findByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, int, int, boolean)
|
|
827
|
*/
|
|
828
|
public List<TaxonBase> findByNameTitleCache(Class<? extends TaxonBase>clazz, String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageNumber, Integer pageSize, List<String> propertyPaths) {
|
|
829
|
|
|
830
|
boolean doCount = false;
|
|
831
|
Query query = prepareTaxaByName(clazz, "titleCache", queryString, classification, matchMode, namedAreas, pageSize, pageNumber, doCount);
|
|
832
|
if (query != null){
|
|
833
|
List<TaxonBase> results = query.list();
|
|
834
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
835
|
return results;
|
|
836
|
}
|
|
837
|
return new ArrayList<TaxonBase>();
|
|
838
|
|
|
839
|
}
|
|
840
|
|
|
841
|
/*
|
|
842
|
* (non-Javadoc)
|
|
843
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countMatchesByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, boolean)
|
|
844
|
*/
|
|
845
|
public int countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted) {
|
|
846
|
checkNotInPriorView("TaxonDaoHibernateImpl.countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted)");
|
|
847
|
Criteria crit = getSession().createCriteria(type);
|
|
848
|
crit.add(Restrictions.ilike("titleCache", matchMode.queryStringFrom(queryString)));
|
|
849
|
crit.setProjection(Projections.rowCount());
|
|
850
|
int result = ((Integer)crit.list().get(0)).intValue();
|
|
851
|
return result;
|
|
852
|
}
|
|
853
|
|
|
854
|
/*
|
|
855
|
* (non-Javadoc)
|
|
856
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countMatchesByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, boolean, java.util.List)
|
|
857
|
*/
|
|
858
|
public int countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted, List<Criterion> criteria) {
|
|
859
|
checkNotInPriorView("TaxonDaoHibernateImpl.countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted, List<Criterion> criteria)");
|
|
860
|
Criteria crit = getSession().createCriteria(type);
|
|
861
|
crit.add(Restrictions.ilike("titleCache", matchMode.queryStringFrom(queryString)));
|
|
862
|
if(criteria != null){
|
|
863
|
for (Criterion criterion : criteria) {
|
|
864
|
crit.add(criterion);
|
|
865
|
}
|
|
866
|
}
|
|
867
|
crit.setProjection(Projections.rowCount());
|
|
868
|
int result = ((Integer)crit.list().get(0)).intValue();
|
|
869
|
return result;
|
|
870
|
}
|
|
871
|
|
|
872
|
/*
|
|
873
|
* (non-Javadoc)
|
|
874
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction)
|
|
875
|
*/
|
|
876
|
public int countTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Direction direction) {
|
|
877
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
878
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
879
|
Query query = null;
|
|
880
|
|
|
881
|
if(type == null) {
|
|
882
|
query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship."+direction+" = :relatedTaxon");
|
|
883
|
} else {
|
|
884
|
query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship."+direction+" = :relatedTaxon and taxonRelationship.type = :type");
|
|
885
|
query.setParameter("type",type);
|
|
886
|
}
|
|
887
|
query.setParameter("relatedTaxon", taxon);
|
|
888
|
|
|
889
|
return ((Long)query.uniqueResult()).intValue();
|
|
890
|
} else {
|
|
891
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonRelationship.class,auditEvent.getRevisionNumber());
|
|
892
|
query.add(AuditEntity.relatedId(direction.toString()).eq(taxon.getId()));
|
|
893
|
query.addProjection(AuditEntity.id().count("id"));
|
|
894
|
|
|
895
|
if(type != null) {
|
|
896
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
897
|
}
|
|
898
|
|
|
899
|
return ((Long)query.getSingleResult()).intValue();
|
|
900
|
}
|
|
901
|
}
|
|
902
|
|
|
903
|
/*
|
|
904
|
* (non-Javadoc)
|
|
905
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countSynonyms(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType)
|
|
906
|
*/
|
|
907
|
public int countSynonyms(Taxon taxon, SynonymRelationshipType type) {
|
|
908
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
909
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
910
|
Criteria criteria = getSession().createCriteria(SynonymRelationship.class);
|
|
911
|
|
|
912
|
criteria.add(Restrictions.eq("relatedTo", taxon));
|
|
913
|
if(type != null) {
|
|
914
|
criteria.add(Restrictions.eq("type", type));
|
|
915
|
}
|
|
916
|
criteria.setProjection(Projections.rowCount());
|
|
917
|
return (Integer)criteria.uniqueResult();
|
|
918
|
} else {
|
|
919
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(SynonymRelationship.class,auditEvent.getRevisionNumber());
|
|
920
|
query.add(AuditEntity.relatedId("relatedTo").eq(taxon.getId()));
|
|
921
|
query.addProjection(AuditEntity.id().count("id"));
|
|
922
|
|
|
923
|
if(type != null) {
|
|
924
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
925
|
}
|
|
926
|
|
|
927
|
return ((Long)query.getSingleResult()).intValue();
|
|
928
|
}
|
|
929
|
}
|
|
930
|
|
|
931
|
/*
|
|
932
|
* (non-Javadoc)
|
|
933
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countSynonyms(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType)
|
|
934
|
*/
|
|
935
|
public int countSynonyms(Synonym synonym, SynonymRelationshipType type) {
|
|
936
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
937
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
938
|
Criteria criteria = getSession().createCriteria(SynonymRelationship.class);
|
|
939
|
|
|
940
|
criteria.add(Restrictions.eq("relatedFrom", synonym));
|
|
941
|
if(type != null) {
|
|
942
|
criteria.add(Restrictions.eq("type", type));
|
|
943
|
}
|
|
944
|
|
|
945
|
criteria.setProjection(Projections.rowCount());
|
|
946
|
return (Integer)criteria.uniqueResult();
|
|
947
|
} else {
|
|
948
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(SynonymRelationship.class,auditEvent.getRevisionNumber());
|
|
949
|
query.add(AuditEntity.relatedId("relatedFrom").eq(synonym.getId()));
|
|
950
|
query.addProjection(AuditEntity.id().count("id"));
|
|
951
|
|
|
952
|
if(type != null) {
|
|
953
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
954
|
}
|
|
955
|
|
|
956
|
return ((Long)query.getSingleResult()).intValue();
|
|
957
|
}
|
|
958
|
}
|
|
959
|
|
|
960
|
/*
|
|
961
|
* (non-Javadoc)
|
|
962
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countTaxaByName(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.name.Rank)
|
|
963
|
*/
|
|
964
|
public int countTaxaByName(Class<? extends TaxonBase> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank) {
|
|
965
|
