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// $Id$
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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.api.service;
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import java.util.ArrayList;
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import java.util.Comparator;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Service;
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import org.springframework.transaction.annotation.Transactional;
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import eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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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.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.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.persistence.dao.BeanInitializer;
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import eu.etaxonomy.cdm.persistence.dao.common.IOrderedTermVocabularyDao;
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import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;
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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.OrderHint;
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@Service
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@Transactional(readOnly = true)
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public class TaxonServiceImpl extends IdentifiableServiceBase<TaxonBase,ITaxonDao> implements ITaxonService{
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private static final Logger logger = Logger.getLogger(TaxonServiceImpl.class);
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@Autowired
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private ITaxonNameDao nameDao;
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@Autowired
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private IOrderedTermVocabularyDao orderedVocabularyDao;
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@Autowired
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private IDescriptionDao descriptionDao;
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@Autowired
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private BeanInitializer defaultBeanInitializer;
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private Comparator<? super TaxonNode> taxonNodeComparator;
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@Autowired
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public void setTaxonNodeComparator(ITaxonNodeComparator<? super TaxonNode> taxonNodeComparator){
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this.taxonNodeComparator = (Comparator<? super TaxonNode>) taxonNodeComparator;
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}
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/**
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* Constructor
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*/
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public TaxonServiceImpl(){
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if (logger.isDebugEnabled()) { logger.debug("Load TaxonService Bean"); }
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}
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/**
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* FIXME Candidate for harmonization
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* rename searchByName ?
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*/
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public List<TaxonBase> searchTaxaByName(String name, ReferenceBase sec) {
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return dao.getTaxaByName(name, sec);
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}
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/**
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* FIXME Candidate for harmonization
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* list(Synonym.class, ...)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllSynonyms(int, int)
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*/
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public List<Synonym> getAllSynonyms(int limit, int start) {
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return dao.getAllSynonyms(limit, start);
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}
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/**
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* FIXME Candidate for harmonization
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* list(Taxon.class, ...)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllTaxa(int, int)
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*/
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public List<Taxon> getAllTaxa(int limit, int start) {
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return dao.getAllTaxa(limit, start);
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}
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/**
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* FIXME Candidate for harmonization
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* merge with getRootTaxa(ReferenceBase sec, ..., ...)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#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);
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}
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/**
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* FIXME Candidate for harmonization
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* merge with getRootTaxa(ReferenceBase sec, ..., ...)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase, boolean)
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*/
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public List<Taxon> getRootTaxa(ReferenceBase sec, CdmFetch cdmFetch, boolean onlyWithChildren) {
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if (cdmFetch == null){
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cdmFetch = CdmFetch.NO_FETCH();
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}
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return dao.getRootTaxa(sec, cdmFetch, onlyWithChildren, false);
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}
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/**
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* FIXME Candidate for harmonization
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* merge with getRootTaxa(ReferenceBase sec, ..., ...)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase, boolean, boolean)
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*/
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public List<Taxon> getRootTaxa(ReferenceBase sec, boolean onlyWithChildren,
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boolean withMisapplications) {
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return dao.getRootTaxa(sec, null, onlyWithChildren, withMisapplications);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.name.Rank, eu.etaxonomy.cdm.model.reference.ReferenceBase, boolean, boolean)
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*/
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public List<Taxon> getRootTaxa(Rank rank, ReferenceBase sec, boolean onlyWithChildren,
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boolean withMisapplications, List<String> propertyPaths) {
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return dao.getRootTaxa(rank, sec, null, onlyWithChildren, withMisapplications, propertyPaths);
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}
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public List<RelationshipBase> getAllRelationships(int limit, int start){
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return dao.getAllRelationships(limit, start);
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}
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/**
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* FIXME Candidate for harmonization
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* is this the same as termService.getVocabulary(VocabularyEnum.TaxonRelationshipType) ?
