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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.Collection;
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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.Transactional;
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import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
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import eu.etaxonomy.cdm.api.service.config.TaxonNodeDeletionConfigurator;
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import eu.etaxonomy.cdm.api.service.config.TaxonNodeDeletionConfigurator.ChildHandling;
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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.HomotypicalGroup;
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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.ITaxonNodeComparator;
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import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
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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.initializer.IBeanInitializer;
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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(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.getLogger(TaxonNodeServiceImpl.class);
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@Autowired
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private IBeanInitializer defaultBeanInitializer;
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private Comparator<? super TaxonNode> taxonNodeComparator;
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@Autowired
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private ITaxonService taxonService;
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@Autowired
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private IClassificationService classService;
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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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@Override
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public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode,
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List<String> propertyPaths, boolean recursive, boolean sorted) {
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taxonNode = dao.load(taxonNode.getUuid());
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List<TaxonNode> childNodes;
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if (recursive == true){
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childNodes = dao.listChildrenOf(taxonNode, null, null, null, recursive);
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}else{
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childNodes = new ArrayList<TaxonNode>(taxonNode.getChildNodes());
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}
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if (sorted){
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Collections.sort(childNodes, taxonNodeComparator);
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}
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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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@Override
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@Transactional(readOnly = false)
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public Synonym makeTaxonNodeASynonymOfAnotherTaxonNode(TaxonNode oldTaxonNode,
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TaxonNode newAcceptedTaxonNode,
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SynonymRelationshipType synonymRelationshipType,
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Reference citation,
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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)this.taxonService.load(newAcceptedTaxonNode.getTaxon().getUuid());
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// Move oldTaxon to newTaxon
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//TaxonNameBase<?,?> synonymName = oldTaxon.getName();
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TaxonNameBase<?,?> synonymName = (TaxonNameBase)HibernateProxyHelper.deproxy(oldTaxon.getName());
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HomotypicalGroup group = synonymName.getHomotypicalGroup();
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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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//set homotypic group
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HomotypicalGroup newAcceptedTaxonHomotypicalgroup = newAcceptedTaxon.getHomotypicGroup();
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HibernateProxyHelper.deproxy(newAcceptedTaxonHomotypicalgroup);
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HibernateProxyHelper.deproxy(newAcceptedTaxon.getName());
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// Move Synonym Relations to new Taxon
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SynonymRelationship synonmyRelationship = newAcceptedTaxon.addSynonymName(synonymName,
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synonymRelationshipType, citation, citationMicroReference);
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HomotypicalGroup homotypicalGroupAcceptedTaxon = synonmyRelationship.getSynonym().getHomotypicGroup();
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// Move Synonym Relations to new Taxon
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// From ticket 3163 we can move taxon with accepted name having homotypic synonyms
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List<Synonym> synonymsInHomotypicalGroup = null;