checkNotInPriorView("TaxonDaoHibernateImpl.countTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank)");
|
|
966
|
Criteria criteria = null;
|
|
967
|
|
|
968
|
if(clazz == null) {
|
|
969
|
criteria = getSession().createCriteria(TaxonBase.class);
|
|
970
|
} else {
|
|
971
|
criteria = getSession().createCriteria(clazz);
|
|
972
|
}
|
|
973
|
|
|
974
|
criteria.setFetchMode( "name", FetchMode.JOIN );
|
|
975
|
criteria.createAlias("name", "name");
|
|
976
|
|
|
977
|
if(genusOrUninomial == null) {
|
|
978
|
criteria.add(Restrictions.isNull("name.genusOrUninomial"));
|
|
979
|
} else if(!genusOrUninomial.equals("*")) {
|
|
980
|
criteria.add(Restrictions.eq("name.genusOrUninomial", genusOrUninomial));
|
|
981
|
}
|
|
982
|
|
|
983
|
if(infraGenericEpithet == null) {
|
|
984
|
criteria.add(Restrictions.isNull("name.infraGenericEpithet"));
|
|
985
|
} else if(!infraGenericEpithet.equals("*")) {
|
|
986
|
criteria.add(Restrictions.eq("name.infraGenericEpithet", infraGenericEpithet));
|
|
987
|
}
|
|
988
|
|
|
989
|
if(specificEpithet == null) {
|
|
990
|
criteria.add(Restrictions.isNull("name.specificEpithet"));
|
|
991
|
} else if(!specificEpithet.equals("*")) {
|
|
992
|
criteria.add(Restrictions.eq("name.specificEpithet", specificEpithet));
|
|
993
|
|
|
994
|
}
|
|
995
|
|
|
996
|
if(infraSpecificEpithet == null) {
|
|
997
|
criteria.add(Restrictions.isNull("name.infraSpecificEpithet"));
|
|
998
|
} else if(!infraSpecificEpithet.equals("*")) {
|
|
999
|
criteria.add(Restrictions.eq("name.infraSpecificEpithet", infraSpecificEpithet));
|
|
1000
|
}
|
|
1001
|
|
|
1002
|
if(rank != null) {
|
|
1003
|
criteria.add(Restrictions.eq("name.rank", rank));
|
|
1004
|
}
|
|
1005
|
|
|
1006
|
criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));
|
|
1007
|
|
|
1008
|
return (Integer)criteria.uniqueResult();
|
|
1009
|
}
|
|
1010
|
|
|
1011
|
/*
|
|
1012
|
* (non-Javadoc)
|
|
1013
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#findTaxaByName(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, java.lang.Integer, java.lang.Integer)
|
|
1014
|
*/
|
|
1015
|
public List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank, Integer pageSize, Integer pageNumber) {
|
|
1016
|
checkNotInPriorView("TaxonDaoHibernateImpl.findTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank, Integer pageSize, Integer pageNumber)");
|
|
1017
|
Criteria criteria = null;
|
|
1018
|
|
|
1019
|
if(clazz == null) {
|
|
1020
|
criteria = getSession().createCriteria(TaxonBase.class);
|
|
1021
|
} else {
|
|
1022
|
criteria = getSession().createCriteria(clazz);
|
|
1023
|
}
|
|
1024
|
|
|
1025
|
criteria.setFetchMode( "name", FetchMode.JOIN );
|
|
1026
|
criteria.createAlias("name", "name");
|
|
1027
|
|
|
1028
|
if(genusOrUninomial == null) {
|
|
1029
|
criteria.add(Restrictions.isNull("name.genusOrUninomial"));
|
|
1030
|
} else if(!genusOrUninomial.equals("*")) {
|
|
1031
|
criteria.add(Restrictions.eq("name.genusOrUninomial", genusOrUninomial));
|
|
1032
|
}
|
|
1033
|
|
|
1034
|
if(infraGenericEpithet == null) {
|
|
1035
|
criteria.add(Restrictions.isNull("name.infraGenericEpithet"));
|
|
1036
|
} else if(!infraGenericEpithet.equals("*")) {
|
|
1037
|
criteria.add(Restrictions.eq("name.infraGenericEpithet", infraGenericEpithet));
|
|
1038
|
}
|
|
1039
|
|
|
1040
|
if(specificEpithet == null) {
|
|
1041
|
criteria.add(Restrictions.isNull("name.specificEpithet"));
|
|
1042
|
} else if(!specificEpithet.equals("*")) {
|
|
1043
|
criteria.add(Restrictions.eq("name.specificEpithet", specificEpithet));
|
|
1044
|
|
|
1045
|
}
|
|
1046
|
|
|
1047
|
if(infraSpecificEpithet == null) {
|
|
1048
|
criteria.add(Restrictions.isNull("name.infraSpecificEpithet"));
|
|
1049
|
} else if(!infraSpecificEpithet.equals("*")) {
|
|
1050
|
criteria.add(Restrictions.eq("name.infraSpecificEpithet", infraSpecificEpithet));
|
|
1051
|
}
|
|
1052
|
|
|
1053
|
if(rank != null) {
|
|
1054
|
criteria.add(Restrictions.eq("name.rank", rank));
|
|
1055
|
}
|
|
1056
|
|
|
1057
|
if(pageSize != null) {
|
|
1058
|
criteria.setMaxResults(pageSize);
|
|
1059
|
if(pageNumber != null) {
|
|
1060
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
1061
|
} else {
|
|
1062
|
criteria.setFirstResult(0);
|
|
1063
|
}
|
|
1064
|
}
|
|
1065
|
|
|
1066
|
return (List<TaxonBase>)criteria.list();
|
|
1067
|
}
|
|
1068
|
|
|
1069
|
/*
|
|
1070
|
* (non-Javadoc)
|
|
1071
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction)
|
|
1072
|
*/
|
|
1073
|
public List<TaxonRelationship> getTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths, Direction direction) {
|
|
1074
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
1075
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
1076
|
Criteria criteria = getSession().createCriteria(TaxonRelationship.class);
|
|
1077
|
|
|
1078
|
criteria.add(Restrictions.eq("relatedTo", taxon));
|
|
1079
|
if(type != null) {
|
|
1080
|
criteria.add(Restrictions.eq("type", type));
|
|
1081
|
}
|
|
1082
|
|
|
1083
|
addOrder(criteria,orderHints);
|
|
1084
|
|
|
1085
|
if(pageSize != null) {
|
|
1086
|
criteria.setMaxResults(pageSize);
|
|
1087
|
if(pageNumber != null) {
|
|
1088
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
1089
|
} else {
|
|
1090
|
criteria.setFirstResult(0);
|
|
1091
|
}
|
|
1092
|
}
|
|
1093
|
|
|
1094
|
List<TaxonRelationship> result = (List<TaxonRelationship>)criteria.list();
|
|
1095
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1096
|
|
|
1097
|
return result;
|
|
1098
|
} else {
|
|
1099
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonRelationship.class,auditEvent.getRevisionNumber());
|
|
1100
|
query.add(AuditEntity.relatedId("relatedTo").eq(taxon.getId()));
|
|
1101
|
|
|
1102
|
if(type != null) {
|
|
1103
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
1104
|
}
|
|
1105
|
|
|
1106
|
if(pageSize != null) {
|
|
1107
|
query.setMaxResults(pageSize);
|
|
1108
|
if(pageNumber != null) {
|
|
1109
|
query.setFirstResult(pageNumber * pageSize);
|
|
1110
|
} else {
|
|
1111
|
query.setFirstResult(0);
|
|
1112
|
}
|
|
1113
|
}
|
|
1114
|
|
|
1115
|
List<TaxonRelationship> result = (List<TaxonRelationship>)query.getResultList();
|
|
1116
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1117
|
|
|
1118
|
// Ugly, but for now, there is no way to sort on a related entity property in Envers,
|
|
1119
|
// and we can't live without this functionality in CATE as it screws up the whole
|
|
1120
|
// taxon tree thing
|
|
1121
|
if(orderHints != null && !orderHints.isEmpty()) {
|
|
1122
|
