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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.Arrays;
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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.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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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.security.core.Authentication;
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import org.springframework.stereotype.Service;
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import org.springframework.transaction.annotation.Transactional;
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import org.springframework.transaction.interceptor.TransactionAspectSupport;
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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.PublishForSubtreeConfigurator;
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import eu.etaxonomy.cdm.api.service.config.SecundumForSubtreeConfigurator;
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import eu.etaxonomy.cdm.api.service.config.SubtreeCloneConfigurator;
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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.dto.CreateTaxonDTO;
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import eu.etaxonomy.cdm.api.service.dto.TaxonDistributionDTO;
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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.AbstractPagerImpl;
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import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
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import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
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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.Language;
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import eu.etaxonomy.cdm.model.common.LanguageString;
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import eu.etaxonomy.cdm.model.common.TreeIndex;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
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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.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.permission.Operation;
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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.ITaxonTreeNode;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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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.TaxonNodeAgentRelation;
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import eu.etaxonomy.cdm.model.taxon.TaxonNodeStatus;
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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.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.persistence.dao.common.Restriction;
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import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
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import eu.etaxonomy.cdm.persistence.dao.reference.IOriginalSourceDao;
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import eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeFilterDao;
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import eu.etaxonomy.cdm.persistence.dto.MergeResult;
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import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
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import eu.etaxonomy.cdm.persistence.permission.ICdmPermissionEvaluator;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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/**
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* @author n.hoffmann
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* @since Apr 9, 2010
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*/
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@Service
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@Transactional(readOnly = true)
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public class TaxonNodeServiceImpl
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extends AnnotatableServiceBase<TaxonNode, ITaxonNodeDao>
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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 IReferenceService referenceService;
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@Autowired
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private IDescriptiveDataSetService dataSetService;
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@Autowired
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private IAgentService agentService;
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@Autowired
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private INameService nameService;
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@Autowired
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private IOriginalSourceDao sourceDao;
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@Autowired
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private ITaxonNodeFilterDao nodeFilterDao;
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@Autowired
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private IReferenceDao referenceDao;
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@Autowired
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private IClassificationDao classificationDao;
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@Autowired
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IProgressMonitorService progressMonitorService;
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@Autowired
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private ICdmPermissionEvaluator permissionEvaluator;
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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 includeUnpublished,
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TaxonNodeSortMode 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, recursive, includeUnpublished, null);
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}else if (includeUnpublished){
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childNodes = new ArrayList<>(taxonNode.getChildNodes());
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}else{
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childNodes = new ArrayList<>();
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for (TaxonNode node:taxonNode.getChildNodes()){
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if (node.getTaxon().isPublish()){