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*/
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@Deprecated
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public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary() {
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String taxonRelTypeVocabularyId = "15db0cf7-7afc-4a86-a7d4-221c73b0c9ac";
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UUID uuid = UUID.fromString(taxonRelTypeVocabularyId);
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OrderedTermVocabulary<TaxonRelationshipType> taxonRelTypeVocabulary =
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(OrderedTermVocabulary)orderedVocabularyDao.findByUuid(uuid);
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return taxonRelTypeVocabulary;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#makeTaxonSynonym(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.Taxon)
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*/
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@Transactional(readOnly = false)
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public Synonym makeTaxonSynonym(Taxon oldTaxon, Taxon newAcceptedTaxon, SynonymRelationshipType synonymRelationshipType, ReferenceBase citation, String citationMicroReference) {
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if (oldTaxon == null || newAcceptedTaxon == null || oldTaxon.getName() == null){
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throw new IllegalArgumentException();
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}
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// Move oldTaxon to newTaxon
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TaxonNameBase<?,?> synonymName = oldTaxon.getName();
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if (synonymRelationshipType == null){
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if (synonymName.isHomotypic(newAcceptedTaxon.getName())){
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synonymRelationshipType = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF();
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}else{
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//TODO synonymType
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synonymRelationshipType = SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
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}
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}
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SynonymRelationship synRel = newAcceptedTaxon.addSynonymName(synonymName, synonymRelationshipType, citation, citationMicroReference);
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//Move Synonym Relations to new Taxon
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for(SynonymRelationship synRelation : oldTaxon.getSynonymRelations()){
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newAcceptedTaxon.addSynonym(synRelation.getSynonym(), synRelation.getType(),
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synRelation.getCitation(), synRelation.getCitationMicroReference());
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}
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//Move Taxon RelationShips to new Taxon
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Set<TaxonRelationship> removableTaxonRels = new HashSet<TaxonRelationship>();
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for(TaxonRelationship taxonRelation : oldTaxon.getTaxonRelations()){
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//CHILDREN
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if (taxonRelation.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())){
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if (taxonRelation.getFromTaxon() == oldTaxon){
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removableTaxonRels.add(taxonRelation);
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// oldTaxon.removeTaxonRelation(taxonRelation);
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}else if(taxonRelation.getToTaxon() == oldTaxon){
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newAcceptedTaxon.addTaxonomicChild(taxonRelation.getFromTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
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removableTaxonRels.add(taxonRelation);
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// oldTaxon.removeTaxonRelation(taxonRelation);
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}else{
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logger.warn("Taxon is not part of its own Taxonrelationship");
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}
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}
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//MISAPPLIED NAMES
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if (taxonRelation.getType().equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){
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if (taxonRelation.getFromTaxon() == oldTaxon){
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newAcceptedTaxon.addMisappliedName(taxonRelation.getToTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
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removableTaxonRels.add(taxonRelation);
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// oldTaxon.removeTaxonRelation(taxonRelation);
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}else if(taxonRelation.getToTaxon() == oldTaxon){
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newAcceptedTaxon.addMisappliedName(taxonRelation.getFromTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
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removableTaxonRels.add(taxonRelation);
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// oldTaxon.removeTaxonRelation(taxonRelation);