SortedSet<TaxonRelationship> sortedList = new TreeSet<TaxonRelationship>(new TaxonRelationshipFromTaxonComparator());
|
|
1123
|
sortedList.addAll(result);
|
|
1124
|
return new ArrayList<TaxonRelationship>(sortedList);
|
|
1125
|
}
|
|
1126
|
|
|
1127
|
return result;
|
|
1128
|
}
|
|
1129
|
}
|
|
1130
|
|
|
1131
|
class TaxonRelationshipFromTaxonComparator implements Comparator<TaxonRelationship> {
|
|
1132
|
|
|
1133
|
public int compare(TaxonRelationship o1, TaxonRelationship o2) {
|
|
1134
|
return o1.getFromTaxon().getTitleCache().compareTo(o2.getFromTaxon().getTitleCache());
|
|
1135
|
}
|
|
1136
|
|
|
1137
|
}
|
|
1138
|
|
|
1139
|
class SynonymRelationshipFromTaxonComparator implements Comparator<SynonymRelationship> {
|
|
1140
|
|
|
1141
|
public int compare(SynonymRelationship o1, SynonymRelationship o2) {
|
|
1142
|
return o1.getSynonym().getTitleCache().compareTo(o2.getSynonym().getTitleCache());
|
|
1143
|
}
|
|
1144
|
|
|
1145
|
}
|
|
1146
|
|
|
1147
|
/*
|
|
1148
|
* (non-Javadoc)
|
|
1149
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getSynonyms(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
|
1150
|
*/
|
|
1151
|
public List<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1152
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
1153
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
1154
|
Criteria criteria = getSession().createCriteria(SynonymRelationship.class);
|
|
1155
|
|
|
1156
|
criteria.add(Restrictions.eq("relatedTo", taxon));
|
|
1157
|
if(type != null) {
|
|
1158
|
criteria.add(Restrictions.eq("type", type));
|
|
1159
|
}
|
|
1160
|
|
|
1161
|
addOrder(criteria,orderHints);
|
|
1162
|
|
|
1163
|
if(pageSize != null) {
|
|
1164
|
criteria.setMaxResults(pageSize);
|
|
1165
|
if(pageNumber != null) {
|
|
1166
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
1167
|
} else {
|
|
1168
|
criteria.setFirstResult(0);
|
|
1169
|
}
|
|
1170
|
}
|
|
1171
|
|
|
1172
|
List<SynonymRelationship> result = (List<SynonymRelationship>)criteria.list();
|
|
1173
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1174
|
|
|
1175
|
return result;
|
|
1176
|
} else {
|
|
1177
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(SynonymRelationship.class,auditEvent.getRevisionNumber());
|
|
1178
|
query.add(AuditEntity.relatedId("relatedTo").eq(taxon.getId()));
|
|
1179
|
|
|
1180
|
if(type != null) {
|
|
1181
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
1182
|
}
|
|
1183
|
|
|
1184
|
if(pageSize != null) {
|
|
1185
|
query.setMaxResults(pageSize);
|
|
1186
|
if(pageNumber != null) {
|
|
1187
|
query.setFirstResult(pageNumber * pageSize);
|
|
1188
|
} else {
|
|
1189
|
query.setFirstResult(0);
|
|
1190
|
}
|
|
1191
|
}
|
|
1192
|
|
|
1193
|
List<SynonymRelationship> result = (List<SynonymRelationship>)query.getResultList();
|
|
1194
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1195
|
|
|
1196
|
return result;
|
|
1197
|
}
|
|
1198
|
}
|
|
1199
|
|
|
1200
|
/*
|
|
1201
|
* (non-Javadoc)
|
|
1202
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getSynonyms(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
|
1203
|
*/
|
|
1204
|
public List<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1205
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
1206
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
1207
|
Criteria criteria = getSession().createCriteria(SynonymRelationship.class);
|
|
1208
|
|
|
1209
|
criteria.add(Restrictions.eq("relatedFrom", synonym));
|
|
1210
|
if(type != null) {
|
|
1211
|
criteria.add(Restrictions.eq("type", type));
|
|
1212
|
}
|
|
1213
|
|
|
1214
|
addOrder(criteria,orderHints);
|
|
1215
|
|
|
1216
|
if(pageSize != null) {
|
|
1217
|
criteria.setMaxResults(pageSize);
|
|
1218
|
if(pageNumber != null) {
|
|
1219
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
1220
|
} else {
|
|
1221
|
criteria.setFirstResult(0);
|
|
1222
|
}
|
|
1223
|
}
|
|
1224
|
|
|
1225
|
List<SynonymRelationship> result = (List<SynonymRelationship>)criteria.list();
|
|
1226
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1227
|
|
|
1228
|
return result;
|
|
1229
|
} else {
|
|
1230
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(SynonymRelationship.class,auditEvent.getRevisionNumber());
|
|
1231
|
query.add(AuditEntity.relatedId("relatedFrom").eq(synonym.getId()));
|
|
1232
|
|
|
1233
|
if(type != null) {
|
|
1234
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
1235
|
}
|
|
1236
|
|
|
1237
|
if(pageSize != null) {
|
|
1238
|
query.setMaxResults(pageSize);
|
|
1239
|
if(pageNumber != null) {
|
|
1240
|
query.setFirstResult(pageNumber * pageSize);
|
|
1241
|
} else {
|
|
1242
|
query.setFirstResult(0);
|
|
1243
|
}
|
|
1244
|
}
|
|
1245
|
|
|
1246
|
List<SynonymRelationship> result = (List<SynonymRelationship>)query.getResultList();
|
|
1247
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1248
|
|
|
1249
|
return result;
|
|
1250
|
}
|
|
1251
|
}
|
|
1252
|
|
|
1253
|
@Override
|
|
1254
|
public void rebuildIndex() {
|
|
1255
|
FullTextSession fullTextSession = Search.getFullTextSession(getSession());
|
|
1256
|
|
|
1257
|
for(TaxonBase taxonBase : list(null,null)) { // re-index all taxon base
|
|
1258
|
Hibernate.initialize(taxonBase.getName());
|
|
1259
|
fullTextSession.index(taxonBase);
|
|
1260
|
}
|
|
1261
|
fullTextSession.flushToIndexes();
|
|
1262
|
}
|
|
1263
|
|
|
1264
|
@Override
|
|
1265
|
public String suggestQuery(String queryString) {
|
|
1266
|
checkNotInPriorView("TaxonDaoHibernateImpl.suggestQuery(String queryString)");
|
|
1267
|
String alternativeQueryString = null;
|
|
1268
|
if (alternativeSpellingSuggestionParser != null) {
|
|
1269
|
try {
|
|
1270
|
|
|
1271
|
alternativeSpellingSuggestionParser.parse(queryString);
|
|
1272
|
org.apache.lucene.search.Query alternativeQuery = alternativeSpellingSuggestionParser.suggest(queryString);
|
|
1273
|
if (alternativeQuery != null) {
|
|
1274
|
alternativeQueryString = alternativeQuery
|
|
1275
|
.toString("name.titleCache");
|
|
1276
|
}
|
|
1277
|
|
|
1278
|
} catch (ParseException e) {
|
|
1279
|
throw new QueryParseException(e, queryString);
|
|
1280
|
}
|
|
1281
|
}
|
|
1282
|
return alternativeQueryString;
|
|
1283
|
}
|
|
1284
|
|
|
1285
|
/*
|
|
1286
|
* (non-Javadoc)
|
|
1287
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheOfAcceptedTaxa(eu.etaxonomy.cdm.model.taxon.Classification)
|
|
1288
|
*/
|
|
1289
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification) {
|
|
1290
|
|
|
1291
|
int classificationId = classification.getId();
|
|
1292
|
|
|
1293
|
