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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.Propagation;
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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.config.MatchingTaxonConfigurator;
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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.common.IProgressMonitor;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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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.RelationshipBase.Direction;
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import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
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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.media.MediaUtils;
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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.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.persistence.dao.common.IOrderedTermVocabularyDao;
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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.strategy.cache.common.IIdentifiableEntityCacheStrategy;
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/**
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* @author a.kohlbecker
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* @date 10.09.2010
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*
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*/
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@Service
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@Transactional(propagation = Propagation.SUPPORTS, 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 INameService nameService;
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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, Reference 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(Reference sec, ..., ...)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference, boolean)
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*/
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public List<Taxon> getRootTaxa(Reference 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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/* (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.Reference, boolean, boolean)
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*/
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public List<Taxon> getRootTaxa(Rank rank, Reference sec, boolean onlyWithChildren,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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllRelationships(int, int)
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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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/*
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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){
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TaxonNameBase<?,?> synonymName = synonym.getName();
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synonymName.removeTaxonBase(synonym);
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TaxonNameBase<?,?> taxonName = acceptedTaxon.getName();
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taxonName.removeTaxonBase(acceptedTaxon);
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synonym.setName(taxonName);
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acceptedTaxon.setName(synonymName);
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// the accepted taxon needs a new uuid because the concept has changed
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// FIXME this leads to an error "HibernateException: immutable natural identifier of an instance of eu.etaxonomy.cdm.model.taxon.Taxon was altered"
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//acceptedTaxon.setUuid(UUID.randomUUID());
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#changeSynonymToAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)
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*/
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//TODO correct delete handling still needs to be implemented / checked
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@Override
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@Transactional(readOnly = false)
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public Taxon changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, boolean deleteSynonym, boolean copyCitationInfo, Reference citation, String microCitation) throws IllegalArgumentException{
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TaxonNameBase<?,?> acceptedName = acceptedTaxon.getName();
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TaxonNameBase<?,?> synonymName = synonym.getName();
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HomotypicalGroup synonymHomotypicGroup = synonymName.getHomotypicalGroup();
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//check synonym is not homotypic
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if (acceptedName.getHomotypicalGroup().equals(synonymHomotypicGroup)){
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String message = "The accepted taxon and the synonym are part of the same homotypical group and therefore can not be both accepted.";
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throw new IllegalArgumentException(message);
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}
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Taxon newAcceptedTaxon = Taxon.NewInstance(synonymName, acceptedTaxon.getSec());
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SynonymRelationshipType relTypeForGroup = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF();
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List<Synonym> heteroSynonyms = acceptedTaxon.getSynonymsInGroup(synonymHomotypicGroup);
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for (Synonym heteroSynonym : heteroSynonyms){
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if (synonym.equals(heteroSynonym)){
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acceptedTaxon.removeSynonym(heteroSynonym, false);
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}else{
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//move synonyms in same homotypic group to new accepted taxon
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heteroSynonym.replaceAcceptedTaxon(newAcceptedTaxon, relTypeForGroup, copyCitationInfo, citation, microCitation);
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}
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}
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//synonym.getName().removeTaxonBase(synonym);
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//TODO correct delete handling still needs to be implemented / checked
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if (deleteSynonym){
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// deleteSynonym(synonym, taxon, false);
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try {
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this.dao.flush();
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this.delete(synonym);
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} catch (Exception e) {
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logger.info("Can't delete old synonym from database");
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}
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}
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return newAcceptedTaxon;
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}
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public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference citation, String microcitation){
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// Get name from synonym
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TaxonNameBase<?, ?> synonymName = synonym.getName();
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// remove synonym from taxon
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toTaxon.removeSynonym(synonym);
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// Create a taxon with synonym name
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Taxon fromTaxon = Taxon.NewInstance(synonymName, null);
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// Add taxon relation
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fromTaxon.addTaxonRelation(toTaxon, taxonRelationshipType, citation, microcitation);
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// since we are swapping names, we have to detach the name from the synonym completely.
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// Otherwise the synonym will still be in the list of typified names.
