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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.UpdateResult.Status;
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import eu.etaxonomy.cdm.api.service.config.NodeDeletionConfigurator.ChildHandling;
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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.dto.CdmEntityIdentifier;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.api.service.pager.PagerUtils;
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import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
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import eu.etaxonomy.cdm.hibernate.HHH_9751_Util;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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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.HomotypicGroupTaxonComparator;
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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.TaxonNodeAgentRelation;
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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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import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
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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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@Autowired
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private ITaxonService taxonService;
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@Autowired
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private IAgentService agentService;
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@Override
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public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode,
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List<String> propertyPaths, boolean recursive, NodeSortMode sortMode) {
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getSession().refresh(taxonNode);
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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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HHH_9751_Util.removeAllNull(childNodes);
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if (sortMode != null){
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Comparator<TaxonNode> comparator = sortMode.newComparator();
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Collections.sort(childNodes, comparator);
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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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/**
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* {@inheritDoc}
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*/
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@Override
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public Pager<TaxonNodeDto> pageChildNodesDTOs(UUID taxonNodeUuid, boolean recursive,
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boolean doSynonyms, NodeSortMode sortMode,
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Integer pageSize, Integer pageIndex) {
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TaxonNode parentNode = dao.load(taxonNodeUuid);
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List<CdmBase> allRecords = new ArrayList<>();
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//acceptedTaxa
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List<TaxonNode> childNodes = loadChildNodesOfTaxonNode(parentNode, null, recursive, sortMode);
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allRecords.addAll(childNodes);
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//add synonyms if pager is not yet full synonyms
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List<Synonym> synList = new ArrayList<>(parentNode.getTaxon().getSynonyms());
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Collections.sort(synList, new HomotypicGroupTaxonComparator(null));
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//TODO: test sorting
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allRecords.addAll(synList);
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List<TaxonNodeDto> dtos = new ArrayList<>(pageSize==null?25:pageSize);
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int start = PagerUtils.startFor(pageSize, pageIndex);
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int limit = PagerUtils.limitFor(pageSize);
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Long totalCount = Long.valueOf(allRecords.size());
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if(PagerUtils.hasResultsInRange(totalCount, pageIndex, pageSize)) {
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TaxonNameBase<?,?> parentName = null;
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for(int i = start; i < Math.min(totalCount, start + limit); i++) {
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CdmBase record = allRecords.get(i);