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//the synonyms of the homotypical group of the old taxon
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if (synonymRelationshipType.equals(SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF())){
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synonymsInHomotypicalGroup = oldTaxon.getSynonymsInGroup(group);
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}
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for(SynonymRelationship synRelation : oldTaxon.getSynonymRelations()){
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SynonymRelationshipType srt;
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if(synRelation.getSynonym().getName().getHomotypicalGroup()!= null
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&& synRelation.getSynonym().getName().getHomotypicalGroup().equals(newAcceptedTaxon.getName().getHomotypicalGroup())) {
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srt = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF();
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} else if(synRelation.getType() != null && synRelation.getType().equals(SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF())) {
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if (synonymRelationshipType.equals(SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF())){
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srt = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF();
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} else{
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srt = SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
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}
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} else {
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srt = synRelation.getType();
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}
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newAcceptedTaxon.addSynonym(synRelation.getSynonym(),
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srt,
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synRelation.getCitation(),
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synRelation.getCitationMicroReference());
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/*if (synonymsInHomotypicalGroup.contains(synRelation.getSynonym()) && srt.equals(SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF())){
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homotypicalGroupAcceptedTaxon.addTypifiedName(synRelation.getSynonym().getName());
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}*/
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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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fromTaxon.addTaxonRelation(newAcceptedTaxon, taxonRelationship.getType(),
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taxonRelationship.getCitation(), taxonRelationship.getCitationMicroReference());
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taxonService.saveOrUpdate(fromTaxon);
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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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fromTaxon.removeTaxonRelation(taxonRelationship);
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toTaxon.removeTaxonRelation(taxonRelationship);
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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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List<TaxonDescription> descriptions = new ArrayList<TaxonDescription>( oldTaxon.getDescriptions()); //to avoid concurrent modification errors (newAcceptedTaxon.addDescription() modifies also oldtaxon.descritpions())
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for(TaxonDescription description : descriptions){
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String message = "Description copied from former accepted taxon: %s (Old title: %s)";
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message = String.format(message, oldTaxon.getTitleCache(), description.getTitleCache());
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description.setTitleCache(message, true);
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//oldTaxon.removeDescription(description, false);
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newAcceptedTaxon.addDescription(description);
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}
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oldTaxon.clearDescriptions();
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taxonService.update(newAcceptedTaxon);
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TaxonDeletionConfigurator conf = new TaxonDeletionConfigurator();
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conf.setDeleteSynonymsIfPossible(false);
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DeleteResult result = taxonService.isDeletable(oldTaxon, conf);
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// conf.setDeleteNameIfPossible(false);
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if (result.isOk()){
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result = taxonService.deleteTaxon(oldTaxon, conf, null);
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}else{
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TaxonNodeDeletionConfigurator config = new TaxonNodeDeletionConfigurator();
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config.setDeleteTaxon(false);
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conf.setTaxonNodeConfig(config);
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result = deleteTaxonNode(oldTaxonNode, conf);