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synonym.getName().removeTaxonBase(synonym);
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return fromTaxon;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#changeHomotypicalGroupOfSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.name.HomotypicalGroup, eu.etaxonomy.cdm.model.taxon.Taxon, boolean, boolean)
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*/
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@Transactional(readOnly = false)
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@Override
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public void changeHomotypicalGroupOfSynonym(Synonym synonym, HomotypicalGroup newHomotypicalGroup, Taxon targetTaxon,
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boolean removeFromOtherTaxa, boolean setBasionymRelationIfApplicable){
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// Get synonym name
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TaxonNameBase synonymName = synonym.getName();
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HomotypicalGroup oldHomotypicalGroup = synonymName.getHomotypicalGroup();
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// Switch groups
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oldHomotypicalGroup.removeTypifiedName(synonymName);
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newHomotypicalGroup.addTypifiedName(synonymName);
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//remove existing basionym relationships
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synonymName.removeBasionyms();
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//add basionym relationship
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if (setBasionymRelationIfApplicable){
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Set<TaxonNameBase> basionyms = newHomotypicalGroup.getBasionyms();
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for (TaxonNameBase basionym : basionyms){
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synonymName.addBasionym(basionym);
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}
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}
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//set synonym relationship correctly
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// SynonymRelationship relToTaxon = null;
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boolean relToTargetTaxonExists = false;
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Set<SynonymRelationship> existingRelations = synonym.getSynonymRelations();
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for (SynonymRelationship rel : existingRelations){
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Taxon acceptedTaxon = rel.getAcceptedTaxon();
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boolean isTargetTaxon = acceptedTaxon != null && acceptedTaxon.equals(targetTaxon);
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HomotypicalGroup acceptedGroup = acceptedTaxon.getHomotypicGroup();
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boolean isHomotypicToTaxon = acceptedGroup.equals(newHomotypicalGroup);
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SynonymRelationshipType newRelationType = isHomotypicToTaxon? SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF() : SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
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rel.setType(newRelationType);
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//TODO handle citation and microCitation
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if (isTargetTaxon){
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relToTargetTaxonExists = true;
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}else{
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if (removeFromOtherTaxa){
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acceptedTaxon.removeSynonym(synonym, false);
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}else{
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//do nothing
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}
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}
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}
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if (targetTaxon != null && ! relToTargetTaxonExists ){
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Taxon acceptedTaxon = targetTaxon;
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HomotypicalGroup acceptedGroup = acceptedTaxon.getHomotypicGroup();
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boolean isHomotypicToTaxon = acceptedGroup.equals(newHomotypicalGroup);
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SynonymRelationshipType relType = isHomotypicToTaxon? SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF() : SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
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//TODO handle citation and microCitation
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Reference citation = null;