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if (record.isInstanceOf(TaxonNode.class)){
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dtos.add(new TaxonNodeDto(CdmBase.deproxy(record, TaxonNode.class)));
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}else if (record.isInstanceOf(Synonym.class)){
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Synonym synonym = CdmBase.deproxy(record, Synonym.class);
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parentName = parentName == null? parentNode.getTaxon().getName(): parentName;
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boolean isHomotypic = synonym.getName().isHomotypic(parentName);
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dtos.add(new TaxonNodeDto(synonym, isHomotypic));
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}
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}
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}
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return new DefaultPagerImpl<TaxonNodeDto>(pageIndex, totalCount, pageSize , dtos);
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}
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@Override
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public TaxonNodeDto parentDto(UUID taxonNodeUuid) {
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TaxonNode taxonNode = dao.load(taxonNodeUuid);
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if(taxonNode.getParent() != null) {
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return new TaxonNodeDto(taxonNode.getParent());
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}
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return null;
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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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@Override
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@Transactional(readOnly = false)
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public DeleteResult 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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Classification classification = oldTaxonNode.getClassification();
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Taxon oldTaxon = 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 = HibernateProxyHelper.deproxy(oldTaxon.getName());
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HomotypicalGroup group = synonymName.getHomotypicalGroup();
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group = HibernateProxyHelper.deproxy(group, HomotypicalGroup.class);
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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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newAcceptedTaxonHomotypicalgroup = HibernateProxyHelper.deproxy(newAcceptedTaxonHomotypicalgroup, HomotypicalGroup.class);
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TaxonNameBase newAcceptedTaxonName = HibernateProxyHelper.deproxy(newAcceptedTaxon.getName(), TaxonNameBase.class);
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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(newAcceptedTaxonName.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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List<TaxonNode> childNodes = new ArrayList<TaxonNode>();
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for (TaxonNode childNode : oldTaxonNode.getChildNodes()){
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childNodes.add(childNode);
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}
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for(TaxonNode childNode :childNodes){
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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 = HibernateProxyHelper.deproxy(taxonRelationship.getFromTaxon());
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Taxon toTaxon = 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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taxonService.update(oldTaxon);
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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.getUuid(), conf, classification.getUuid());
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}else{
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result.setStatus(Status.OK);
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TaxonNodeDeletionConfigurator config = new TaxonNodeDeletionConfigurator();
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config.setDeleteElement(false);
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conf.setTaxonNodeConfig(config);
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result.includeResult(deleteTaxonNode(oldTaxonNode, conf));
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}
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result.addUpdatedObject(newAcceptedTaxon);
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result.addUpdatedObject(oldTaxon);
