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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.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.apache.lucene.analysis.SimpleAnalyzer;
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import org.apache.lucene.queryParser.ParseException;
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import org.apache.lucene.queryParser.QueryParser;
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import org.apache.lucene.search.Sort;
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import org.apache.lucene.search.SortField;
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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.LazyInitializationException;
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import org.hibernate.Query;
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import org.hibernate.Transaction;
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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.search.FullTextQuery;
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import org.hibernate.search.FullTextSession;
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import org.hibernate.search.Search;
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import org.hibernate.search.SearchFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import org.springframework.dao.DataAccessException;
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import org.springframework.stereotype.Repository;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.common.OriginalSource;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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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.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.persistence.dao.QueryParseException;
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import eu.etaxonomy.cdm.persistence.dao.common.ITitledDao;
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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.taxon.ITaxonDao;
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import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
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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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@SuppressWarnings("unused")
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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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}
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@Autowired
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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.ReferenceBase)
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*/
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public List<Taxon> getRootTaxa(ReferenceBase 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.reference.ReferenceBase, eu.etaxonomy.cdm.persistence.fetch.CdmFetch, java.lang.Boolean, java.lang.Boolean)
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*/
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public List<Taxon> getRootTaxa(ReferenceBase 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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// String query = "from Taxon root ";
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// query += " where root.taxonomicParentCache is NULL ";
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// if (sec != null){
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// query += " AND root.sec.id = :sec ";
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// }
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// Query q = getSession().createQuery(query);
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// if (sec != null){
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// q.setInteger("sec", sec.getId());
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// }
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Criteria crit = getSession().createCriteria(Taxon.class);
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crit.add(Restrictions.isNull("taxonomicParentCache"));
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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.warn("no child taxa fetch");
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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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for(Taxon taxon : (List<Taxon>) crit.list()){
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//childTaxa
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//TODO create restriction instead
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if (onlyWithChildren == false || taxon.hasTaxonomicChildren()){
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if (withMisapplications == true || ! taxon.isMisappliedName()){
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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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public List<TaxonBase> getTaxaByName(String queryString, ReferenceBase sec) {
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return getTaxaByName(queryString, true, sec);
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}
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public List<TaxonBase> getTaxaByName(String queryString, Boolean accepted, ReferenceBase 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){
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if(sec.getId() == 0){
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getSession().save(sec);
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}
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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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List<TaxonBase> results = criteria.list();
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return results;
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}
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public List<TaxonBase> getAllTaxonBases(Integer pagesize, Integer page) {
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Criteria crit = getSession().createCriteria(TaxonBase.class);
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List<TaxonBase> results = crit.list();
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// TODO add page & pagesize criteria
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return results;
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}
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public List<Synonym> getAllSynonyms(Integer limit, Integer start) {
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Criteria crit = getSession().createCriteria(Synonym.class);
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List<Synonym> results = crit.list();
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return results;
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}
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public List<Taxon> getAllTaxa(Integer limit, Integer start) {
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Criteria crit = getSession().createCriteria(Taxon.class);
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List<Taxon> results = crit.list();
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return results;
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}
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public List<RelationshipBase> getAllRelationships(Integer limit, Integer start) {
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Criteria crit = getSession().createCriteria(RelationshipBase.class);
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List<RelationshipBase> results = crit.list();
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return results;
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}
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@Override
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public UUID delete(TaxonBase taxonBase) throws DataAccessException{
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//getSession().update(taxonBase); doesn't work with lazy collections
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//annotations
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try {
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Set<Annotation> annotations = taxonBase.getAnnotations();
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for (Annotation annotation: annotations){
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taxonBase.removeAnnotation(annotation);
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}
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} catch (LazyInitializationException e) {
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logger.warn("LazyInitializationException: " + e);
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}
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//markers
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try {
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Set<Marker> markers = taxonBase.getMarkers();
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for (Marker marker: markers){
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taxonBase.removeMarker(marker);
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}
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} catch (LazyInitializationException e) {
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logger.warn("LazyInitializationException: " + e);
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}
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//originalSource
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try {
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Set<OriginalSource> origSources = taxonBase.getSources();
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for (OriginalSource source: origSources){
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taxonBase.removeSource(source);
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}
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} catch (LazyInitializationException e) {
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logger.warn("LazyInitializationException: " + e);
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}
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//is Taxon
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taxonBase.getName().removeTaxonBase(taxonBase);
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if (taxonBase instanceof Taxon){
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//taxonRelationships
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Taxon taxon = (Taxon)taxonBase;
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Set<TaxonRelationship> taxRels = taxon.getTaxonRelations();
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for (TaxonRelationship taxRel: taxRels){
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taxon.removeTaxonRelation(taxRel);
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} ;
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//SynonymRelationships
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Set<SynonymRelationship> synRels = taxon.getSynonymRelations();
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for (SynonymRelationship synRel: synRels){
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taxon.removeSynonymRelation(synRel);
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} ;
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}//is Synonym
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else if (taxonBase instanceof Synonym){
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Synonym synonym = (Synonym)taxonBase;
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Set<SynonymRelationship> synRels = synonym.getSynonymRelations();
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for (SynonymRelationship synRel: synRels){
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synonym.removeSynonymRelation(synRel);
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} ;
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}
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return super.delete(taxonBase);
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}
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// TODO add generic return type !!