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String microCitation = null;
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acceptedTaxon.addSynonym(synonym, relType, citation, microCitation);
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}
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
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*/
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@Override
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public void updateTitleCache(Class<? extends TaxonBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<TaxonBase> cacheStrategy, IProgressMonitor monitor) {
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if (clazz == null){
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clazz = TaxonBase.class;
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}
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super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
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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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|
334
|
/* (non-Javadoc)
|
|
335
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#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)
|
|
336
|
*/
|
|
337
|
public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
|
|
338
|
Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank);
|
|
339
|
|
|
340
|
List<TaxonBase> results = new ArrayList<TaxonBase>();
|
|
341
|
if(numberOfResults > 0) { // no point checking again
|
|
342
|
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber);
|
|
343
|
}
|
|
344
|
|
|
345
|
return new DefaultPagerImpl<TaxonBase>(pageNumber, numberOfResults, pageSize, results);
|
|
346
|
}
|
|
347
|
|
|
348
|
/* (non-Javadoc)
|
|
349
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listTaxaByName(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)
|
|
350
|
*/
|
|
351
|
public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
|
|
352
|
Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank);
|
|
353
|
|
|
354
|
List<TaxonBase> results = new ArrayList<TaxonBase>();
|
|
355
|
if(numberOfResults > 0) { // no point checking again
|
|
356
|
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber);
|
|
357
|
}
|
|
358
|
|
|
359
|
return results;
|
|
360
|
}
|
|
361
|
|
|
362
|
/* (non-Javadoc)
|
|
363
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listToTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
|
364
|
*/
|
|
365
|
public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
|
|
366
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);
|
|
367
|
|
|
368
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
|
369
|
if(numberOfResults > 0) { // no point checking again
|
|
370
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedTo);
|
|
371
|
}
|
|
372
|
return results;
|
|
373
|
}
|
|
374
|
|
|
375
|
/* (non-Javadoc)
|
|
376
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#pageToTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
|
377
|
*/
|
|
378
|
public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
379
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);
|
|
380
|
|
|
381
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
|
382
|
if(numberOfResults > 0) { // no point checking again
|
|
383
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedTo);
|
|
384
|
}
|
|
385
|
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
386
|
}
|
|
387
|
|
|
388
|
/* (non-Javadoc)
|
|
389
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listFromTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
|
390
|
*/
|
|
391
|
public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
|
|
392
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom);
|
|
393
|
|
|
394
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
|
395
|
if(numberOfResults > 0) { // no point checking again
|
|
396
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedFrom);
|
|
397
|
}
|
|
398
|
return results;
|
|
399
|
}
|
|
400
|
|
|
401
|
/* (non-Javadoc)
|
|
402
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#pageFromTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
|
403
|
*/
|
|
404
|
public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
405
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom);
|
|
406
|
|
|
407
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
|
408
|
if(numberOfResults > 0) { // no point checking again
|
|
409
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedFrom);
|
|
410
|
}
|
|
411
|
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
412
|
}
|
|
413
|
|
|
414
|
/* (non-Javadoc)
|
|
415
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#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)
|
|
416
|
*/
|
|
417
|
public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
418
|
Integer numberOfResults = dao.countSynonyms(taxon, type);
|
|
419
|
|
|
420
|
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
|
421
|
if(numberOfResults > 0) { // no point checking again
|
|
422
|
results = dao.getSynonyms(taxon, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