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//oldTaxonNode.delete();
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return result;
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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 UpdateResult 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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TaxonNode oldTaxonNode = dao.load(oldTaxonNodeUuid);
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TaxonNode oldTaxonParentNode = oldTaxonNode.getParent();
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TaxonNode newTaxonNode = dao.load(newAcceptedTaxonNodeUUID);
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UpdateResult result = makeTaxonNodeASynonymOfAnotherTaxonNode(oldTaxonNode,
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newTaxonNode,
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synonymRelationshipType,
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citation,
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citationMicroReference);
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result.addUpdatedCdmId(new CdmEntityIdentifier(oldTaxonParentNode.getId(), TaxonNode.class));
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result.addUpdatedCdmId(new CdmEntityIdentifier(newTaxonNode.getId(), TaxonNode.class));
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result.setCdmEntity(oldTaxonParentNode);
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return result;
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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(List<TaxonNode> list, 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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List<TaxonNode> taxonNodes = new ArrayList<TaxonNode>(list);
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for (TaxonNode treeNode:taxonNodes){
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if (treeNode != null){
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TaxonNode taxonNode;
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taxonNode = HibernateProxyHelper.deproxy(treeNode, TaxonNode.class);
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TaxonNode parent = taxonNode.getParent();
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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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List<TaxonNode> children = new ArrayList<TaxonNode> ();
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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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374
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changeDeleteTaxon = true;
|
375
|
}
|
376
|
DeleteResult resultNodes = deleteTaxonNodes(children, config);
|
377
|
if (!resultNodes.isOk()){
|
378
|
result.addExceptions(resultNodes.getExceptions());
|
379
|
result.setStatus(resultNodes.getStatus());
|
380
|
}
|
381
|
if (changeDeleteTaxon){
|
382
|
config.getTaxonNodeConfig().setDeleteTaxon(false);
|
383
|
}
|
384
|
|
385
|
} else {
|
386
|
//move the children to the parent
|
387
|
|
388
|
for (TaxonNode child: childNodesList){
|
389
|
parent.addChildNode(child, child.getReference(), child.getMicroReference());
|
390
|
}
|
391
|
|
392
|
}
|
393
|
}
|
394
|
|
395
|
classification = taxonNode.getClassification();
|
396
|
|
397
|
if (classification.getRootNode().equals(taxonNode)){
|
398
|
classification.removeRootNode();
|
399
|
classification = null;
|
400
|
}else if (classification.getChildNodes().contains(taxonNode)){
|
401
|
Taxon taxon = taxonNode.getTaxon();
|
402
|
classification.deleteChildNode(taxonNode);
|
403
|
|
404
|
//node is rootNode
|
405
|
if (taxon != null){
|
406
|
|
407
|
if (config.getTaxonNodeConfig().isDeleteTaxon()){
|
408
|
taxonService.saveOrUpdate(taxon);
|
409
|
saveOrUpdate(taxonNode);
|
410
|
|
411
|
TaxonDeletionConfigurator configNew = new TaxonDeletionConfigurator();
|
412
|
DeleteResult resultTaxon = taxonService.deleteTaxon(taxon.getUuid(), configNew, classification.getUuid());
|
413
|
if (!resultTaxon.isOk()){
|
414
|
result.addExceptions(resultTaxon.getExceptions());
|
415
|
result.setStatus(resultTaxon.getStatus());
|
416
|
}
|
417
|
|
418
|
}
|
419
|
}
|
420
|
classification = null;
|
421
|
|
422
|
} else {
|
423
|
classification = null;
|
424
|
Taxon taxon = taxonNode.getTaxon();
|
425
|
taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);
|
426
|
if (taxon != null){
|
427
|
taxon.removeTaxonNode(taxonNode);
|
428
|
if (config.getTaxonNodeConfig().isDeleteTaxon()){
|
429
|
TaxonDeletionConfigurator configNew = new TaxonDeletionConfigurator();
|
430
|
saveOrUpdate(taxonNode);
|
431
|
taxonService.saveOrUpdate(taxon);
|
432
|
DeleteResult resultTaxon = taxonService.deleteTaxon(taxon.getUuid(), configNew, null);
|
433
|
|
434
|
if (!resultTaxon.isOk()){
|
435
|
result.addExceptions(resultTaxon.getExceptions());
|
436
|
result.setStatus(resultTaxon.getStatus());
|
437
|
}
|
438
|
}
|
439
|
}
|
440
|
|
441
|