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childNodes.add(node);
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}
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}
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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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@Override
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public List<TaxonNode> listChildrenOf(TaxonNode node, Integer pageSize, Integer pageIndex,
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boolean recursive, boolean includeUnpublished, List<String> propertyPaths){
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return dao.listChildrenOf(node, pageSize, pageIndex, recursive, includeUnpublished, propertyPaths);
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}
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@Override
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public TaxonNodeDto getParentUuidAndTitleCache(ITaxonTreeNode child) {
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UUID uuid = child.getUuid();
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int id = child.getId();
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TaxonNodeDto uuidAndTitleCache = new TaxonNodeDto(uuid, id, null);
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return getParentUuidAndTitleCache(uuidAndTitleCache);
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}
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@Override
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public TaxonNodeDto getParentUuidAndTitleCache(TaxonNodeDto child) {
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return dao.getParentUuidAndTitleCache(child);
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}
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@Override
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public List<TaxonNodeDto> listChildNodesAsTaxonNodeDto(TaxonNodeDto parent) {
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return dao.listChildNodesAsTaxonNodeDto(parent);
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}
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@Override
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public List<TaxonNodeDto> getUuidAndTitleCache(Integer limit, String pattern, UUID classificationUuid) {
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return dao.getUuidAndTitleCache(limit, pattern, classificationUuid, true);
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}
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@Override
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public List<TaxonNodeDto> listChildNodesAsTaxonNodeDto(ITaxonTreeNode parent) {
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List<String> propertyPaths = new ArrayList<>();
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propertyPaths.add("parent");
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parent = dao.load(parent.getId(), propertyPaths);
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TaxonNodeDto uuidAndTitleCache = new TaxonNodeDto(parent);
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return listChildNodesAsTaxonNodeDto(uuidAndTitleCache);
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}
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@Override
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public List<TaxonNodeDto> taxonNodeDtoParentRank(Classification classification, Rank rank, TaxonName name) {
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return dao.getParentTaxonNodeDtoForRank(classification, rank, name);
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}
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@Override
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public List<TaxonNodeDto> taxonNodeDtoParentRank(Classification classification, Rank rank, TaxonBase<?> taxonBase) {
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return dao.getParentTaxonNodeDtoForRank(classification, rank, taxonBase);
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}
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@Override
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public Pager<TaxonNodeDto> pageChildNodesDTOs(UUID taxonNodeUuid, boolean recursive, boolean includeUnpublished,
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boolean doSynonyms, TaxonNodeSortMode 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, includeUnpublished, 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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if (doSynonyms){
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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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}
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List<TaxonNodeDto> dtos = new ArrayList<>(pageSize==null?25:pageSize);
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long totalCount = Long.valueOf(allRecords.size());
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TaxonName parentName = null;
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for(CdmBase item : PagerUtils.pageList(allRecords, pageIndex, pageSize)) {
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if (item.isInstanceOf(TaxonNode.class)){
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dtos.add(new TaxonNodeDto(CdmBase.deproxy(item, TaxonNode.class)));
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}else if (item.isInstanceOf(Synonym.class)){
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Synonym synonym = CdmBase.deproxy(item, 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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return new DefaultPagerImpl<>(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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if (taxonNodeUuid == null){
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return null;
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}
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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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public TaxonNodeDto dto(UUID taxonNodeUuid) {
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if (taxonNodeUuid == null){
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return null;
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}
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TaxonNode taxonNode = dao.load(taxonNodeUuid);
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if (taxonNode != null){
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return new TaxonNodeDto(taxonNode);
