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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.Collections;
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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.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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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.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.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.persistence.dao.BeanInitializer;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
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/**
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* @author n.hoffmann
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* @created Apr 9, 2010
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* @version 1.0
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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 TaxonNodeServiceImpl extends AnnotatableServiceBase<TaxonNode, ITaxonNodeDao> implements ITaxonNodeService{
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private static final Logger logger = Logger
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.getLogger(TaxonNodeServiceImpl.class);
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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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public TaxonNode getTaxonNodeByUuid(UUID uuid) {
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return dao.findByUuid(uuid);
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}
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public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode,
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List<String> propertyPaths) {
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taxonNode = dao.load(taxonNode.getUuid());
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List<TaxonNode> childNodes = new ArrayList<TaxonNode>(taxonNode.getChildNodes());
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Collections.sort(childNodes, taxonNodeComparator);
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defaultBeanInitializer.initializeAll(childNodes, propertyPaths);
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return childNodes;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ServiceBase#setDao(eu.etaxonomy.cdm.persistence.dao.common.ICdmEntityDao)
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*/
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@Override
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@Autowired
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protected void setDao(ITaxonNodeDao dao) {
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this.dao = dao;
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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 makeTaxonNodeASynonymOfAnotherTaxonNode(TaxonNode oldTaxonNode, TaxonNode newAcceptedTaxonNode, SynonymRelationshipType synonymRelationshipType, Reference citation, String citationMicroReference) {
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// TODO at the moment this method only moves synonym-, concept relations and descriptions to the new accepted taxon
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// in a future version we also want to move cdm data like annotations, marker, so., but we will need a policy for that
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if (oldTaxonNode == null || newAcceptedTaxonNode == null || oldTaxonNode.getTaxon().getName() == null){
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throw new IllegalArgumentException("A mandatory parameter was null.");
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}
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if(oldTaxonNode.equals(newAcceptedTaxonNode)){
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throw new IllegalArgumentException("Taxon can not be made synonym of its own.");
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}
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Taxon oldTaxon = (Taxon) HibernateProxyHelper.deproxy(oldTaxonNode.getTaxon());
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Taxon newAcceptedTaxon = (Taxon) HibernateProxyHelper.deproxy(newAcceptedTaxonNode.getTaxon());
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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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synonymRelationshipType = SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
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}
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}
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SynonymRelationship synonmyRelationship = 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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// CHILD NODES
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if(oldTaxonNode.getChildNodes() != null && oldTaxonNode.getChildNodes().size() != 0){
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for(TaxonNode childNode : oldTaxonNode.getChildNodes()){
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newAcceptedTaxonNode.addChildNode(childNode, childNode.getReference(), childNode.getMicroReference(), childNode.getSynonymToBeUsed());
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}
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}
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//Move Taxon RelationShips to new Taxon
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Set<TaxonRelationship> obsoleteTaxonRelationships = new HashSet<TaxonRelationship>();
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for(TaxonRelationship taxonRelationship : oldTaxon.getTaxonRelations()){
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Taxon fromTaxon = (Taxon) HibernateProxyHelper.deproxy(taxonRelationship.getFromTaxon());
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Taxon toTaxon = (Taxon) HibernateProxyHelper.deproxy(taxonRelationship.getToTaxon());
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if (fromTaxon == oldTaxon){
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newAcceptedTaxon.addTaxonRelation(taxonRelationship.getToTaxon(), taxonRelationship.getType(),
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taxonRelationship.getCitation(), taxonRelationship.getCitationMicroReference());
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}else if(toTaxon == oldTaxon){
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taxonRelationship.getFromTaxon().addTaxonRelation(newAcceptedTaxon, taxonRelationship.getType(),
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taxonRelationship.getCitation(), taxonRelationship.getCitationMicroReference());
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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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// Remove old relationships
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taxonRelationship.setToTaxon(null);
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taxonRelationship.setFromTaxon(null);
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}
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//Move descriptions to new taxon
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for(TaxonDescription description : oldTaxon.getDescriptions()){
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description.setTitleCache("Description copied from former accepted taxon: " + oldTaxon.getTitleCache() + "(Old title: " + description.getTitleCache() + ")");
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newAcceptedTaxon.addDescription(description);
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}
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oldTaxonNode.delete();
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return synonmyRelationship.getSynonym();
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}
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}
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