423
|
}
|
|
424
|
|
|
425
|
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
426
|
}
|
|
427
|
|
|
428
|
/* (non-Javadoc)
|
|
429
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#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)
|
|
430
|
*/
|
|
431
|
public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
432
|
Integer numberOfResults = dao.countSynonyms(synonym, type);
|
|
433
|
|
|
434
|
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
|
435
|
if(numberOfResults > 0) { // no point checking again
|
|
436
|
results = dao.getSynonyms(synonym, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
437
|
}
|
|
438
|
|
|
439
|
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
440
|
}
|
|
441
|
|
|
442
|
/* (non-Javadoc)
|
|
443
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getHomotypicSynonymsByHomotypicGroup(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)
|
|
444
|
*/
|
|
445
|
public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths){
|
|
446
|
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
|
|
447
|
return t.getHomotypicSynonymsByHomotypicGroup();
|
|
448
|
}
|
|
449
|
|
|
450
|
/* (non-Javadoc)
|
|
451
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getHeterotypicSynonymyGroups(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)
|
|
452
|
*/
|
|
453
|
public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths){
|
|
454
|
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
|
|
455
|
List<HomotypicalGroup> homotypicalGroups = t.getHeterotypicSynonymyGroups();
|
|
456
|
List<List<Synonym>> heterotypicSynonymyGroups = new ArrayList<List<Synonym>>(homotypicalGroups.size());
|
|
457
|
for(HomotypicalGroup homotypicalGroup : homotypicalGroups){
|
|
458
|
heterotypicSynonymyGroups.add(t.getSynonymsInGroup(homotypicalGroup));
|
|
459
|
}
|
|
460
|
return heterotypicSynonymyGroups;
|
|
461
|
}
|
|
462
|
|
|
463
|
public List<UuidAndTitleCache<TaxonBase>> findTaxaAndNamesForEditor(ITaxonServiceConfigurator configurator){
|
|
464
|
|
|
465
|
List<UuidAndTitleCache<TaxonBase>> result = new ArrayList<UuidAndTitleCache<TaxonBase>>();
|
|
466
|
Class<? extends TaxonBase> clazz = null;
|
|
467
|
if ((configurator.isDoTaxa() && configurator.isDoSynonyms())) {
|
|
468
|
clazz = TaxonBase.class;
|
|
469
|
//propertyPath.addAll(configurator.getTaxonPropertyPath());
|
|
470
|
//propertyPath.addAll(configurator.getSynonymPropertyPath());
|
|
471
|
} else if(configurator.isDoTaxa()) {
|
|
472
|
clazz = Taxon.class;
|
|
473
|
//propertyPath = configurator.getTaxonPropertyPath();
|
|
474
|
} else if (configurator.isDoSynonyms()) {
|
|
475
|
clazz = Synonym.class;
|
|
476
|
//propertyPath = configurator.getSynonymPropertyPath();
|
|
477
|
}
|
|
478
|
|
|
479
|
|
|
480
|
result = dao.getTaxaByNameForEditor(clazz, configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas());
|
|
481
|
return result;
|
|
482
|
}
|
|
483
|
|
|
484
|
/* (non-Javadoc)
|
|
485
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaAndNames(eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator)
|
|
486
|
*/
|
|
487
|
public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator) {
|
|
488
|
|
|
489
|
List<IdentifiableEntity> results = new ArrayList<IdentifiableEntity>();
|
|
490
|
int numberOfResults = 0; // overall number of results (as opposed to number of results per page)
|
|
491
|
List<TaxonBase> taxa = null;
|
|
492
|
|
|
493
|
// Taxa and synonyms
|
|
494
|
long numberTaxaResults = 0L;
|
|
495
|
|
|
496
|
Class<? extends TaxonBase> clazz = null;
|
|
497
|
List<String> propertyPath = new ArrayList<String>();
|
|
498
|
if(configurator.getTaxonPropertyPath() != null){
|
|
499
|
propertyPath.addAll(configurator.getTaxonPropertyPath());
|
|
500
|
}
|
|
501
|
if ((configurator.isDoTaxa() && configurator.isDoSynonyms())) {
|
|
502
|
clazz = TaxonBase.class;
|
|
503
|
//propertyPath.addAll(configurator.getTaxonPropertyPath());
|
|
504
|
//propertyPath.addAll(configurator.getSynonymPropertyPath());
|
|
505
|
} else if(configurator.isDoTaxa()) {
|
|
506
|
clazz = Taxon.class;
|
|
507
|
//propertyPath = configurator.getTaxonPropertyPath();
|
|
508
|
} else if (configurator.isDoSynonyms()) {
|
|
509
|
clazz = Synonym.class;
|
|
510
|
//propertyPath = configurator.getSynonymPropertyPath();
|
|
511
|
}
|
|
512
|
|
|
513
|
if(clazz != null){
|
|
514
|
if(configurator.getPageSize() != null){ // no point counting if we need all anyway
|
|
515
|
numberTaxaResults =
|
|
516
|
dao.countTaxaByName(clazz,
|
|
517
|
configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(),
|
|
518
|
configurator.getNamedAreas());
|
|
519
|
}
|
|
520
|
|
|
521
|
if(configurator.getPageSize() == null || numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){ // no point checking again if less results
|
|
522
|
taxa = dao.getTaxaByName(clazz,
|
|
523
|
configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(),
|
|
524
|
configurator.getNamedAreas(), configurator.getPageSize(),
|
|
525
|
configurator.getPageNumber(), propertyPath);
|
|
526
|
}
|
|
527
|
}
|
|
528
|
|
|
529
|