String queryString = "SELECT nodes.uuid, taxa.titleCache FROM TaxonNode AS nodes LEFT JOIN TaxonBase AS taxa ON nodes.taxon_id = taxa.id WHERE taxa.DTYPE = 'Taxon' AND nodes.classification_id = " + classificationId;
|
|
1294
|
|
|
1295
|
List<Object[]> result = getSession().createSQLQuery(queryString).list();
|
|
1296
|
|
|
1297
|
if(result.size() == 0){
|
|
1298
|
return null;
|
|
1299
|
}else{
|
|
1300
|
List<UuidAndTitleCache<TaxonNode>> list = new ArrayList<UuidAndTitleCache<TaxonNode>>(result.size());
|
|
1301
|
|
|
1302
|
for (Object object : result){
|
|
1303
|
|
|
1304
|
Object[] objectArray = (Object[]) object;
|
|
1305
|
|
|
1306
|
UUID uuid = UUID.fromString((String) objectArray[0]);
|
|
1307
|
String titleCache = (String) objectArray[1];
|
|
1308
|
|
|
1309
|
list.add(new UuidAndTitleCache(TaxonNode.class, uuid, titleCache));
|
|
1310
|
}
|
|
1311
|
|
|
1312
|
return list;
|
|
1313
|
}
|
|
1314
|
}
|
|
1315
|
|
|
1316
|
|
|
1317
|
public class UuidAndTitleCacheOfAcceptedTaxon{
|
|
1318
|
UUID uuid;
|
|
1319
|
|
|
1320
|
String titleCache;
|
|
1321
|
|
|
1322
|
public UuidAndTitleCacheOfAcceptedTaxon(UUID uuid, String titleCache){
|
|
1323
|
this.uuid = uuid;
|
|
1324
|
this.titleCache = titleCache;
|
|
1325
|
}
|
|
1326
|
|
|
1327
|
public UUID getUuid() {
|
|
1328
|
return uuid;
|
|
1329
|
}
|
|
1330
|
|
|
1331
|
public void setUuid(UUID uuid) {
|
|
1332
|
this.uuid = uuid;
|
|
1333
|
}
|
|
1334
|
|
|
1335
|
public String getTitleCache() {
|
|
1336
|
return titleCache;
|
|
1337
|
}
|
|
1338
|
|
|
1339
|
public void setTitleCache(String titleCache) {
|
|
1340
|
this.titleCache = titleCache;
|
|
1341
|
}
|
|
1342
|
}
|
|
1343
|
|
|
1344
|
@Override
|
|
1345
|
public TaxonBase find(LSID lsid) {
|
|
1346
|
TaxonBase taxonBase = super.find(lsid);
|
|
1347
|
if(taxonBase != null) {
|
|
1348
|
List<String> propertyPaths = new ArrayList<String>();
|
|
1349
|
propertyPaths.add("createdBy");
|
|
1350
|
propertyPaths.add("updatedBy");
|
|
1351
|
propertyPaths.add("name");
|
|
1352
|
propertyPaths.add("sec");
|
|
1353
|
propertyPaths.add("relationsToThisTaxon");
|
|
1354
|
propertyPaths.add("relationsToThisTaxon.fromTaxon");
|
|
1355
|
propertyPaths.add("relationsToThisTaxon.toTaxon");
|
|
1356
|
propertyPaths.add("relationsFromThisTaxon");
|
|
1357
|
propertyPaths.add("relationsFromThisTaxon.toTaxon");
|
|
1358
|
propertyPaths.add("relationsToThisTaxon.type");
|
|
1359
|
propertyPaths.add("synonymRelations");
|
|
1360
|
propertyPaths.add("synonymRelations.synonym");
|
|
1361
|
propertyPaths.add("synonymRelations.type");
|
|
1362
|
propertyPaths.add("descriptions");
|
|
1363
|
|
|
1364
|
defaultBeanInitializer.initialize(taxonBase, propertyPaths);
|
|
1365
|
}
|
|
1366
|
return taxonBase;
|
|
1367
|
}
|
|
1368
|
|
|
1369
|
public List<TaxonBase> getTaxaByCommonName(String queryString,
|
|
1370
|
Classification classification, MatchMode matchMode,
|
|
1371
|
Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber) {
|
|
1372
|
// TODO Auto-generated method stub
|
|
1373
|
return null;
|
|
1374
|
}
|
|
1375
|
|
|
1376
|
|
|
1377
|
public List<Synonym> createAllInferredSynonyms(Taxon taxon, Classification tree){
|
|
1378
|
List <Synonym> inferredSynonyms = new ArrayList<Synonym>();
|
|
1379
|
|
|
1380
|
inferredSynonyms.addAll(createInferredSynonyms(taxon, tree, SynonymRelationshipType.INFERRED_EPITHET_OF()));
|
|
1381
|
inferredSynonyms.addAll(createInferredSynonyms(taxon, tree, SynonymRelationshipType.INFERRED_GENUS_OF()));
|
|
1382
|
inferredSynonyms.addAll(createInferredSynonyms(taxon, tree, SynonymRelationshipType.POTENTIAL_COMBINATION_OF()));
|
|
1383
|
|
|
1384
|
return inferredSynonyms;
|
|
1385
|
}
|
|
1386
|
|
|
1387
|
|
|
1388
|
/**
|
|
1389
|
* Returns an existing ZoologicalName or extends an internal hashmap if it does not exist.
|
|
1390
|
* Very likely only useful for createInferredSynonyms().
|
|
1391
|
* @param uuid
|
|
1392
|
* @param zooHashMap
|
|
1393
|
* @return
|
|
1394
|
*/
|
|
1395
|
private ZoologicalName getZoologicalName(UUID uuid, HashMap <UUID, ZoologicalName> zooHashMap) {
|
|
1396
|
ZoologicalName taxonName = this.taxonNameDao.findZoologicalNameByUUID(uuid);
|
|
1397
|
if (taxonName == null) {
|
|
1398
|
taxonName = zooHashMap.get(uuid);
|
|
1399
|
}
|
|
1400
|
return taxonName;
|
|
1401
|
}
|
|
1402
|
|
|
1403
|
public List<Synonym> createInferredSynonyms(Taxon taxon, Classification tree, SynonymRelationshipType type){
|
|
1404
|
List <Synonym> inferredSynonyms = new ArrayList<Synonym>();
|
|
1405
|
List<Synonym> inferredSynonymsToBeRemoved = new ArrayList<Synonym>();
|
|
1406
|
|
|
1407
|
HashMap <UUID, ZoologicalName> zooHashMap = new HashMap<UUID, ZoologicalName>();
|
|
1408
|
UUID uuid;
|
|
1409
|
|
|
1410
|
uuid= taxon.getName().getUuid();
|
|
1411
|
ZoologicalName taxonName = getZoologicalName(uuid, zooHashMap);
|
|
1412
|
String epithetOfTaxon = taxonName.getSpecificEpithet();
|
|
1413
|
String genusOfTaxon = taxonName.getGenusOrUninomial();
|
|
1414
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
|
1415
|
List<String> taxonNames = new ArrayList<String>();
|
|
1416
|
|
|
1417
|
for (TaxonNode node: nodes){
|
|
1418
|
HashMap<String, String> synonymsGenus = new HashMap<String, String>(); // Changed this to be able to store the idInSource to a genusName
|
|
1419
|
List<String> synonymsEpithet = new ArrayList<String>();
|
|
1420
|
|
|
1421
|
if (node.getClassification().equals(tree)){
|
|
1422
|
if (!node.isTopmostNode()){
|
|
1423
|
TaxonNode parent = (TaxonNode)node.getParent();
|
|
1424
|
parent = (TaxonNode)HibernateProxyHelper.deproxy(parent);
|
|
1425
|
TaxonNameBase parentName = parent.getTaxon().getName();
|
|
1426
|
parentName = (TaxonNameBase)HibernateProxyHelper.deproxy(parentName);
|
|
1427
|
|
|
1428
|
//create inferred synonyms for species, subspecies or subgenus
|
|
1429
|
if (parentName.isGenus() || parentName.isSpecies() || parentName.getRank().equals(Rank.SUBGENUS())){
|
|
1430
|
|
|
1431
|
Synonym inferredEpithet;
|
|
1432
|
Synonym inferredGenus = null;
|
|
1433
|
Synonym potentialCombination;
|
|
1434
|
|
|
1435
|
List<String> propertyPaths = new ArrayList<String>();
|
|
1436
|
propertyPaths.add("synonym");
|
|
1437
|
propertyPaths.add("synonym.name");
|
|
1438
|
List<OrderHint> orderHints = new ArrayList<OrderHint>();
|
|
1439
|
orderHints.add(new OrderHint("relatedFrom.titleCache", SortOrder.ASCENDING));
|
|
1440
|
|
|
1441
|
List<SynonymRelationship> synonymRelationshipsOfGenus = getSynonyms(parent.getTaxon(), SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), null, null,orderHints,propertyPaths);
|
|
1442