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public List findByName(String queryString, ITitledDao.MATCH_MODE matchMode, int page, int pagesize, boolean onlyAcccepted) {
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ArrayList<Criterion> criteria = new ArrayList<Criterion>();
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//TODO ... Restrictions.eq(propertyName, value)
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return super.findByTitle(queryString, matchMode, page, pagesize, criteria);
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}
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public int countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted) {
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Criteria crit = getSession().createCriteria(type);
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crit.add(Restrictions.ilike("persistentTitleCache", matchMode.queryStringFrom(queryString)));
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crit.setProjection(Projections.rowCount());
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int result = ((Integer)crit.list().get(0)).intValue();
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return result;
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}
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public int countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted, List<Criterion> criteria) {
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Criteria crit = getSession().createCriteria(type);
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crit.add(Restrictions.ilike("persistentTitleCache", matchMode.queryStringFrom(queryString)));
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if(criteria != null){
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for (Criterion criterion : criteria) {
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crit.add(criterion);
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}
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}
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crit.setProjection(Projections.rowCount());
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int result = ((Integer)crit.list().get(0)).intValue();
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return result;
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}
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public int countRelatedTaxa(Taxon taxon, TaxonRelationshipType type) {
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Query query = null;
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if(type == null) {
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query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship.relatedTo = :relatedTo");
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} else {
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query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship.relatedTo = :relatedTo and taxonRelationship.type = :type");
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query.setParameter("type",type);
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}
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query.setParameter("relatedTo", taxon);
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return ((Long)query.uniqueResult()).intValue();
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}
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public int countSynonyms(Taxon taxon, SynonymRelationshipType type) {
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Query query = null;
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if(type == null) {
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query = getSession().createQuery("select count(synonymRelationship) from SynonymRelationship synonymRelationship where synonymRelationship.relatedTo = :relatedTo");
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} else {
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query = getSession().createQuery("select count(synonymRelationship) from SynonymRelationship synonymRelationship where synonymRelationship.relatedTo = :relatedTo and synonymRelationship.type = :type");
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query.setParameter("type",type);
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}
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query.setParameter("relatedTo", taxon);
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return ((Long)query.uniqueResult()).intValue();
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}
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public int countTaxa(String queryString, Boolean accepted) {
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QueryParser queryParser = new QueryParser("name.persistentTitleCache", new SimpleAnalyzer());
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try {
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org.apache.lucene.search.Query query = queryParser.parse(queryString);
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FullTextSession fullTextSession = Search.createFullTextSession(this.getSession());
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org.hibernate.search.FullTextQuery fullTextQuery = null;
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if(accepted == null) {
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fullTextQuery = fullTextSession.createFullTextQuery(query, TaxonBase.class);
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} else {
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if(accepted) {
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fullTextQuery = fullTextSession.createFullTextQuery(query, Taxon.class);