if (logger.isDebugEnabled()) { logger.debug(numberTaxaResults + " matching taxa counted"); }
|
|
530
|
|
|
531
|
if(taxa != null){
|
|
532
|
results.addAll(taxa);
|
|
533
|
}
|
|
534
|
|
|
535
|
numberOfResults += numberTaxaResults;
|
|
536
|
|
|
537
|
// Names without taxa
|
|
538
|
if (configurator.isDoNamesWithoutTaxa()) {
|
|
539
|
int numberNameResults = 0;
|
|
540
|
|
|
541
|
List<? extends TaxonNameBase<?,?>> names =
|
|
542
|
nameDao.findByName(configurator.getTitleSearchStringSqlized(), configurator.getMatchMode(),
|
|
543
|
configurator.getPageSize(), configurator.getPageNumber(), null, configurator.getTaxonNamePropertyPath());
|
|
544
|
if (logger.isDebugEnabled()) { logger.debug(names.size() + " matching name(s) found"); }
|
|
545
|
if (names.size() > 0) {
|
|
546
|
for (TaxonNameBase<?,?> taxonName : names) {
|
|
547
|
if (taxonName.getTaxonBases().size() == 0) {
|
|
548
|
results.add(taxonName);
|
|
549
|
numberNameResults++;
|
|
550
|
}
|
|
551
|
}
|
|
552
|
if (logger.isDebugEnabled()) { logger.debug(numberNameResults + " matching name(s) without taxa found"); }
|
|
553
|
numberOfResults += numberNameResults;
|
|
554
|
}
|
|
555
|
}
|
|
556
|
|
|
557
|
// Taxa from common names
|
|
558
|
|
|
559
|
if (configurator.isDoTaxaByCommonNames()) {
|
|
560
|
taxa = null;
|
|
561
|
numberTaxaResults = 0;
|
|
562
|
if(configurator.getPageSize() != null){// no point counting if we need all anyway
|
|
563
|
numberTaxaResults = dao.countTaxaByCommonName(configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas());
|
|
564
|
}
|
|
565
|
if(configurator.getPageSize() == null || numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){
|
|
566
|
taxa = dao.getTaxaByCommonName(configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas(), configurator.getPageSize(), configurator.getPageNumber(), configurator.getTaxonPropertyPath());
|
|
567
|
}
|
|
568
|
if(taxa != null){
|
|
569
|
results.addAll(taxa);
|
|
570
|
}
|
|
571
|
numberOfResults += numberTaxaResults;
|
|
572
|
|
|
573
|
}
|
|
574
|
|
|
575
|
return new DefaultPagerImpl<IdentifiableEntity>
|
|
576
|
(configurator.getPageNumber(), numberOfResults, configurator.getPageSize(), results);
|
|
577
|
}
|
|
578
|
|
|
579
|
public List<UuidAndTitleCache<TaxonBase>> getTaxonUuidAndTitleCache(){
|
|
580
|
return dao.getUuidAndTitleCache();
|
|
581
|
}
|
|
582
|
|
|
583
|
/* (non-Javadoc)
|
|
584
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllMedia(eu.etaxonomy.cdm.model.taxon.Taxon, int, int, int, java.lang.String[])
|
|
585
|
*/
|
|
586
|
public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes){
|
|
587
|
List<MediaRepresentation> medRep = new ArrayList<MediaRepresentation>();
|
|
588
|
taxon = (Taxon)dao.load(taxon.getUuid());
|
|
589
|
Set<TaxonDescription> descriptions = taxon.getDescriptions();
|
|
590
|
for (TaxonDescription taxDesc: descriptions){
|
|
591
|
Set<DescriptionElementBase> elements = taxDesc.getElements();
|
|
592
|
for (DescriptionElementBase descElem: elements){
|
|
593
|
for(Media media : descElem.getMedia()){
|
|
594
|
|
|
595
|
//find the best matching representation
|
|
596
|
medRep.add(MediaUtils.findBestMatchingRepresentation(media, null, size, height, widthOrDuration, mimeTypes));
|
|
597
|
|
|
598
|
}
|
|
599
|
}
|
|
600
|
}
|
|
601
|
return medRep;
|
|
602
|
}
|
|
603
|
|
|
604
|
/* (non-Javadoc)
|
|
605
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaByID(java.util.Set)
|
|
606
|
*/
|
|
607
|
public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs) {
|
|
608
|
return this.dao.findById(listOfIDs);
|
|
609
|
}
|
|
610
|
|
|
611
|
/* (non-Javadoc)
|
|
612
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#countAllRelationships()
|
|
613
|
*/
|
|
614
|
public int countAllRelationships() {
|
|
615
|
return this.dao.countAllRelationships();
|
|
616
|
}
|
|
617
|
|
|
618
|
/* (non-Javadoc)
|
|
619
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#createAllInferredSynonyms(eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.model.taxon.Taxon)
|
|
620
|
*/
|
|
621
|
public List<Synonym> createAllInferredSynonyms(Classification tree,
|
|
622
|
Taxon taxon) {
|
|
623
|
|
|
624
|
return this.dao.createAllInferredSynonyms(taxon, tree);
|
|
625
|
}
|
|
626
|
|
|
627
|
/* (non-Javadoc)
|
|
628
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#createInferredSynonyms(eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType)
|
|
629
|
*/
|
|
630
|
public List<Synonym> createInferredSynonyms(Classification tree, Taxon taxon, SynonymRelationshipType type) {
|
|
631
|
|
|
632
|
return this.dao.createInferredSynonyms(taxon, tree, type);
|
|
633
|
}
|
|
634
|
|
|
635
|
/* (non-Javadoc)
|
|
636
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNames(java.util.List)
|
|
637
|
*/
|
|
638
|
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath) {
|
|
639
|
|
|
640
|
return this.dao.findIdenticalTaxonNames(propertyPath);
|
|
641
|
}
|
|
642
|
|
|
643
|
|
|
644
|
/* (non-Javadoc)
|
|
645
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#deleteSynonym(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.Synonym, boolean)
|
|
646
|
*/
|
|
647
|
//TODO move to dao??