|
List<SynonymRelationship> synonymRelationshipsOfTaxon= getSynonyms(taxon, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), null, null,orderHints,propertyPaths);
|
|
1443
|
|
|
1444
|
if (type.equals(SynonymRelationshipType.INFERRED_EPITHET_OF())){
|
|
1445
|
|
|
1446
|
for (SynonymRelationship synonymRelationOfGenus:synonymRelationshipsOfGenus){
|
|
1447
|
TaxonNameBase synName;
|
|
1448
|
ZoologicalName inferredSynName;
|
|
1449
|
Synonym syn = synonymRelationOfGenus.getSynonym();
|
|
1450
|
HibernateProxyHelper.deproxy(syn);
|
|
1451
|
|
|
1452
|
// Determine the idInSource
|
|
1453
|
String idInSource = getIdInSource(syn);
|
|
1454
|
|
|
1455
|
// Determine the sourceReference
|
|
1456
|
Reference sourceReference = syn.getSec();
|
|
1457
|
|
|
1458
|
synName = syn.getName();
|
|
1459
|
ZoologicalName zooName = getZoologicalName(synName.getUuid(), zooHashMap);
|
|
1460
|
String synGenusName = zooName.getGenusOrUninomial();
|
|
1461
|
if (synGenusName != null && !synonymsGenus.containsKey(synGenusName)){
|
|
1462
|
synonymsGenus.put(synGenusName, idInSource);
|
|
1463
|
}
|
|
1464
|
inferredSynName = ZoologicalName.NewInstance(Rank.SPECIES());
|
|
1465
|
|
|
1466
|
// DEBUG
|
|
1467
|
if (epithetOfTaxon == null) {
|
|
1468
|
logger.error("This specificEpithet is NULL");
|
|
1469
|
}
|
|
1470
|
|
|
1471
|
inferredSynName.setSpecificEpithet(epithetOfTaxon);
|
|
1472
|
inferredSynName.setGenusOrUninomial(synGenusName);
|
|
1473
|
inferredEpithet = Synonym.NewInstance(inferredSynName, null);
|
|
1474
|
|
|
1475
|
// Set the sourceReference
|
|
1476
|
inferredEpithet.setSec(sourceReference);
|
|
1477
|
|
|
1478
|
// Add the original source
|
|
1479
|
if (idInSource != null) {
|
|
1480
|
IdentifiableSource originalSource = IdentifiableSource.NewInstance(idInSource, "InferredEpithetOf", syn.getSec(), null);
|
|
1481
|
|
|
1482
|
// Add the citation
|
|
1483
|
Reference citation = getCitation(syn);
|
|
1484
|
if (citation != null) {
|
|
1485
|
originalSource.setCitation(citation);
|
|
1486
|
inferredEpithet.addSource(originalSource);
|
|
1487
|
}
|
|
1488
|
}
|
|
1489
|
|
|
1490
|
taxon.addSynonym(inferredEpithet, SynonymRelationshipType.INFERRED_GENUS_OF());
|
|
1491
|
inferredSynonyms.add(inferredEpithet);
|
|
1492
|
inferredSynName.generateTitle();
|
|
1493
|
zooHashMap.put(inferredSynName.getUuid(), inferredSynName);
|
|
1494
|
taxonNames.add(inferredSynName.getNameCache());
|
|
1495
|
}
|
|
1496
|
|
|
1497
|
if (!taxonNames.isEmpty()){
|
|
1498
|
List<String> synNotInCDM = this.taxaByNameNotInDB(taxonNames);
|
|
1499
|
ZoologicalName name;
|
|
1500
|
if (!synNotInCDM.isEmpty()){
|
|
1501
|
inferredSynonymsToBeRemoved.clear();
|
|
1502
|
|
|
1503
|
for (Synonym syn :inferredSynonyms){
|
|
1504
|
name = getZoologicalName(syn.getName().getUuid(), zooHashMap);
|
|
1505
|
if (!synNotInCDM.contains(name.getNameCache())){
|
|
1506
|
inferredSynonymsToBeRemoved.add(syn);
|
|
1507
|
}
|
|
1508
|
}
|
|
1509
|
|
|
1510
|
// Remove identified Synonyms from inferredSynonyms
|
|
1511
|
for (Synonym synonym : inferredSynonymsToBeRemoved) {
|
|
1512
|
inferredSynonyms.remove(synonym);
|
|
1513
|
}
|
|
1514
|
}
|
|
1515
|
}
|
|
1516
|
|
|
1517
|
}else if (type.equals(SynonymRelationshipType.INFERRED_GENUS_OF())){
|
|
1518
|
|
|
1519
|
|
|
1520
|
for (SynonymRelationship synonymRelationOfTaxon:synonymRelationshipsOfTaxon){
|
|
1521
|
TaxonNameBase synName;
|
|
1522
|
ZoologicalName inferredSynName;
|
|
1523
|
|
|
1524
|
Synonym syn = synonymRelationOfTaxon.getSynonym();
|
|
1525
|
synName =syn.getName();
|
|
1526
|
HibernateProxyHelper.deproxy(syn);
|
|
1527
|
|
|
1528
|
// Determine the idInSource
|
|
1529
|
String idInSource = getIdInSource(syn);
|
|
1530
|
|
|
1531
|
// Determine the sourceReference
|
|
1532
|
Reference sourceReference = syn.getSec();
|
|
1533
|
|
|
1534
|
synName = syn.getName();
|
|
1535
|
ZoologicalName zooName = getZoologicalName(synName.getUuid(), zooHashMap);
|
|
1536
|
String speciesEpithetName = zooName.getSpecificEpithet();
|
|
1537
|
if (synonymsEpithet != null && !synonymsEpithet.contains(speciesEpithetName)){
|
|
1538
|
synonymsEpithet.add(speciesEpithetName);
|
|
1539
|
}
|
|
1540
|
inferredSynName = ZoologicalName.NewInstance(Rank.SPECIES());
|
|
1541
|
inferredSynName.setSpecificEpithet(speciesEpithetName);
|
|
1542
|
inferredSynName.setGenusOrUninomial(genusOfTaxon);
|
|
1543
|
inferredGenus = Synonym.NewInstance(inferredSynName, null);
|
|
1544
|
|
|
1545
|
// Set the sourceReference
|
|
1546
|
inferredGenus.setSec(sourceReference);
|
|
1547
|
|
|
1548
|
// Add the original source
|
|
1549
|
if (idInSource != null) {
|
|
1550
|
IdentifiableSource originalSource = IdentifiableSource.NewInstance(idInSource, "InferredGenusOf", syn.getSec(), null);
|
|
1551
|
|
|
1552
|
// Add the citation
|
|
1553
|
Reference citation = getCitation(syn);
|
|
1554
|
if (citation != null) {
|
|
1555
|
originalSource.setCitation(citation);
|
|
1556
|
inferredGenus.addSource(originalSource);
|
|
1557
|
}
|
|
1558
|
}
|
|
1559
|
|
|
1560
|
taxon.addSynonym(inferredGenus, SynonymRelationshipType.INFERRED_EPITHET_OF());
|
|
1561
|
inferredSynonyms.add(inferredGenus);
|
|
1562
|
inferredSynName.generateTitle();
|
|
1563
|
zooHashMap.put(inferredSynName.getUuid(), inferredSynName);
|
|
1564
|
taxonNames.add(inferredSynName.getNameCache());
|
|
1565
|
}
|
|
1566
|
|
|
1567
|
if (!taxonNames.isEmpty()){
|
|
1568
|
List<String> synNotInCDM = this.taxaByNameNotInDB(taxonNames);
|
|
1569
|
ZoologicalName name;
|
|
1570
|
if (!synNotInCDM.isEmpty()){
|
|
1571
|
inferredSynonymsToBeRemoved.clear();
|
|
1572
|
|
|
1573
|
for (Synonym syn :inferredSynonyms){
|
|
1574
|
name = getZoologicalName(syn.getName().getUuid(), zooHashMap);
|
|
1575
|
if (!synNotInCDM.contains(name.getNameCache())){
|
|
1576
|
inferredSynonymsToBeRemoved.add(syn);
|
|
1577
|
}
|
|
1578
|
}
|
|
1579
|
|
|
1580
|
// Remove identified Synonyms from inferredSynonyms
|
|
1581
|
for (Synonym synonym : inferredSynonymsToBeRemoved) {
|
|
1582
|
inferredSynonyms.remove(synonym);
|
|
1583
|
}
|
|
1584
|
}
|
|
1585
|
}
|
|
1586
|
|
|
1587
|
}else if (type.equals(SynonymRelationshipType.POTENTIAL_COMBINATION_OF())){
|
|
1588
|
|
|
1589
|
Reference sourceReference = null; // TODO: Determination of sourceReference is redundant
|
|
1590
|
|
|
1591
|
for (SynonymRelationship synonymRelationOfGenus:synonymRelationshipsOfGenus){
|
|
1592
|
TaxonNameBase synName;
|
|
1593
|
Synonym syn = synonymRelationOfGenus.getSynonym();
|
|
1594
|
synName =syn.getName();
|
|
1595
|
|
|
1596
|