}
|
442
|
|
443
|
result.addUpdatedObject(parent);
|
444
|
if(result.getCdmEntity() == null){
|
445
|
result.setCdmEntity(taxonNode);
|
446
|
}
|
447
|
UUID uuid = dao.delete(taxonNode);
|
448
|
logger.debug("Deleted node " +uuid.toString());
|
449
|
|
450
|
}
|
451
|
}
|
452
|
/*if (classification != null){
|
453
|
result.addUpdatedObject(classification);
|
454
|
DeleteResult resultClassification = classService.delete(classification);
|
455
|
if (!resultClassification.isOk()){
|
456
|
result.addExceptions(resultClassification.getExceptions());
|
457
|
result.setStatus(resultClassification.getStatus());
|
458
|
}
|
459
|
}*/
|
460
|
return result;
|
461
|
|
462
|
}
|
463
|
|
464
|
|
465
|
@Override
|
466
|
@Transactional(readOnly = false)
|
467
|
public DeleteResult deleteTaxonNodes(Collection<UUID> nodeUuids, TaxonDeletionConfigurator config) {
|
468
|
List<TaxonNode> nodes = new ArrayList<TaxonNode>();
|
469
|
for(UUID nodeUuid : nodeUuids) {
|
470
|
nodes.add(dao.load(nodeUuid));
|
471
|
}
|
472
|
return deleteTaxonNodes(nodes, config);
|
473
|
}
|
474
|
|
475
|
|
476
|
|
477
|
@Override
|
478
|
@Transactional(readOnly = false)
|
479
|
public DeleteResult deleteTaxonNode(UUID nodeUUID, TaxonDeletionConfigurator config) {
|
480
|
|
481
|
TaxonNode node = HibernateProxyHelper.deproxy(dao.load(nodeUUID), TaxonNode.class);
|
482
|
return deleteTaxonNode(node, config);
|
483
|
}
|
484
|
|
485
|
@Override
|
486
|
@Transactional(readOnly = false)
|
487
|
public DeleteResult deleteTaxonNode(TaxonNode node, TaxonDeletionConfigurator config) {
|
488
|
DeleteResult result = new DeleteResult();
|
489
|
if (node == null){
|
490
|
result.setAbort();
|
491
|
result.addException(new Exception("The TaxonNode was already deleted."));
|
492
|
return result;
|
493
|
}
|
494
|
Taxon taxon = null;
|
495
|
try{
|
496
|
taxon = HibernateProxyHelper.deproxy(node.getTaxon());
|
497
|
}catch(NullPointerException e){
|
498
|
result.setAbort();
|
499
|
result.addException(new Exception("The Taxon was already deleted."));
|
500
|
|
501
|
}
|
502
|
TaxonNode parent = HibernateProxyHelper.deproxy(node.getParent(), TaxonNode.class);
|
503
|
if (config == null){
|
504
|
config = new TaxonDeletionConfigurator();
|
505
|
}
|
506
|
|
507
|
|
508
|
|
509
|
if (config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.MOVE_TO_PARENT)){
|
510
|
Object[] children = node.getChildNodes().toArray();
|
511
|
TaxonNode childNode;
|
512
|
for (Object child: children){
|
513
|
childNode = (TaxonNode) child;
|
514
|
parent.addChildNode(childNode, childNode.getReference(), childNode.getMicroReference());
|
515
|
}
|
516
|
}else{
|
517
|
deleteTaxonNodes(node.getChildNodes(), config);
|
518
|
}
|
519
|
|
520
|
if (taxon != null){
|
521
|
if (config.getTaxonNodeConfig().isDeleteTaxon() && (config.isDeleteInAllClassifications() || taxon.getTaxonNodes().size() == 1)){
|
522
|
result = taxonService.deleteTaxon(taxon.getUuid(), config, node.getClassification().getUuid());
|
523
|
result.addUpdatedObject(parent);
|
524
|
if (result.isOk()){
|
525
|
return result;
|
526
|
}
|
527
|
} else {
|
528
|
result.addUpdatedObject(taxon);
|
529
|
}
|
530
|
}
|
531
|
result.setCdmEntity(node);
|
532
|
boolean success = taxon.removeTaxonNode(node);
|
533
|
dao.save(parent);
|
534
|
taxonService.saveOrUpdate(taxon);
|
535
|
result.addUpdatedObject(parent);
|
536
|
|
537
|
if (success){
|
538
|
result.setStatus(Status.OK);
|
539
|
parent = HibernateProxyHelper.deproxy(parent, TaxonNode.class);
|
540
|
int index = parent.getChildNodes().indexOf(node);
|
541
|
if (index > -1){
|
542
|
parent.removeChild(index);
|
543
|
}
|
544
|
if (!dao.delete(node, config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.DELETE)).equals(null)){
|
545
|
return result;
|
546
|
} else {
|
547
|
result.setError();
|
548
|
return result;
|
549
|
}
|
550
|
}else{
|
551
|
if (dao.findByUuid(node.getUuid()) != null){
|
552
|
result.setError();
|
553
|
result.addException(new Exception("The node can not be removed from the taxon."));
|
554
|
}
|
555
|
return result;
|
556
|
}
|
557
|
|
558
|
|
559
|
|
560
|
}
|
561
|
|
562
|
|
563
|
/* (non-Javadoc)
|
564
|
* @see eu.etaxonomy.cdm.api.service.ITaxonNodeService#listAllNodesForClassification(eu.etaxonomy.cdm.model.taxon.Classification, int, int)
|
565
|
*/
|
566
|
@Override
|
567
|
public List<TaxonNode> listAllNodesForClassification(Classification classification, Integer start, Integer end) {
|
568
|
return dao.getTaxonOfAcceptedTaxaByClassification(classification, start, end);
|
569
|
}
|
570
|
|
571
|
@Override
|
572
|
public int countAllNodesForClassification(Classification classification) {
|
573
|
return dao.countTaxonOfAcceptedTaxaByClassification(classification);
|
574
|
}
|
575
|
|
576
|
@Override
|
577
|
@Transactional
|
578
|
public UpdateResult moveTaxonNode(UUID taxonNodeUuid, UUID targetNodeUuid, int movingType){
|
579
|
TaxonNode taxonNode = HibernateProxyHelper.deproxy(dao.load(taxonNodeUuid), TaxonNode.class);
|
580
|
TaxonNode targetNode = HibernateProxyHelper.deproxy(dao.load(targetNodeUuid), TaxonNode.class);