|
|
648
|
@Transactional(readOnly = false)
|
|
649
|
@Override
|
|
650
|
public void deleteSynonym(Synonym synonym, Taxon taxon, boolean removeNameIfPossible) {
|
|
651
|
//remove synonymRelationship
|
|
652
|
Set<Taxon> taxonSet = new HashSet<Taxon>();
|
|
653
|
if (taxon != null){
|
|
654
|
taxonSet.add(taxon);
|
|
655
|
}else{
|
|
656
|
taxonSet.addAll(synonym.getAcceptedTaxa());
|
|
657
|
}
|
|
658
|
Set<SynonymRelationship> synRels = synonym.getSynonymRelations();
|
|
659
|
for (Taxon taxon2 : taxonSet){
|
|
660
|
dao.deleteSynonymRelationships(synonym, taxon2);
|
|
661
|
}
|
|
662
|
|
|
663
|
//TODO remove name from homotypical group?
|
|
664
|
|
|
665
|
//remove synonym (if necessary)
|
|
666
|
if (synonym.getSynonymRelations().isEmpty()){
|
|
667
|
dao.delete(synonym);
|
|
668
|
}
|
|
669
|
|
|
670
|
if (removeNameIfPossible){
|
|
671
|
TaxonNameBase name = synonym.getName();
|
|
672
|
nameService.delete(name);
|
|
673
|
//check is used
|
|
674
|
//name relationship
|
|
675
|
//concept
|
|
676
|
//descriptionElementSource
|
|
677
|
//
|
|
678
|
}
|
|
679
|
}
|
|
680
|
|
|
681
|
|
|
682
|
/* (non-Javadoc)
|
|
683
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNameIds(java.util.List)
|
|
684
|
*/
|
|
685
|
public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath) {
|
|
686
|
|
|
687
|
return this.dao.findIdenticalNamesNew(propertyPath);
|
|
688
|
}
|
|
689
|
|
|
690
|
/* (non-Javadoc)
|
|
691
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getPhylumName(eu.etaxonomy.cdm.model.name.TaxonNameBase)
|
|
692
|
*/
|
|
693
|
public String getPhylumName(TaxonNameBase name){
|
|
694
|
return this.dao.getPhylumName(name);
|
|
695
|
}
|
|
696
|
|
|
697
|
/* (non-Javadoc)
|
|
698
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#deleteSynonymRelationships(eu.etaxonomy.cdm.model.taxon.Synonym)
|
|
699
|
*/
|
|
700
|
public long deleteSynonymRelationships(Synonym syn) {
|
|
701
|
return dao.deleteSynonymRelationships(syn, null);
|
|
702
|
}
|
|
703
|
|
|
704
|
|
|
705
|
/* (non-Javadoc)
|
|
706
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listSynonymRelationships(eu.etaxonomy.cdm.model.taxon.TaxonBase, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction)
|
|
707
|
*/
|
|
708
|
public List<SynonymRelationship> listSynonymRelationships(
|
|
709
|
TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber,
|
|
710
|
List<OrderHint> orderHints, List<String> propertyPaths, Direction direction) {
|
|
711
|
Integer numberOfResults = dao.countSynonymRelationships(taxonBase, type, direction);
|
|
712
|
|
|
713
|
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
|
714
|
if(numberOfResults > 0) { // no point checking again
|
|
715
|
results = dao.getSynonymRelationships(taxonBase, type, pageSize, pageNumber, orderHints, propertyPaths, direction);
|
|
716
|
}
|
|
717
|
return results;
|
|
718
|
}
|
|
719
|
|
|
720
|
/* (non-Javadoc)
|
|
721
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findBestMatchingTaxon(java.lang.String)
|
|
722
|
*/
|
|
723
|
@Override
|
|
724
|
public Taxon findBestMatchingTaxon(String taxonName) {
|
|
725
|
MatchingTaxonConfigurator config = MatchingTaxonConfigurator.NewInstance();
|
|
726
|
config.setTaxonNameTitle(taxonName);
|
|
727
|
return findBestMatchingTaxon(config);
|
|
728
|
}
|
|
729
|
|
|
730
|
|
|
731
|
|
|
732
|
@Override
|
|
733
|