HibernateProxyHelper.deproxy(syn);
|
|
1597
|
|
|
1598
|
// Set the sourceReference
|
|
1599
|
sourceReference = syn.getSec();
|
|
1600
|
|
|
1601
|
// Determine the idInSource
|
|
1602
|
String idInSource = getIdInSource(syn);
|
|
1603
|
|
|
1604
|
ZoologicalName zooName = getZoologicalName(synName.getUuid(), zooHashMap);
|
|
1605
|
String synGenusName = zooName.getGenusOrUninomial();
|
|
1606
|
if (synGenusName != null && !synonymsGenus.containsKey(synGenusName)){
|
|
1607
|
synonymsGenus.put(synGenusName, idInSource);
|
|
1608
|
}
|
|
1609
|
}
|
|
1610
|
|
|
1611
|
ZoologicalName inferredSynName;
|
|
1612
|
for (SynonymRelationship synonymRelationOfTaxon:synonymRelationshipsOfTaxon){
|
|
1613
|
|
|
1614
|
Synonym syn = synonymRelationOfTaxon.getSynonym();
|
|
1615
|
HibernateProxyHelper.deproxy(syn);
|
|
1616
|
|
|
1617
|
// Set sourceReference
|
|
1618
|
sourceReference = syn.getSec();
|
|
1619
|
|
|
1620
|
ZoologicalName zooName = getZoologicalName(syn.getName().getUuid(), zooHashMap);
|
|
1621
|
String epithetName = zooName.getSpecificEpithet();
|
|
1622
|
if (epithetName != null && !synonymsEpithet.contains(epithetName)){
|
|
1623
|
synonymsEpithet.add(epithetName);
|
|
1624
|
}
|
|
1625
|
}
|
|
1626
|
for (String epithetName:synonymsEpithet){
|
|
1627
|
for (String genusName: synonymsGenus.keySet()){
|
|
1628
|
inferredSynName = ZoologicalName.NewInstance(Rank.SPECIES());
|
|
1629
|
inferredSynName.setSpecificEpithet(epithetName);
|
|
1630
|
inferredSynName.setGenusOrUninomial(genusName);
|
|
1631
|
potentialCombination = Synonym.NewInstance(inferredSynName, null);
|
|
1632
|
|
|
1633
|
// Set the sourceReference
|
|
1634
|
potentialCombination.setSec(sourceReference);
|
|
1635
|
|
|
1636
|
// Add the original source
|
|
1637
|
String idInSource = synonymsGenus.get(genusName);
|
|
1638
|
if (idInSource != null) {
|
|
1639
|
IdentifiableSource originalSource = IdentifiableSource.NewInstance(idInSource, "PotentialCombinationOf", sourceReference, null);
|
|
1640
|
|
|
1641
|
// Add the citation
|
|
1642
|
if (sourceReference != null) {
|
|
1643
|
originalSource.setCitation(sourceReference);
|
|
1644
|
potentialCombination.addSource(originalSource);
|
|
1645
|
}
|
|
1646
|
}
|
|
1647
|
|
|
1648
|
inferredSynonyms.add(potentialCombination);
|
|
1649
|
inferredSynName.generateTitle();
|
|
1650
|
zooHashMap.put(inferredSynName.getUuid(), inferredSynName);
|
|
1651
|
taxonNames.add(inferredSynName.getNameCache());
|
|
1652
|
}
|
|
1653
|
|
|
1654
|
if (!taxonNames.isEmpty()){
|
|
1655
|
List<String> synNotInCDM = this.taxaByNameNotInDB(taxonNames);
|
|
1656
|
ZoologicalName name;
|
|
1657
|
if (!synNotInCDM.isEmpty()){
|
|
1658
|
inferredSynonymsToBeRemoved.clear();
|
|
1659
|
|
|
1660
|
for (Synonym syn :inferredSynonyms){
|
|
1661
|
try{
|
|
1662
|
name = (ZoologicalName) syn.getName();
|
|
1663
|
}catch (ClassCastException e){
|
|
1664
|
name = getZoologicalName(syn.getName().getUuid(), zooHashMap);
|
|
1665
|
}
|
|
1666
|
if (!synNotInCDM.contains(name.getNameCache())){
|
|
1667
|
inferredSynonymsToBeRemoved.add(syn);
|
|
1668
|
}
|
|
1669
|
}
|
|
1670
|
|
|
1671
|
// Remove identified Synonyms from inferredSynonyms
|
|
1672
|
for (Synonym synonym : inferredSynonymsToBeRemoved) {
|
|
1673
|
inferredSynonyms.remove(synonym);
|
|
1674
|
}
|
|
1675
|
}
|
|
1676
|
}
|
|
1677
|
}
|
|
1678
|
}else {
|
|
1679
|
logger.info("The synonymrelationship type is not defined.");
|
|
1680
|
return null;
|
|
1681
|
}
|
|
1682
|
}
|
|
1683
|
}
|
|
1684
|
}
|
|
1685
|
}
|
|
1686
|
|
|
1687
|
|
|
1688
|
return inferredSynonyms;
|
|
1689
|
}
|
|
1690
|
|
|
1691
|
|
|
1692
|
/**
|
|
1693
|
* Returns the idInSource for a given Synonym.
|
|
1694
|
* @param syn
|
|
1695
|
*/
|
|
1696
|
private String getIdInSource(Synonym syn) {
|
|
1697
|
String idInSource = null;
|
|
1698
|
Set<IdentifiableSource> sources = syn.getSources();
|
|
1699
|
if (sources.size() == 1) {
|
|
1700
|
IdentifiableSource source = sources.iterator().next();
|
|
1701
|
if (source != null) {
|
|
1702
|
idInSource = source.getIdInSource();
|
|
1703
|
}
|
|
1704
|
} else if (sources.size() > 1) {
|
|
1705
|
int count = 1;
|
|
1706
|
idInSource = "";
|
|
1707
|
for (IdentifiableSource source : sources) {
|
|
1708
|
idInSource += source.getIdInSource();
|
|
1709
|
if (count < sources.size()) {
|
|
1710
|
idInSource += "; ";
|
|
1711
|
}
|
|
1712
|
count++;
|
|
1713
|
}
|
|
1714
|
}
|
|
1715
|
|
|
1716
|
return idInSource;
|
|
1717
|
}
|
|
1718
|
|
|
1719
|
/**
|
|
1720
|
* Returns the citation for a given Synonym.
|
|
1721
|
* @param syn
|
|
1722
|
*/
|
|
1723
|
private Reference getCitation(Synonym syn) {
|
|
1724
|
Reference citation = null;
|
|
1725
|
Set<IdentifiableSource> sources = syn.getSources();
|
|
1726
|
if (sources.size() == 1) {
|
|
1727
|
IdentifiableSource source = sources.iterator().next();
|
|
1728
|
if (source != null) {
|
|
1729
|
citation = source.getCitation();
|
|
1730
|
}
|
|
1731
|
} else if (sources.size() > 1) {
|
|
1732
|
logger.warn("This Synonym has more than one source: " + syn.getUuid() + " (" + syn.getTitleCache() +")");
|
|
1733
|
}
|
|
1734
|
|
|
1735
|
return citation;
|
|
1736
|
}
|
|
1737
|
|
|
1738
|
/* private void xxx(List<SynonymRelationship> synonymRelationships, HashMap <UUID, ZoologicalName> zooHashMap, SynonymRelationshipType type, String addString){
|
|
1739
|
|
|
1740
|
for (SynonymRelationship synonymRelation:synonymRelationships){
|
|
1741
|
TaxonNameBase synName;
|
|
1742
|
NonViralName inferredSynName;
|
|
1743
|
Synonym syn = synonymRelation.getSynonym();
|
|
1744
|
HibernateProxyHelper.deproxy(syn);
|
|
1745
|
|
|
1746
|
synName = syn.getName();
|
|
1747
|
ZoologicalName zooName = zooHashMap.get(synName.getUuid());
|
|
1748
|
String synGenusName = zooName.getGenusOrUninomial();
|
|
1749
|
|
|
1750
|
switch(type.getId()){
|
|
1751
|
case SynonymRelationshipType.INFERRED_EPITHET_OF().getId():
|
|
1752
|
inferredSynName.setSpecificEpithet(addString);
|
|
1753
|
break;
|
|
1754
|
case SynonymRelationshipType.INFERRED_GENUS_OF().getId():
|
|
1755
|
break;
|
|
1756
|
case SynonymRelationshipType.POTENTIAL_COMBINATION_OF().getId():
|
|
1757
|
break;
|
|
1758
|
default:
|
|
1759
|
}
|
|
1760
|
if (!synonymsGenus.contains(synGenusName)){
|
|
1761
|
synonymsGenus.add(synGenusName);
|
|
1762
|
}
|
|
1763
|
inferredSynName = NonViralName.NewInstance(Rank.SPECIES());
|
|
1764
|
inferredSynName.setSpecificEpithet(epithetOfTaxon);
|
|
1765
|
inferredSynName.setGenusOrUninomial(synGenusName);
|
|
1766
|
inferredEpithet = Synonym.NewInstance(inferredSynName, null);