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} else {
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fullTextQuery = fullTextSession.createFullTextQuery(query, Synonym.class);
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}
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}
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Integer result = fullTextQuery.getResultSize();
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return result;
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} catch (ParseException e) {
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throw new QueryParseException(e, queryString);
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}
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}
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public int countTaxaByName(String queryString, Boolean accepted, ReferenceBase 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){
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if(sec.getId() == 0){
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getSession().save(sec);
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}
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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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criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));
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return (Integer)criteria.uniqueResult();
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}
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public int countTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank) {
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Criteria criteria = null;
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if(accepted == null) {
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criteria = getSession().createCriteria(TaxonBase.class);
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} else {
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if(accepted) {
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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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}
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criteria.setFetchMode( "name", FetchMode.JOIN );
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criteria.createAlias("name", "name");
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if(genusOrUninomial != null) {
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criteria.add(Restrictions.eq("name.genusOrUninomial", genusOrUninomial));
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}
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if(infraGenericEpithet != null) {
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criteria.add(Restrictions.eq("name.infraGenericEpithet", infraGenericEpithet));
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}
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if(specificEpithet != null) {
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criteria.add(Restrictions.eq("name.specificEpithet", specificEpithet));
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}
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if(infraSpecificEpithet != null) {
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criteria.add(Restrictions.eq("name.infraSpecificEpithet", infraSpecificEpithet));
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}
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if(rank != null) {
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criteria.add(Restrictions.eq("name.rank", rank));
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}
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criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));
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408
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return (Integer)criteria.uniqueResult();
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}
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412
|
public List<TaxonBase> findTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank, Integer pageSize, Integer pageNumber) {
|
413
|
Criteria criteria = null;
|
414
|
|
415
|
if(accepted == null) {
|
416
|
criteria = getSession().createCriteria(TaxonBase.class);
|
417
|
} else {
|
418
|
if(accepted) {
|
419
|
criteria = getSession().createCriteria(Taxon.class);
|
420
|
} else {
|
421
|
criteria = getSession().createCriteria(Synonym.class);
|
422
|
}
|
423
|
}
|
424
|
|
425
|
criteria.setFetchMode( "name", FetchMode.JOIN );
|
426
|
criteria.createAlias("name", "name");
|
427
|
|
428
|
if(genusOrUninomial != null) {
|
429
|
criteria.add(Restrictions.eq("name.genusOrUninomial", genusOrUninomial));
|
430
|
}
|
431
|
|
432
|
if(infraGenericEpithet != null) {
|
433
|
criteria.add(Restrictions.eq("name.infraGenericEpithet", infraGenericEpithet));
|
434
|
} else {
|
435
|
criteria.add(Restrictions.isNull("name.infraGenericEpithet"));
|
436
|
}
|
437
|
|
438
|
if(specificEpithet != null) {
|
439
|
criteria.add(Restrictions.eq("name.specificEpithet", specificEpithet));
|
440
|
}
|
441
|
|
442
|
if(infraSpecificEpithet != null) {
|
443
|
criteria.add(Restrictions.eq("name.infraSpecificEpithet", infraSpecificEpithet));
|
444
|
}
|
445
|
|
446
|
if(rank != null) {
|
447
|
criteria.add(Restrictions.eq("name.rank", rank));
|
448
|
}
|
449
|
|
450
|
if(pageSize != null) {
|
451
|
criteria.setMaxResults(pageSize);
|
452
|
if(pageNumber != null) {
|
453
|
criteria.setFirstResult(pageNumber * pageSize);
|
454
|
} else {
|
455
|