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}else{
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logger.warn("Taxon is not part of its own Taxonrelationship");
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}
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}
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//Concept Relationships
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//FIXME implement
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// if (taxonRelation.getType().equals(TaxonRelationshipType.MISAPPLIEDNAMEFOR())){
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// if (taxonRelation.getFromTaxon() == oldTaxon){
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// newAcceptedTaxon.addMisappliedName(taxonRelation.getToTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
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// removableTaxonRels.add(taxonRelation);
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// }else if(taxonRelation.getToTaxon() == oldTaxon){
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// newAcceptedTaxon.addMisappliedName(taxonRelation.getFromTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
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// removableTaxonRels.add(taxonRelation);
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// }else{
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// logger.warn("Taxon is not part of its own Taxonrelationship");
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// }
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// }
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}
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for(TaxonRelationship taxonRel : removableTaxonRels) {
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oldTaxon.removeTaxonRelation(taxonRel);
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}
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//Move Descriptions to new Taxon
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for(TaxonDescription taxDescription : oldTaxon.getDescriptions()){
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newAcceptedTaxon.addDescription(taxDescription);
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}
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//delete old Taxon
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this.dao.saveOrUpdate(newAcceptedTaxon);
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// FIXME implement
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// this.dao.delete(oldTaxon);
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//return
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// this.dao.flush();
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return synRel.getSynonym();
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}
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/*
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#swapSynonymWithAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym)
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*/
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@Transactional(readOnly = false)
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public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, SynonymRelationshipType synonymRelationshipType){
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// create a new synonym with the old acceptedName
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TaxonNameBase oldAcceptedTaxonName = acceptedTaxon.getName();
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// remove synonym from oldAcceptedTaxon
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acceptedTaxon.removeSynonym(synonym);
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// make synonym name the accepted taxons name
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TaxonNameBase newAcceptedTaxonName = synonym.getName();
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acceptedTaxon.setName(newAcceptedTaxonName);
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// add the new synonym to the acceptedTaxon
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if(synonymRelationshipType == null){
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synonymRelationshipType = SynonymRelationshipType.SYNONYM_OF();
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}
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acceptedTaxon.addSynonymName(oldAcceptedTaxonName, synonymRelationshipType);
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}
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/*
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#makeSynonymAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)
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*/
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public Taxon makeSynonymAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon){
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Taxon newAcceptedTaxon = Taxon.NewInstance(synonym.getName(), acceptedTaxon.getSec());
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acceptedTaxon.removeSynonym(synonym);
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return newAcceptedTaxon;
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}
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public void generateTitleCache() {
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generateTitleCache(true);
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}
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//TODO
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public void generateTitleCache(boolean forceProtected) {
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logger.warn("generateTitleCache not yet fully implemented!");