|
|
1767
|
taxon.addSynonym(inferredEpithet, SynonymRelationshipType.INFERRED_GENUS_OF());
|
|
1768
|
inferredSynonyms.add(inferredEpithet);
|
|
1769
|
inferredSynName.generateTitle();
|
|
1770
|
taxonNames.add(inferredSynName.getNameCache());
|
|
1771
|
}
|
|
1772
|
|
|
1773
|
|
|
1774
|
if (!taxonNames.isEmpty()){
|
|
1775
|
List<String> synNotInCDM = this.taxaByNameNotInDB(taxonNames);
|
|
1776
|
ZoologicalName name;
|
|
1777
|
if (!synNotInCDM.isEmpty()){
|
|
1778
|
for (Synonym syn :inferredSynonyms){
|
|
1779
|
name =zooHashMap.get(syn.getName().getUuid());
|
|
1780
|
if (!synNotInCDM.contains(name.getNameCache())){
|
|
1781
|
inferredSynonyms.remove(syn);
|
|
1782
|
}
|
|
1783
|
}
|
|
1784
|
}
|
|
1785
|
}
|
|
1786
|
}*/
|
|
1787
|
|
|
1788
|
/*
|
|
1789
|
* (non-Javadoc)
|
|
1790
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countAllRelationships()
|
|
1791
|
*/
|
|
1792
|
public int countAllRelationships() {
|
|
1793
|
List<RelationshipBase> relationships = this.getAllRelationships(null, 0);
|
|
1794
|
return relationships.size();
|
|
1795
|
}
|
|
1796
|
|
|
1797
|
|
|
1798
|
public List<String> taxaByNameNotInDB(List<String> taxonNames){
|
|
1799
|
List<TaxonBase> notInDB = new ArrayList<TaxonBase>();
|
|
1800
|
//get all taxa, already in db
|
|
1801
|
Query query = getSession().createQuery("from TaxonNameBase t where t.nameCache IN (:taxonList)");
|
|
1802
|
query.setParameterList("taxonList", taxonNames);
|
|
1803
|
List<TaxonNameBase> taxaInDB = query.list();
|
|
1804
|
//compare the original list with the result of the query
|
|
1805
|
for (TaxonNameBase taxonName: taxaInDB){
|
|
1806
|
if (taxonName.isInstanceOf(NonViralName.class)) {
|
|
1807
|
NonViralName nonViralName = CdmBase.deproxy(taxonName, NonViralName.class);
|
|
1808
|
String nameCache = nonViralName.getNameCache();
|
|
1809
|
if (taxonNames.contains(nameCache)){
|
|
1810
|
taxonNames.remove(nameCache);
|
|
1811
|
}
|
|
1812
|
}
|
|
1813
|
}
|
|
1814
|
|
|
1815
|
return taxonNames;
|
|
1816
|
}
|
|
1817
|
|
|
1818
|
//TODO: mal nur mit UUID probieren (ohne fetch all properties), vielleicht geht das schneller?
|
|
1819
|
public List<UUID> findIdenticalTaxonNameIds(List<String> propertyPaths){
|
|
1820
|
Query query=getSession().createQuery("select tmb2 from ZoologicalName tmb, ZoologicalName tmb2 fetch all properties where tmb.id != tmb2.id and tmb.nameCache = tmb2.nameCache");
|
|
1821
|
List<UUID> zooNames = query.list();
|
|
1822
|
|
|
1823
|
return zooNames;
|
|
1824
|
|
|
1825
|
}
|
|
1826
|
|
|
1827
|
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPaths) {
|
|
1828
|
|
|
1829
|
Query query=getSession().createQuery("select tmb2 from ZoologicalName tmb, ZoologicalName tmb2 fetch all properties where tmb.id != tmb2.id and tmb.nameCache = tmb2.nameCache");
|
|
1830
|
|
|
1831
|
List<TaxonNameBase> zooNames = query.list();
|
|
1832
|
|
|
1833
|
TaxonNameComparator taxComp = new TaxonNameComparator();
|
|
1834
|
Collections.sort(zooNames, taxComp);
|
|
1835
|
|
|
1836
|
for (TaxonNameBase taxonNameBase: zooNames){
|
|
1837
|
defaultBeanInitializer.initialize(taxonNameBase, propertyPaths);
|
|
1838
|
}
|
|
1839
|
|
|
1840
|
return zooNames;
|
|
1841
|
}
|
|
1842
|
|
|
1843
|
public List<TaxonNameBase> findIdenticalNamesNew(List<String> propertyPaths){
|
|
1844
|
|
|
1845
|
//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)
|
|
1846
|
Query query = getSession().createQuery("Select id from Reference where titleCache like 'Fauna Europaea database'");
|
|
1847
|
List<String> secRefFauna = query.list();
|
|
1848
|
query = getSession().createQuery("Select id from Reference where titleCache like 'ERMS'");
|
|
1849
|
List<String> secRefErms = query.list();
|
|
1850
|
//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");
|
|
1851
|
//Get all names of fauna europaea
|
|
1852
|
query = getSession().createQuery("select zn.nameCache from ZoologicalName zn, TaxonBase tb where tb.name = zn and tb.sec.id = :secRefFauna");
|
|
1853
|
query.setParameter("secRefFauna", secRefFauna.get(0));
|
|
1854
|
List<String> namesFauna= query.list();
|
|
1855
|
|
|
1856
|
//Get all names of erms
|
|
1857
|
|
|
1858
|
query = getSession().createQuery("select zn.nameCache from ZoologicalName zn, TaxonBase tb where tb.name = zn and tb.sec.id = :secRefErms");
|
|
1859
|
query.setParameter("secRefErms", secRefErms.get(0));
|
|
1860
|
|
|
1861
|
List<String> namesErms = query.list();
|
|
1862
|
/*TaxonNameComparator comp = new TaxonNameComparator();
|
|
1863
|
Collections.sort(namesFauna);
|
|
1864
|
Collections.sort(namesErms);
|
|
1865
|
*/
|
|
1866
|
List <String> identicalNames = new ArrayList<String>();
|
|
1867
|
String predecessor = "";
|
|
1868
|
|
|
1869
|
for (String nameFauna: namesFauna){
|
|
1870
|
if (namesErms.contains(nameFauna)){
|
|
1871
|
identicalNames.add(nameFauna);
|
|
1872
|
}
|
|
1873
|
}
|
|
1874
|
|
|
1875
|
|
|
1876
|
query = getSession().createQuery("from ZoologicalName zn where zn.nameCache IN (:identicalNames)");
|
|
1877
|
query.setParameterList("identicalNames", identicalNames);
|
|
1878
|
List<TaxonNameBase> result = query.list();
|
|
1879
|
TaxonNameBase temp = result.get(0);
|
|
1880
|
|
|
1881
|
Iterator<OriginalSourceBase> sources = temp.getSources().iterator();
|
|
1882
|
|
|
1883
|
TaxonNameComparator taxComp = new TaxonNameComparator();
|
|
1884
|
Collections.sort(result, taxComp);
|
|
1885
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
1886
|
return result;
|
|
1887
|
|
|
1888
|
}
|
|
1889
|
|
|
1890
|
|
|
1891
|
|
|
1892
|
public String getPhylumName(TaxonNameBase name){
|
|
1893
|
List results = new ArrayList();
|
|
1894
|
try{
|
|
1895
|
Query query = getSession().createSQLQuery("select getPhylum("+ name.getId()+");");
|
|
1896
|
results = query.list();
|
|
1897
|
}catch(Exception e){
|
|
1898
|
System.err.println(name.getUuid());
|
|
1899
|
return null;
|
|
1900
|
}
|
|
1901
|
System.err.println("phylum of "+ name.getTitleCache() );
|
|
1902
|
return (String)results.get(0);
|
|
1903
|
}
|
|
1904
|
|
|
1905
|
|
|
1906
|
public long countTaxaByCommonName(String searchString,
|
|
1907
|
Classification classification, MatchMode matchMode,
|
|
1908
|
Set<NamedArea> namedAreas) {
|
|
1909
|
boolean doCount = true;
|
|
1910
|
Query query = prepareTaxaByCommonName(searchString, classification, matchMode, namedAreas, null, null, doCount);
|
|
1911
|
if (query != null && !query.list().isEmpty()) {
|
|
1912
|
Object o = query.uniqueResult();
|
|
1913
|
if(o != null) {
|
|
1914
|
return (Long)o;
|
|
1915
|
}
|
|
1916
|
}
|
|
1917