criteria.setFirstResult(0);
|
456
|
}
|
457
|
}
|
458
|
|
459
|
return (List<TaxonBase>)criteria.list();
|
460
|
}
|
461
|
|
462
|
public List<TaxonRelationship> getRelatedTaxa(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber) {
|
463
|
Query query = null;
|
464
|
|
465
|
if(type == null) {
|
466
|
query = getSession().createQuery("select taxonRelationship from TaxonRelationship taxonRelationship join fetch taxonRelationship.relatedFrom where taxonRelationship.relatedTo = :relatedTo");
|
467
|
} else {
|
468
|
query = getSession().createQuery("select taxonRelationship from TaxonRelationship taxonRelationship join fetch taxonRelationship.relatedFrom where taxonRelationship.relatedTo = :relatedTo and taxonRelationship.type = :type");
|
469
|
query.setParameter("type",type);
|
470
|
}
|
471
|
|
472
|
query.setParameter("relatedTo", taxon);
|
473
|
|
474
|
if(pageSize != null) {
|
475
|
query.setMaxResults(pageSize);
|
476
|
if(pageNumber != null) {
|
477
|
query.setFirstResult(pageNumber * pageSize);
|
478
|
} else {
|
479
|
query.setFirstResult(0);
|
480
|
}
|
481
|
}
|
482
|
|
483
|
return (List<TaxonRelationship>)query.list();
|
484
|
}
|
485
|
|
486
|
public List<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber) {
|
487
|
Query query = null;
|
488
|
|
489
|
if(type == null) {
|
490
|
query = getSession().createQuery("select synonymRelationship from SynonymRelationship synonymRelationship join fetch synonymRelationship.relatedFrom where synonymRelationship.relatedTo = :relatedTo");
|
491
|
} else {
|
492
|
query = getSession().createQuery("select synonymRelationship from SynonymRelationship synonymRelationship join fetch synonymRelationship.relatedFrom where synonymRelationship.relatedTo = :relatedTo and synonymRelationship.type = :type");
|
493
|
query.setParameter("type",type);
|
494
|
}
|
495
|
|
496
|
query.setParameter("relatedTo", taxon);
|
497
|
|
498
|
if(pageSize != null) {
|
499
|
query.setMaxResults(pageSize);
|
500
|
if(pageNumber != null) {
|
501
|
query.setFirstResult(pageNumber * pageSize);
|
502
|
} else {
|
503
|
query.setFirstResult(0);
|
504
|
}
|
505
|
}
|
506
|
|
507
|
return (List<SynonymRelationship>)query.list();
|
508
|
}
|
509
|
|
510
|
public List<TaxonBase> searchTaxa(String queryString, Boolean accepted, Integer pageSize, Integer pageNumber) {
|
511
|
QueryParser queryParser = new QueryParser("name.persistentTitleCache", new SimpleAnalyzer());
|
512
|
List<TaxonBase> results = new ArrayList<TaxonBase>();
|
513
|
|
514
|
try {
|
515
|
org.apache.lucene.search.Query query = queryParser.parse(queryString);
|
516
|
|
517
|
FullTextSession fullTextSession = Search.createFullTextSession(getSession());
|
518
|
org.hibernate.search.FullTextQuery fullTextQuery = null;
|
519
|
Criteria criteria = null;
|
520
|
|
521
|
if(accepted == null) {
|
522
|
fullTextQuery = fullTextSession.createFullTextQuery(query, TaxonBase.class);
|
523
|
criteria = getSession().createCriteria( TaxonBase.class );
|
524
|
} else {
|
525
|
if(accepted) {
|
526
|
fullTextQuery = fullTextSession.createFullTextQuery(query, Taxon.class);
|
527
|
criteria = getSession().createCriteria( Taxon.class );
|
528
|
} else {
|
529
|
fullTextQuery = fullTextSession.createFullTextQuery(query, Synonym.class);
|
530
|
criteria = getSession().createCriteria( Synonym.class );
|
531
|
}
|
532
|
}
|
533
|
|
534
|
org.apache.lucene.search.Sort sort = new Sort(new SortField("name.titleCache_forSort"));
|
535
|
fullTextQuery.setSort(sort);
|
536
|
|
537
|
criteria.setFetchMode( "name", FetchMode.JOIN );
|
538
|
fullTextQuery.setCriteriaQuery(criteria);
|
539
|
|
540
|
if(pageSize != null) {
|
541
|
fullTextQuery.setMaxResults(pageSize);
|
542
|
if(pageNumber != null) {
|
543
|
fullTextQuery.setFirstResult(pageNumber * pageSize);
|
544
|
} else {
|
545
|
fullTextQuery.setFirstResult(0);
|
546
|
}
|
547
|
}
|
548
|
|
549
|
return (List<TaxonBase>)fullTextQuery.list();
|
550
|
|
551
|
} catch (ParseException e) {
|
552
|
throw new QueryParseException(e, queryString);
|
553
|
}
|
554
|
}
|
555
|
|
556
|
public void purgeIndex() {
|
557
|
FullTextSession fullTextSession = Search.createFullTextSession(getSession());
|
558
|
|
559
|
fullTextSession.purgeAll(type); // remove all taxon base from indexes
|
560
|
// fullTextSession.flushToIndexes() not implemented in 3.0.0.GA
|
561
|
}
|
562
|
|
563
|
public void rebuildIndex() {
|
564
|
FullTextSession fullTextSession = Search.createFullTextSession(getSession());
|
565
|
|
566
|
for(TaxonBase taxonBase : list(null,null)) { // re-index all taxon base
|
567
|
Hibernate.initialize(taxonBase.getName());
|
568
|
fullTextSession.index(taxonBase);
|
569
|
}
|
570
|
// fullTextSession.flushToIndexes() not implemented in 3.0.0.GA
|
571
|
}
|
572
|
|
573
|
public void optimizeIndex() {
|
574
|
FullTextSession fullTextSession = Search.createFullTextSession(getSession());
|
575
|
SearchFactory searchFactory = fullTextSession.getSearchFactory();
|
576
|
searchFactory.optimize(type); // optimize the indices ()
|
577
|
// fullTextSession.flushToIndexes() not implemented in 3.0.0.GA
|
578
|
}
|
579
|
|
580
|
public String suggestQuery(String queryString) {
|
581
|
try {
|
582
|
String alternativeQueryString = null;
|
583
|
alternativeSpellingSuggestionParser.parse(queryString);
|
584
|
org.apache.lucene.search.Query alternativeQuery = alternativeSpellingSuggestionParser.suggest(queryString);
|
585
|
if(alternativeQuery != null) {
|
586
|
alternativeQueryString = alternativeQuery.toString("name.persistentTitleCache");
|
587
|
}
|
588
|
return alternativeQueryString;
|
589
|
} catch (ParseException e) {
|
590
|
throw new QueryParseException(e, queryString);
|
591
|
}
|
592
|
}
|
593
|
}
|