public Taxon findBestMatchingTaxon(MatchingTaxonConfigurator config) {
|
|
734
|
|
|
735
|
Taxon bestCandidate = null;
|
|
736
|
try{
|
|
737
|
// 1. search for acceptet taxa
|
|
738
|
List<TaxonBase> taxonList = dao.findByNameTitleCache(Taxon.class, config.getTaxonNameTitle(), null, MatchMode.EXACT, null, 0, null, null);
|
|
739
|
boolean bestCandidateMatchesSecUuid = false;
|
|
740
|
boolean bestCandidateIsInClassification = false;
|
|
741
|
int countEqualCandidates = 0;
|
|
742
|
for(TaxonBase taxonBaseCandidate : taxonList){
|
|
743
|
if(taxonBaseCandidate instanceof Taxon){
|
|
744
|
Taxon newCanditate = CdmBase.deproxy(taxonBaseCandidate, Taxon.class);
|
|
745
|
boolean newCandidateMatchesSecUuid = isMatchesSecUuid(newCanditate, config);
|
|
746
|
if (! newCandidateMatchesSecUuid && config.isOnlyMatchingSecUuid() ){
|
|
747
|
continue;
|
|
748
|
}else if(newCandidateMatchesSecUuid && ! bestCandidateMatchesSecUuid){
|
|
749
|
bestCandidate = newCanditate;
|
|
750
|
countEqualCandidates = 1;
|
|
751
|
bestCandidateMatchesSecUuid = true;
|
|
752
|
continue;
|
|
753
|
}
|
|
754
|
|
|
755
|
boolean newCandidateInClassification = isInClassification(newCanditate, config);
|
|
756
|
if (! newCandidateInClassification && config.isOnlyMatchingClassificationUuid()){
|
|
757
|
continue;
|
|
758
|
}else if (newCandidateInClassification && ! bestCandidateIsInClassification){
|
|
759
|
bestCandidate = newCanditate;
|
|
760
|
countEqualCandidates = 1;
|
|
761
|
bestCandidateIsInClassification = true;
|
|
762
|
continue;
|
|
763
|
}
|
|
764
|
if (bestCandidate == null){
|
|
765
|
bestCandidate = newCanditate;
|
|
766
|
countEqualCandidates = 1;
|
|
767
|
continue;
|
|
768
|
}
|
|
769
|
|
|
770
|
}else{ //not Taxon.class
|
|
771
|
continue;
|
|
772
|
}
|
|
773
|
countEqualCandidates++;
|
|
774
|
|
|
775
|
}
|
|
776
|
if (bestCandidate != null){
|
|
777
|
if(countEqualCandidates > 1){
|
|
778
|
logger.info(countEqualCandidates + " equally matching TaxonBases found, using first accepted Taxon: " + bestCandidate.getTitleCache());
|
|
779
|
return bestCandidate;
|
|
780
|
} else {
|
|
781
|
logger.info("using accepted Taxon: " + bestCandidate.getTitleCache());
|
|
782
|
return bestCandidate;
|
|
783
|
}
|
|
784
|
}
|
|
785
|
|
|
786
|
|
|
787
|
// 2. search for synonyms
|
|
788
|
if (config.isIncludeSynonyms()){
|
|
789
|
List<TaxonBase> synonymList = dao.findByNameTitleCache(Synonym.class, config.getTaxonNameTitle(), null, MatchMode.EXACT, null, 0, null, null);
|
|
790
|
for(TaxonBase taxonBase : synonymList){
|
|
791
|
if(taxonBase instanceof Synonym){
|
|
792
|
Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
|
|
793
|
Set<Taxon> acceptetdCandidates = synonym.getAcceptedTaxa();
|
|
794
|
if(!acceptetdCandidates.isEmpty()){
|
|
795
|
bestCandidate = acceptetdCandidates.iterator().next();
|
|
796
|
if(acceptetdCandidates.size() == 1){
|
|
797
|
logger.info(acceptetdCandidates.size() + " Accepted taxa found for synonym " + taxonBase.getTitleCache() + ", using first one: " + bestCandidate.getTitleCache());
|
|
798
|
return bestCandidate;
|
|
799
|
} else {
|
|
800
|
logger.info("using accepted Taxon " + bestCandidate.getTitleCache() + "for synonym " + taxonBase.getTitleCache());
|
|
801
|
return bestCandidate;
|
|
802
|
}
|
|
803
|
//TODO extend method: search using treeUUID, using SecUUID, first find accepted then include synonyms until a matching taxon is found