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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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonNodeService#makeTaxonNodeASynonymOfAnotherTaxonNode(java.util.UUID, java.util.UUID, java.util.UUID, java.util.UUID, java.lang.String)
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*/
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@Override
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@Transactional(readOnly = false)
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public Synonym makeTaxonNodeASynonymOfAnotherTaxonNode(UUID oldTaxonNodeUuid,
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UUID newAcceptedTaxonNodeUUID,
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SynonymRelationshipType synonymRelationshipType,
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Reference citation,
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String citationMicroReference) {
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return makeTaxonNodeASynonymOfAnotherTaxonNode(dao.load(oldTaxonNodeUuid),
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dao.load(newAcceptedTaxonNodeUUID),
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synonymRelationshipType,
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citation,
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citationMicroReference);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonNodeService#deleteTaxonNodes(java.util.List)
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*/
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@Override
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@Transactional(readOnly = false)
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public DeleteResult deleteTaxonNodes(Set<ITaxonTreeNode> nodes, TaxonDeletionConfigurator config) {
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if (config == null){
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config = new TaxonDeletionConfigurator();
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}
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DeleteResult result = new DeleteResult();
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List<UUID> deletedUUIDs = new ArrayList<UUID>();
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Classification classification = null;
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for (ITaxonTreeNode treeNode:nodes){
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if (treeNode != null){
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if (treeNode instanceof TaxonNode){
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TaxonNode taxonNode;
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taxonNode = HibernateProxyHelper.deproxy(treeNode, TaxonNode.class);
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//check whether the node has children or the children are already deleted
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if(taxonNode.hasChildNodes()){
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Set<ITaxonTreeNode> children = new HashSet<ITaxonTreeNode> ();
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List<TaxonNode> childNodesList = taxonNode.getChildNodes();
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children.addAll(childNodesList);
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int compare = config.getTaxonNodeConfig().getChildHandling().compareTo(ChildHandling.DELETE);
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boolean childHandling = (compare == 0)? true: false;
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if (childHandling){
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boolean changeDeleteTaxon = false;
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if (!config.getTaxonNodeConfig().isDeleteTaxon()){
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config.getTaxonNodeConfig().setDeleteTaxon(true);
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changeDeleteTaxon = true;
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}
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DeleteResult resultNodes = deleteTaxonNodes(children, config);
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if (!resultNodes.isOk()){
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result.addExceptions(resultNodes.getExceptions());
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result.setStatus(resultNodes.getStatus());
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}
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if (changeDeleteTaxon){
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config.getTaxonNodeConfig().setDeleteTaxon(false);
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}
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} else {
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//move the children to the parent
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TaxonNode parent = taxonNode.getParent();
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for (TaxonNode child: childNodesList){
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parent.addChildNode(child, child.getReference(), child.getMicroReference());
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}
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}
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}
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classification = taxonNode.getClassification();
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if (classification.getRootNode().equals(taxonNode)){
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classification.removeRootNode();
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classification = null;
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}else if (classification.getChildNodes().contains(taxonNode)){
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Taxon taxon = taxonNode.getTaxon();