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}
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@Autowired
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protected void setDao(ITaxonDao dao) {
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this.dao = dao;
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}
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public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
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Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank);
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List<TaxonBase> results = new ArrayList<TaxonBase>();
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323
|
if(numberOfResults > 0) { // no point checking again
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324
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results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber);
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325
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}
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326
|
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327
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return new DefaultPagerImpl<TaxonBase>(pageNumber, numberOfResults, pageSize, results);
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328
|
}
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329
|
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330
|
public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
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331
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);
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332
|
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333
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
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334
|
if(numberOfResults > 0) { // no point checking again
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335
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedTo);
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336
|
}
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337
|
return results;
|
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338
|
}
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339
|
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340
|
public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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341
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);
|
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342
|
|
|
343
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
|
344
|
if(numberOfResults > 0) { // no point checking again
|
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345
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedTo);
|
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346
|
}
|
|
347
|
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
348
|
}
|
|
349
|
|
|
350
|
public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
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351
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom);
|
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352
|
|
|
353
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
|
354
|
if(numberOfResults > 0) { // no point checking again
|
|
355
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedFrom);
|
|
356
|
}
|
|
357
|
return results;
|
|
358
|
}
|
|
359
|
|
|
360
|
public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
361
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom);
|
|
362
|
|
|
363
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
|
364
|
if(numberOfResults > 0) { // no point checking again
|
|
365
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedFrom);
|
|
366
|
}
|
|
367
|
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
368
|
}
|
|
369
|
|
|
370
|
public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
371
|
Integer numberOfResults = dao.countSynonyms(taxon, type);
|
|
372
|
|
|
373
|
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
|
374
|
if(numberOfResults > 0) { // no point checking again
|
|
375
|
results = dao.getSynonyms(taxon, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
376
|
}
|
|
377
|
|
|
378
|
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
379
|
}
|
|
380
|
|
|
381
|
public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
382
|
Integer numberOfResults = dao.countSynonyms(synonym, type);
|
|
383
|
|
|
384
|
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
|
385
|
if(numberOfResults > 0) { // no point checking again
|
|
386
|
results = dao.getSynonyms(synonym, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
387
|
}
|
|
388
|
|
|
389
|
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
390
|
}
|
|
391
|
|
|
392
|
public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths){
|
|
393
|
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
|
|
394
|
return t.getHomotypicSynonymsByHomotypicGroup();
|
|
395
|
}
|
|
396
|
|
|
397
|
public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths){
|
|
398
|
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
|
|
399
|
List<HomotypicalGroup> hsgl = t.getHeterotypicSynonymyGroups();
|
|
400
|
List<List<Synonym>> heterotypicSynonymyGroups = new ArrayList<List<Synonym>>(hsgl.size());
|
|
401
|
for(HomotypicalGroup hsg : hsgl){
|
|
402
|
heterotypicSynonymyGroups.add(hsg.getSynonymsInGroup(t.getSec()));
|
|
403
|
}
|
|
404
|
return heterotypicSynonymyGroups;
|
|
405
|
}
|
|
406
|
|
|
407
|
public Pager<TaxonBase> search(Class<? extends TaxonBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
408
|
Integer numberOfResults = dao.count(clazz,queryString);
|
|
409
|
|
|
410
|
List<TaxonBase> results = new ArrayList<TaxonBase>();
|
|
411
|
if(numberOfResults > 0) { // no point checking again