|
|
804
|
}
|
|
805
|
}
|
|
806
|
}
|
|
807
|
}
|
|
808
|
|
|
809
|
} catch (Exception e){
|
|
810
|
logger.error(e);
|
|
811
|
}
|
|
812
|
|
|
813
|
return bestCandidate;
|
|
814
|
}
|
|
815
|
|
|
816
|
private boolean isInClassification(Taxon taxon, MatchingTaxonConfigurator config) {
|
|
817
|
UUID configClassificationUuid = config.getClassificationUuid();
|
|
818
|
if (configClassificationUuid == null){
|
|
819
|
return false;
|
|
820
|
}
|
|
821
|
for (TaxonNode node : taxon.getTaxonNodes()){
|
|
822
|
UUID classUuid = node.getClassification().getUuid();
|
|
823
|
if (configClassificationUuid.equals(classUuid)){
|
|
824
|
return true;
|
|
825
|
}
|
|
826
|
}
|
|
827
|
return false;
|
|
828
|
}
|
|
829
|
|
|
830
|
private boolean isMatchesSecUuid(Taxon taxon, MatchingTaxonConfigurator config) {
|
|
831
|
UUID configSecUuid = config.getSecUuid();
|
|
832
|
if (configSecUuid == null){
|
|
833
|
return false;
|
|
834
|
}
|
|
835
|
UUID taxonSecUuid = (taxon.getSec() == null)? null : taxon.getSec().getUuid();
|
|
836
|
return configSecUuid.equals(taxonSecUuid);
|
|
837
|
}
|
|
838
|
|
|
839
|
/* (non-Javadoc)
|
|
840
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findBestMatchingSynonym(java.lang.String)
|
|
841
|
*/
|
|
842
|
@Override
|
|
843
|
public Synonym findBestMatchingSynonym(String taxonName) {
|
|
844
|
List<TaxonBase> synonymList = dao.findByNameTitleCache(Synonym.class, taxonName, null, MatchMode.EXACT, null, 0, null, null);
|
|
845
|
if(! synonymList.isEmpty()){
|
|
846
|
Synonym result = CdmBase.deproxy(synonymList.iterator().next(), Synonym.class);
|
|
847
|
if(synonymList.size() == 1){
|
|
848
|
logger.info(synonymList.size() + " Synonym found " + result.getTitleCache() );
|
|
849
|
return result;
|
|
850
|
} else {
|
|
851
|
logger.info("Several matching synonyms found. Using first: " + result.getTitleCache());
|
|
852
|
return result;
|
|
853
|
}
|
|
854
|
}
|
|
855
|
return null;
|
|
856
|
}
|
|
857
|
|
|
858
|
/* (non-Javadoc)
|
|
859
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#moveSynonymToAnotherTaxon(eu.etaxonomy.cdm.model.taxon.SynonymRelationship, eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)
|
|
860
|
*/
|
|
861
|
@Override
|
|
862
|
public Taxon moveSynonymToAnotherTaxon(SynonymRelationship synonymRelation,
|
|
863
|
Taxon toTaxon, SynonymRelationshipType synonymRelationshipType, Reference reference, String referenceDetail) {
|
|
864
|
Taxon fromTaxon = synonymRelation.getAcceptedTaxon();
|
|
865
|
|
|
866
|
toTaxon.addSynonym(synonymRelation.getSynonym(), synonymRelationshipType, reference, referenceDetail);
|
|
867
|
|
|
868
|
fromTaxon.removeSynonymRelation(synonymRelation);
|
|
869
|
|
|
870
|
return toTaxon;
|
|
871
|
}
|
|
872
|
|
|
873
|
/* (non-Javadoc)
|
|
874
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheTaxon()
|
|
875
|
*/
|
|
876
|
@Override
|
|
877
|
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheTaxon() {
|
|
878
|
return dao.getUuidAndTitleCacheTaxon();
|
|
879
|
}
|
|
880
|
|
|
881
|
/* (non-Javadoc)
|
|
882
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheSynonym()
|
|
883
|
*/
|
|
884
|
@Override
|
|
885
|
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheSynonym() {
|
|
886
|
return dao.getUuidAndTitleCacheSynonym();
|
|
887
|
}
|
|
888
|
|
|
889
|
}
|