|
return 0;
|
|
1918
|
}
|
|
1919
|
|
|
1920
|
|
|
1921
|
/* (non-Javadoc)
|
|
1922
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#deleteSynonymRelationships(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)
|
|
1923
|
*/
|
|
1924
|
public long deleteSynonymRelationships(Synonym synonym, Taxon taxon) {
|
|
1925
|
|
|
1926
|
String hql = "delete SynonymRelationship sr where sr.relatedFrom = :syn ";
|
|
1927
|
if (taxon != null){
|
|
1928
|
hql += " and sr.relatedTo = :taxon";
|
|
1929
|
}
|
|
1930
|
Session session = this.getSession();
|
|
1931
|
Query q = session.createQuery(hql);
|
|
1932
|
|
|
1933
|
q.setParameter("syn", synonym);
|
|
1934
|
if (taxon != null){
|
|
1935
|
q.setParameter("taxon", taxon);
|
|
1936
|
}
|
|
1937
|
return q.executeUpdate();
|
|
1938
|
}
|
|
1939
|
|
|
1940
|
|
|
1941
|
@Override
|
|
1942
|
public Integer countSynonymRelationships(TaxonBase taxonBase,
|
|
1943
|
SynonymRelationshipType type, Direction relatedfrom) {
|
|
1944
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
1945
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
1946
|
Query query = null;
|
|
1947
|
|
|
1948
|
if(type == null) {
|
|
1949
|
query = getSession().createQuery("select count(synonymRelationship) from SynonymRelationship synonymRelationship where synonymRelationship."+relatedfrom+" = :relatedSynonym");
|
|
1950
|
} else {
|
|
1951
|
query = getSession().createQuery("select count(synonymRelationship) from SynonymRelationship synonymRelationship where synonymRelationship."+relatedfrom+" = :relatedSynonym and synonymRelationship.type = :type");
|
|
1952
|
query.setParameter("type",type);
|
|
1953
|
}
|
|
1954
|
query.setParameter("relatedTaxon", taxonBase);
|
|
1955
|
|
|
1956
|
return ((Long)query.uniqueResult()).intValue();
|
|
1957
|
} else {
|
|
1958
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonRelationship.class,auditEvent.getRevisionNumber());
|
|
1959
|
query.add(AuditEntity.relatedId(relatedfrom.toString()).eq(taxonBase.getId()));
|
|
1960
|
query.addProjection(AuditEntity.id().count("id"));
|
|
1961
|
|
|
1962
|
if(type != null) {
|
|
1963
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
1964
|
}
|
|
1965
|
|
|
1966
|
return ((Long)query.getSingleResult()).intValue();
|
|
1967
|
}
|
|
1968
|
}
|
|
1969
|
|
|
1970
|
|
|
1971
|
@Override
|
|
1972
|
public List<SynonymRelationship> getSynonymRelationships(TaxonBase taxonBase,
|
|
1973
|
SynonymRelationshipType type, Integer pageSize, Integer pageNumber,
|
|
1974
|
List<OrderHint> orderHints, List<String> propertyPaths,
|
|
1975
|
Direction direction) {
|
|
1976
|
|
|
1977
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
1978
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
1979
|
Criteria criteria = getSession().createCriteria(SynonymRelationship.class);
|
|
1980
|
|
|
1981
|
if (direction.equals(Direction.relatedTo)){
|
|
1982
|
criteria.add(Restrictions.eq("relatedTo", taxonBase));
|
|
1983
|
}else{
|
|
1984
|
criteria.add(Restrictions.eq("relatedFrom", taxonBase));
|
|
1985
|
}
|
|
1986
|
if(type != null) {
|
|
1987
|
criteria.add(Restrictions.eq("type", type));
|
|
1988
|
}
|
|
1989
|
|
|
1990
|
addOrder(criteria,orderHints);
|
|
1991
|
|
|
1992
|
if(pageSize != null) {
|
|
1993
|
criteria.setMaxResults(pageSize);
|
|
1994
|
if(pageNumber != null) {
|
|
1995
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
1996
|
} else {
|
|
1997
|
criteria.setFirstResult(0);
|
|
1998
|
}
|
|
1999
|
}
|
|
2000
|
|
|
2001
|
List<SynonymRelationship> result = (List<SynonymRelationship>)criteria.list();
|
|
2002
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
2003
|
|
|
2004
|
return result;
|
|
2005
|
} else {
|
|
2006
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonRelationship.class,auditEvent.getRevisionNumber());
|
|
2007
|
|
|
2008
|
if (direction.equals(Direction.relatedTo)){
|
|
2009
|
query.add(AuditEntity.relatedId("relatedTo").eq(taxonBase.getId()));
|
|
2010
|
}else{
|
|
2011
|
query.add(AuditEntity.relatedId("relatedFrom").eq(taxonBase.getId()));
|
|
2012
|
}
|
|
2013
|
|
|
2014
|
if(type != null) {
|
|
2015
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
2016
|
}
|
|
2017
|
|
|
2018
|
if(pageSize != null) {
|
|
2019
|
query.setMaxResults(pageSize);
|
|
2020
|
if(pageNumber != null) {
|
|
2021
|
query.setFirstResult(pageNumber * pageSize);
|
|
2022
|
} else {
|
|
2023
|
query.setFirstResult(0);
|
|
2024
|
}
|
|
2025
|
}
|
|
2026
|
|
|
2027
|
List<SynonymRelationship> result = (List<SynonymRelationship>)query.getResultList();
|
|
2028
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
2029
|
|
|
2030
|
// Ugly, but for now, there is no way to sort on a related entity property in Envers,
|
|
2031
|
// and we can't live without this functionality in CATE as it screws up the whole
|
|
2032
|
// taxon tree thing
|
|
2033
|
if(orderHints != null && !orderHints.isEmpty()) {
|
|
2034
|
SortedSet<SynonymRelationship> sortedList = new TreeSet<SynonymRelationship>(new SynonymRelationshipFromTaxonComparator());
|
|
2035
|
sortedList.addAll(result);
|
|
2036
|
return new ArrayList<SynonymRelationship>(sortedList);
|
|
2037
|
}
|
|
2038
|
|
|
2039
|
return result;
|
|
2040
|
}
|
|
2041
|
}
|
|
2042
|
|
|
2043
|
|
|
2044
|
/* (non-Javadoc)
|
|
2045
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getUuidAndTitleCacheTaxon()
|
|
2046
|
*/
|
|
2047
|
@Override
|
|
2048
|
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheTaxon() {
|
|
2049
|
String queryString = String.format("select uuid, titleCache from %s where DTYPE = '%s'", type.getSimpleName(), Taxon.class.getSimpleName());
|
|
2050
|
Query query = getSession().createQuery(queryString);
|
|
2051
|
|
|
2052
|
List<UuidAndTitleCache<TaxonBase>> result = getUuidAndTitleCache(query);
|
|
2053
|
|
|
2054
|
return result;
|
|
2055
|
}
|
|
2056
|
|
|
2057
|
|
|
2058
|
/* (non-Javadoc)
|
|
2059
|
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getUuidAndTitleCacheSynonym()
|
|
2060
|
*/
|
|
2061
|
@Override
|
|
2062
|
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheSynonym() {
|
|
2063
|
String queryString = String.format("select uuid, titleCache from %s where DTYPE = '%s'", type.getSimpleName(), Synonym.class.getSimpleName());
|
|
2064
|
Query query = getSession().createQuery(queryString);
|
|
2065
|
|
|
2066
|
List<UuidAndTitleCache<TaxonBase>> result = getUuidAndTitleCache(query);
|
|
2067
|
|
|
2068
|
return result;
|
|
2069
|
}
|
|
2070
|
|
|
2071
|
|
|
2072
|
|
|
2073
|
|
|
2074
|
|
|
2075
|
|
|
2076
|
|
|
2077
|
|
|
2078
|
|
|
2079
|
|
|
2080
|
}
|