|
|
412
|
results = dao.search(clazz,queryString, pageSize, pageNumber, orderHints, propertyPaths);
|
|
413
|
}
|
|
414
|
|
|
415
|
return new DefaultPagerImpl<TaxonBase>(pageNumber, numberOfResults, pageSize, results);
|
|
416
|
}
|
|
417
|
|
|
418
|
|
|
419
|
public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator) {
|
|
420
|
|
|
421
|
List<IdentifiableEntity> results = new ArrayList<IdentifiableEntity>();
|
|
422
|
int numberOfResults = 0; // overall number of results (as opposed to number of results per page)
|
|
423
|
List<TaxonBase> taxa = null;
|
|
424
|
|
|
425
|
// Taxa and synonyms
|
|
426
|
long numberTaxaResults = 0L;
|
|
427
|
|
|
428
|
Class<? extends TaxonBase> clazz = null;
|
|
429
|
if (configurator.isDoTaxa() && configurator.isDoSynonyms()) {
|
|
430
|
clazz = TaxonBase.class;
|
|
431
|
} else if(configurator.isDoTaxa()) {
|
|
432
|
clazz = Taxon.class;
|
|
433
|
} else if (configurator.isDoSynonyms()) {
|
|
434
|
clazz = Synonym.class;
|
|
435
|
}
|
|
436
|
|
|
437
|
if(clazz != null){
|
|
438
|
numberTaxaResults =
|
|
439
|
dao.countTaxaByName(clazz,
|
|
440
|
configurator.getSearchString(), configurator.getTaxonomicTree(), configurator.getMatchMode(),
|
|
441
|
configurator.getNamedAreas());
|
|
442
|
if(numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){ // no point checking again if less results
|
|
443
|
taxa = dao.getTaxaByName(clazz,
|
|
444
|
configurator.getSearchString(), configurator.getTaxonomicTree(), configurator.getMatchMode(),
|
|
445
|
configurator.getNamedAreas(), configurator.getPageSize(),
|
|
446
|
configurator.getPageNumber(), configurator.getTaxonPropertyPath());
|
|
447
|
}
|
|
448
|
}
|
|
449
|
|
|
450
|
if (logger.isDebugEnabled()) { logger.debug(numberTaxaResults + " matching taxa counted"); }
|
|
451
|
|
|
452
|
if(taxa != null){
|
|
453
|
results.addAll(taxa);
|
|
454
|
}
|
|
455
|
|
|
456
|
numberOfResults += numberTaxaResults;
|
|
457
|
|
|
458
|
// Names without taxa
|
|
459
|
|
|
460
|
if (configurator.isDoNamesWithoutTaxa()) {
|
|
461
|
int numberNameResults = 0;
|
|
462
|
//FIXME implement search by area
|
|
463
|
List<? extends TaxonNameBase<?,?>> names =
|
|
464
|
nameDao.findByName(configurator.getSearchString(), configurator.getMatchMode(),
|
|
465
|
configurator.getPageSize(), configurator.getPageNumber(), null, null);
|
|
466
|
if (logger.isDebugEnabled()) { logger.debug(names.size() + " matching name(s) found"); }
|
|
467
|
if (names.size() > 0) {
|
|
468
|
for (TaxonNameBase<?,?> taxonName : names) {
|
|
469
|
if (taxonName.getTaxonBases().size() == 0) {
|
|
470
|
results.add(taxonName);
|
|
471
|
numberNameResults++;
|
|
472
|
}
|
|
473
|
}
|
|
474
|
if (logger.isDebugEnabled()) { logger.debug(numberNameResults + " matching name(s) without taxa found"); }
|
|
475
|
numberOfResults += numberNameResults;
|
|
476
|
}
|
|
477
|
}
|
|
478
|
|
|
479
|
// Taxa from common names
|
|
480
|
// FIXME the matching common names also must be returned
|
|
481
|
// FIXME implement search by area
|
|
482
|
if (configurator.isDoTaxaByCommonNames()) {
|
|
483
|
int numberCommonNameResults = 0;
|
|
484
|
List<CommonTaxonName> commonTaxonNames =
|
|
485
|
descriptionDao.searchDescriptionByCommonName(configurator.getSearchString(),
|
|
486
|
configurator.getMatchMode(), configurator.getPageSize(), configurator.getPageNumber());
|
|
487
|
if (logger.isDebugEnabled()) { logger.debug(commonTaxonNames.size() + " matching common name(s) found"); }
|
|
488
|
if (commonTaxonNames.size() > 0) {
|
|
489
|
for (CommonTaxonName commonTaxonName : commonTaxonNames) {
|
|
490
|
DescriptionBase description = commonTaxonName.getInDescription();
|
|
491
|
description = HibernateProxyHelper.deproxy(description, DescriptionBase.class);
|
|
492
|
if (description instanceof TaxonDescription) {
|
|
493
|
TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(description, TaxonDescription.class);
|
|
494
|
Taxon taxon = taxonDescription.getTaxon();
|
|
495
|
taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);
|
|
496
|
if (!results.contains(taxon) && !taxon.isMisappliedName()) {
|
|
497
|
defaultBeanInitializer.initialize(taxon, configurator.getTaxonPropertyPath());
|
|
498
|
results.add(taxon);
|
|
499
|
numberCommonNameResults++;
|
|
500
|
}
|
|
501
|
} else {
|
|
502
|
logger.warn("Description of " + commonTaxonName.getName() + " is not an instance of TaxonDescription");
|
|
503
|
}
|
|
504
|
}
|
|
505
|
numberOfResults += numberCommonNameResults;
|
|
506
|
}
|
|
507
|
}
|
|
508
|
|
|
509
|
//FIXME does not work any more after model change
|
|
510
|
logger.warn("Sort does currently not work on identifiable entities due to model changes (duplicated implementation of the Comparable interface).");
|
|
511
|
//Collections.sort(results);
|
|
512
|
return new DefaultPagerImpl<IdentifiableEntity>
|
|
513
|
(configurator.getPageNumber(), numberOfResults, configurator.getPageSize(), results);
|
|
514
|
}
|
|
515
|
|
|
516
|
public List<UuidAndTitleCache<TaxonBase>> getTaxonUuidAndTitleCache(){
|
|
517
|
return dao.getUuidAndTitleCache();
|
|
518
|
}
|
|
519
|
|
|
520
|
public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes){
|
|
521
|
List<MediaRepresentation> medRep = new ArrayList<MediaRepresentation>();
|
|
522
|
taxon = (Taxon)dao.load(taxon.getUuid());
|
|
523
|
Set<TaxonDescription> descriptions = taxon.getDescriptions();
|
|
524
|
for (TaxonDescription taxDesc: descriptions){
|
|
525
|
Set<DescriptionElementBase> elements = taxDesc.getElements();
|
|
526
|
for (DescriptionElementBase descElem: elements){
|
|
527
|
for(Media media : descElem.getMedia()){
|
|
528
|
|
|
529
|
//find the best matching representation
|
|
530
|
medRep.add(media.findBestMatchingRepresentation(size, height, widthOrDuration, mimeTypes));
|
|
531
|
|
|
532
|
}
|
|
533
|
}
|
|
534
|
}
|
|
535
|
return medRep;
|
|
536
|
}
|
|
537
|
}
|