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classification.deleteChildNode(taxonNode);
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//node is rootNode
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if (taxon != null){
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if (config.getTaxonNodeConfig().isDeleteTaxon()){
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taxonService.saveOrUpdate(taxon);
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saveOrUpdate(taxonNode);
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TaxonDeletionConfigurator configNew = new TaxonDeletionConfigurator();
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333
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DeleteResult resultTaxon = taxonService.deleteTaxon(taxon, configNew, classification);
|
|
334
|
if (!resultTaxon.isOk()){
|
|
335
|
result.addExceptions(resultTaxon.getExceptions());
|
|
336
|
result.setStatus(resultTaxon.getStatus());
|
|
337
|
}
|
|
338
|
|
|
339
|
}
|
|
340
|
}
|
|
341
|
classification = null;
|
|
342
|
|
|
343
|
}else {
|
|
344
|
classification = null;
|
|
345
|
Taxon taxon = taxonNode.getTaxon();
|
|
346
|
//node is rootNode
|
|
347
|
if (taxon != null){
|
|
348
|
taxonNode.getTaxon().removeTaxonNode(taxonNode);
|
|
349
|
if (config.getTaxonNodeConfig().isDeleteTaxon()){
|
|
350
|
TaxonDeletionConfigurator configNew = new TaxonDeletionConfigurator();
|
|
351
|
saveOrUpdate(taxonNode);
|
|
352
|
taxonService.saveOrUpdate(taxon);
|
|
353
|
DeleteResult resultTaxon = taxonService.deleteTaxon(taxon, configNew, classification);
|
|
354
|
if (!resultTaxon.isOk()){
|
|
355
|
result.addExceptions(resultTaxon.getExceptions());
|
|
356
|
result.setStatus(resultTaxon.getStatus());
|
|
357
|
}
|
|
358
|
}
|
|
359
|
}
|
|
360
|
|
|
361
|
}
|
|
362
|
|
|
363
|
UUID uuid = dao.delete(taxonNode);
|
|
364
|
logger.debug("Deleted node " +uuid.toString());
|
|
365
|
}else {
|
|
366
|
classification = (Classification) treeNode;
|
|
367
|
|
|
368
|
}
|
|
369
|
|
|
370
|
//deletedUUIDs.add(treeNode.getUuid());
|
|
371
|
|
|
372
|
}
|
|
373
|
}
|
|
374
|
if (classification != null){
|
|
375
|
DeleteResult resultClassification = classService.delete(classification);
|
|
376
|
if (!resultClassification.isOk()){
|
|
377
|
result.addExceptions(resultClassification.getExceptions());
|
|
378
|
result.setStatus(resultClassification.getStatus());
|
|
379
|
}
|
|
380
|
}
|
|
381
|
return result;
|
|
382
|
|
|
383
|
}
|
|
384
|
|
|
385
|
@Override
|
|
386
|
@Transactional(readOnly = false)
|
|
387
|
public DeleteResult deleteTaxonNodes(Collection<UUID> nodeUuids, TaxonDeletionConfigurator config) {
|
|
388
|
Set<ITaxonTreeNode> nodes = new HashSet<ITaxonTreeNode>();
|
|
389
|
for(UUID nodeUuid : nodeUuids) {
|
|
390
|
nodes.add(dao.load(nodeUuid));
|
|
391
|
}
|
|
392
|
return deleteTaxonNodes(nodes, config);
|
|
393
|
}
|
|
394
|
|
|
395
|
/* (non-Javadoc)
|
|
396
|
* @see eu.etaxonomy.cdm.api.service.ITaxonNodeService#deleteTaxonNode(java.util.List)
|
|
397
|
*/
|
|
398
|
@Override
|
|
399
|
@Transactional(readOnly = false)
|
|
400
|
public DeleteResult deleteTaxonNode(TaxonNode node, TaxonDeletionConfigurator config) {
|
|
401
|
|
|
402
|
Taxon taxon = (Taxon)HibernateProxyHelper.deproxy(node.getTaxon());
|
|
403
|
if (config == null){
|
|
404
|
config = new TaxonDeletionConfigurator();
|
|
405
|
}
|
|
406
|
if (config.getTaxonNodeConfig().isDeleteTaxon()){
|
|
407
|
return taxonService.deleteTaxon(taxon, config, node.getClassification());
|
|
408
|
} else{
|
|
409
|
DeleteResult result = new DeleteResult();
|
|
410
|
boolean success = taxon.removeTaxonNode(node);
|
|
411
|
if (success){
|
|
412
|
if (!dao.delete(node).equals(null)){
|
|
413
|
return result;
|
|
414
|
} else {
|
|
415
|
result.setError();
|
|
416
|
return result;
|
|
417
|
}
|
|
418
|
}else{
|
|
419
|
result.setError();
|
|
420
|
result.addException(new Exception("The node can not be removed from the taxon."));
|
|
421
|
return result;
|
|
422
|
}
|
|
423
|
|
|
424
|
}
|
|
425
|
|
|
426
|
}
|
|
427
|
|
|
428
|
|
|
429
|
@Override
|
|
430
|
@Transactional(readOnly = false)
|
|
431
|
public DeleteResult deleteTaxonNode(UUID nodeUuid, TaxonDeletionConfigurator config) {
|
|
432
|
DeleteResult dr = deleteTaxonNode(dao.load(nodeUuid), config);
|
|
433
|
return dr;
|
|
434
|
}
|
|
435
|
|
|
436
|
|
|
437
|
@Override
|
|
438
|
@Transactional(readOnly = false)
|
|
439
|
public TaxonNode moveTaxonNode(TaxonNode taxonNode, TaxonNode newParentTaxonNode) {
|
|
440
|
return newParentTaxonNode.addChildNode(taxonNode,
|
|
441
|
newParentTaxonNode.getReference(),
|
|
442
|
newParentTaxonNode.getMicroReference());
|
|
443
|
|
|
444
|
}
|
|
445
|
|
|
446
|
@Override
|
|
447
|
@Transactional(readOnly = false)
|
|
448
|
public TaxonNode moveTaxonNode(UUID taxonNodeUuid, UUID newParentTaxonNodeUuid) {
|
|
449
|
return moveTaxonNode(dao.load(taxonNodeUuid), dao.load(newParentTaxonNodeUuid));
|
|
450
|
|
|
451
|
}
|
|
452
|
|
|
453
|
/* (non-Javadoc)
|
|
454
|
* @see eu.etaxonomy.cdm.api.service.ITaxonNodeService#listAllNodesForClassification(eu.etaxonomy.cdm.model.taxon.Classification, int, int)
|
|
455
|
*/
|
|
456
|
@Override
|
|
457
|
public List<TaxonNode> listAllNodesForClassification(Classification classification, Integer start, Integer end) {
|
|
458
|
return dao.getTaxonOfAcceptedTaxaByClassification(classification, start, end);
|
|
459
|
}
|
|
460
|
|
|
461
|
/* (non-Javadoc)
|
|
462
|
* @see eu.etaxonomy.cdm.api.service.ITaxonNodeService#countAllNodesForClassification(eu.etaxonomy.cdm.model.taxon.Classification)
|
|
463
|
*/
|
|
464
|
@Override
|
|
465
|
public int countAllNodesForClassification(Classification classification) {
|
|
466
|
return dao.countTaxonOfAcceptedTaxaByClassification(classification);
|
|
467
|
}
|
|
468
|
|
|
469
|
|
|
470
|
|
|
471
|
|
|
472
|
}
|