|
581
|
return moveTaxonNode(taxonNode, targetNode, movingType);
|
582
|
}
|
583
|
|
584
|
@Override
|
585
|
@Transactional
|
586
|
public UpdateResult moveTaxonNode(TaxonNode taxonNode, TaxonNode newParent, int movingType){
|
587
|
UpdateResult result = new UpdateResult();
|
588
|
|
589
|
TaxonNode parentParent = HibernateProxyHelper.deproxy(newParent.getParent(), TaxonNode.class);
|
590
|
|
591
|
Integer sortIndex = -1;
|
592
|
if (movingType == 0){
|
593
|
sortIndex = 0;
|
594
|
}else if (movingType == 1){
|
595
|
sortIndex = newParent.getSortIndex();
|
596
|
newParent = parentParent;
|
597
|
} else if (movingType == 2){
|
598
|
sortIndex = newParent.getSortIndex() +1;
|
599
|
newParent = parentParent;
|
600
|
} else{
|
601
|
result.setAbort();
|
602
|
result.addException(new Exception("The moving type "+ movingType +" is not supported."));
|
603
|
}
|
604
|
result.addUpdatedObject(newParent);
|
605
|
result.addUpdatedObject(taxonNode.getParent());
|
606
|
result.setCdmEntity(taxonNode);
|
607
|
|
608
|
newParent.addChildNode(taxonNode, sortIndex, taxonNode.getReference(), taxonNode.getMicroReference());
|
609
|
|
610
|
dao.saveOrUpdate(newParent);
|
611
|
|
612
|
return result;
|
613
|
}
|
614
|
|
615
|
|
616
|
|
617
|
@Override
|
618
|
@Transactional
|
619
|
public UpdateResult moveTaxonNodes(Set<UUID> taxonNodeUuids, UUID newParentNodeUuid, int movingType){
|
620
|
UpdateResult result = new UpdateResult();
|
621
|
TaxonNode targetNode = dao.load(newParentNodeUuid);
|
622
|
for (UUID taxonNodeUuid: taxonNodeUuids){
|
623
|
TaxonNode taxonNode = dao.load(taxonNodeUuid);
|
624
|
result.includeResult(moveTaxonNode(taxonNode,targetNode, movingType));
|
625
|
}
|
626
|
return result;
|
627
|
}
|
628
|
|
629
|
@Override
|
630
|
public Pager<TaxonNodeAgentRelation> pageTaxonNodeAgentRelations(UUID taxonUuid, UUID classificationUuid,
|
631
|
UUID agentUuid, UUID rankUuid, UUID relTypeUuid, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
|
632
|
|
633
|
|
634
|
List<TaxonNodeAgentRelation> records = null;
|
635
|
|
636
|
long count = dao.countTaxonNodeAgentRelations(taxonUuid, classificationUuid, agentUuid, rankUuid, relTypeUuid);
|
637
|
if(PagerUtils.hasResultsInRange(count, pageIndex, pageSize)) {
|
638
|
records = dao.listTaxonNodeAgentRelations(taxonUuid, classificationUuid,
|
639
|
agentUuid, rankUuid, relTypeUuid, PagerUtils.startFor(pageSize, pageIndex), PagerUtils.limitFor(pageSize), propertyPaths);
|
640
|
}
|
641
|
|
642
|
Pager<TaxonNodeAgentRelation> pager = new DefaultPagerImpl<TaxonNodeAgentRelation>(pageIndex, count, pageSize, records);
|
643
|
return pager;
|
644
|
}
|
645
|
|
646
|
@Override
|
647
|
@Transactional
|
648
|
public UpdateResult createNewTaxonNode(UUID parentNodeUuid, Taxon newTaxon, Reference ref, String microref){
|
649
|
UpdateResult result = new UpdateResult();
|
650
|
|
651
|
UUID taxonUUID = taxonService.saveOrUpdate(newTaxon);
|
652
|
newTaxon = (Taxon) taxonService.load(taxonUUID);
|
653
|
|
654
|
TaxonNode parent = dao.load(parentNodeUuid);
|
655
|
TaxonNode child = null;
|
656
|
try{
|
657
|
child = parent.addChildTaxon(newTaxon, parent.getReference(), parent.getMicroReference());
|
658
|
}catch(Exception e){
|
659
|
result.addException(e);
|
660
|
result.setError();
|
661
|
return result;
|
662
|
}
|
663
|
// child = dao.save(child);
|
664
|
|
665
|
dao.saveOrUpdate(parent);
|
666
|
result.addUpdatedObject(parent);
|
667
|
if (child != null){
|
668
|
result.setCdmEntity(child);
|
669
|
}
|
670
|
return result;
|
671
|
|
672
|
}
|
673
|
@Override
|
674
|
@Transactional
|
675
|
public UpdateResult createNewTaxonNode(UUID parentNodeUuid, UUID taxonUuid, Reference ref, String microref){
|
676
|
UpdateResult result = new UpdateResult();
|
677
|
TaxonNode parent = dao.load(parentNodeUuid);
|
678
|
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
|
679
|
TaxonNode child = null;
|
680
|
try{
|
681
|
child = parent.addChildTaxon(taxon, parent.getReference(), parent.getMicroReference());
|
682
|
}catch(Exception e){
|
683
|
result.addException(e);
|
684
|
result.setError();
|
685
|
return result;
|
686
|
}
|
687
|
// child = dao.save(child);
|
688
|
|
689
|
dao.saveOrUpdate(parent);
|
690
|
result.addUpdatedObject(parent);
|
691
|
if (child != null){
|
692
|
result.setCdmEntity(child);
|
693
|
}
|
694
|
return result;
|
695
|
|
696
|
}
|
697
|
|
698
|
@Override
|
699
|
@Transactional
|
700
|
public UpdateResult addTaxonNodeAgentRelation(UUID taxonNodeUUID, UUID agentUUID, DefinedTerm relationshipType){
|
701
|
UpdateResult result = new UpdateResult();
|
702
|
TaxonNode node = dao.load(taxonNodeUUID);
|
703
|
TeamOrPersonBase agent = (TeamOrPersonBase) agentService.load(agentUUID);
|
704
|
node.addAgentRelation(relationshipType, agent);
|
705
|
try{
|
706
|
dao.merge(node, true);
|
707
|
}catch (Exception e){
|
708
|
result.setError();
|
709
|
result.addException(e);
|
710
|
}
|
711
|
result.setCdmEntity(node);
|
712
|
return result;
|
713
|
}
|
714
|
|
715
|
|
716
|
}
|