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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,
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SynonymType synonymType, Reference citation, String citationMicroReference, boolean setNameInSource) {
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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.find(newAcceptedTaxonNode.getTaxon().getUuid());
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newAcceptedTaxon = HibernateProxyHelper.deproxy(newAcceptedTaxon);
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// Move oldTaxon to newTaxon
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//TaxonName synonymName = oldTaxon.getName();
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TaxonName newSynonymName = CdmBase.deproxy(oldTaxon.getName());
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HomotypicalGroup group = CdmBase.deproxy(newSynonymName.getHomotypicalGroup());
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if (synonymType == null){
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if (newSynonymName.isHomotypic(newAcceptedTaxon.getName())){
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synonymType = SynonymType.HOMOTYPIC_SYNONYM_OF();
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}else{
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synonymType = SynonymType.HETEROTYPIC_SYNONYM_OF();
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}
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}
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//set homotypic group
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TaxonName newAcceptedTaxonName = HibernateProxyHelper.deproxy(newAcceptedTaxon.getName(), TaxonName.class);
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newAcceptedTaxon.setName(newAcceptedTaxonName);
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// Move Synonym Relations to new Taxon
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newAcceptedTaxon.addSynonymName(newSynonymName, citation, citationMicroReference, synonymType);
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// Move Synonyms 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 (synonymType.equals(SynonymType.HOMOTYPIC_SYNONYM_OF())){
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synonymsInHomotypicalGroup = oldTaxon.getSynonymsInGroup(group);
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}
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332
|
Set<Synonym> syns = new HashSet<>(oldTaxon.getSynonyms());
|
|
333
|
for(Synonym synonym : syns){
|
|
334
|
SynonymType srt;
|
|
335
|
if(synonym.getHomotypicGroup()!= null
|
|
336
|
&& synonym.getHomotypicGroup().equals(newAcceptedTaxonName.getHomotypicalGroup())) {
|
|
337
|
srt = SynonymType.HOMOTYPIC_SYNONYM_OF();
|
|
338
|
} else if(synonym.getType() != null && synonym.getType().equals(SynonymType.HOMOTYPIC_SYNONYM_OF())) {
|
|
339
|
if (synonymType.equals(SynonymType.HOMOTYPIC_SYNONYM_OF())){
|
|
340
|
srt = SynonymType.HOMOTYPIC_SYNONYM_OF();
|
|
341
|
} else{
|
|
342
|
srt = SynonymType.HETEROTYPIC_SYNONYM_OF();
|
|
343
|
}
|
|
344
|
} else {
|
|
345
|
if (synonymsInHomotypicalGroup != null && synonymsInHomotypicalGroup.contains(synonym)){
|
|
346
|
srt = SynonymType.HOMOTYPIC_SYNONYM_OF();
|
|
347
|
}else{
|
|
348
|
srt = synonym.getType();
|
|
349
|
}
|
|
350
|
|
|
351
|
}
|
|
352
|
|
|
353
|
newAcceptedTaxon.addSynonym(synonym, srt);
|
|
354
|
|
|
355
|
|
|
356
|
/*if (synonymsInHomotypicalGroup.contains(synRelation.getSynonym()) && srt.equals(SynonymType.HETEROTYPIC_SYNONYM_OF())){
|
|
357
|
homotypicalGroupAcceptedTaxon.addTypifiedName(synRelation.getSynonym().getName());
|
|
358
|
}*/
|
|
359
|
|
|
360
|
}
|
|
361
|
|
|
362
|
|
|
363
|
// CHILD NODES
|
|
364
|
if(oldTaxonNode.getChildNodes() != null && oldTaxonNode.getChildNodes().size() != 0){
|
|
365
|
List<TaxonNode> childNodes = new ArrayList<>();
|
|
366
|
for (TaxonNode childNode : oldTaxonNode.getChildNodes()){
|
|
367
|
childNodes.add(childNode);
|
|
368
|
}
|
|
369
|
for(TaxonNode childNode :childNodes){
|
|
370
|
newAcceptedTaxonNode.addChildNode(childNode, childNode.getReference(), childNode.getMicroReference()); // childNode.getSynonymToBeUsed()
|
|
371
|
}
|
|
372
|
}
|
|
373
|
|
|
374
|
//Move Taxon RelationShips to new Taxon
|
|
375
|
for(TaxonRelationship taxonRelationship : oldTaxon.getTaxonRelations()){
|
|
376
|
Taxon fromTaxon = HibernateProxyHelper.deproxy(taxonRelationship.getFromTaxon());
|
|
377
|
Taxon toTaxon = HibernateProxyHelper.deproxy(taxonRelationship.getToTaxon());
|
|
378
|
if (fromTaxon == oldTaxon){
|
|
379
|
newAcceptedTaxon.addTaxonRelation(taxonRelationship.getToTaxon(), taxonRelationship.getType(),
|
|
380
|
taxonRelationship.getCitation(), taxonRelationship.getCitationMicroReference());
|
|
381
|
|
|
382
|
}else if(toTaxon == oldTaxon){
|
|
383
|
fromTaxon.addTaxonRelation(newAcceptedTaxon, taxonRelationship.getType(),
|
|
384
|
taxonRelationship.getCitation(), taxonRelationship.getCitationMicroReference());
|
|
385
|
taxonService.saveOrUpdate(fromTaxon);
|
|
386
|
|
|
387
|
}else{
|
|
388
|
logger.warn("Taxon is not part of its own Taxonrelationship");
|
|
389
|
}
|
|
390
|
// Remove old relationships
|
|
391
|
|
|
392
|
fromTaxon.removeTaxonRelation(taxonRelationship);
|
|
393
|
toTaxon.removeTaxonRelation(taxonRelationship);
|
|
394
|
taxonRelationship.setToTaxon(null);
|
|
395
|
taxonRelationship.setFromTaxon(null);
|
|
396
|
}
|
|
397
|
|
|
398
|
//Move descriptions to new taxon
|
|
399
|
List<TaxonDescription> descriptions = new ArrayList<TaxonDescription>( oldTaxon.getDescriptions()); //to avoid concurrent modification errors (newAcceptedTaxon.addDescription() modifies also oldtaxon.descritpions())
|
|
400
|
for(TaxonDescription description : descriptions){
|
|
401
|
String message = "Description copied from former accepted taxon: %s (Old title: %s)";
|
|
402
|
message = String.format(message, oldTaxon.getTitleCache(), description.getTitleCache());
|
|
403
|
description.setTitleCache(message, true);
|
|
404
|
if (setNameInSource) {
|
|
405
|
for (DescriptionElementBase element: description.getElements()){
|
|
406
|
for (DescriptionElementSource source: element.getSources()){
|
|
407
|
if (source.getNameUsedInSource() == null){
|
|
408
|
source.setNameUsedInSource(newSynonymName);
|
|
409
|
}
|
|
410
|
}
|
|
411
|
}
|
|
412
|
}
|
|
413
|
//oldTaxon.removeDescription(description, false);
|
|
414
|
newAcceptedTaxon.addDescription(description);
|
|
415
|
}
|
|
416
|
oldTaxon.clearDescriptions();
|
|
417
|
|
|
418
|
taxonService.saveOrUpdate(newAcceptedTaxon);
|
|
419
|
|
|
420
|
taxonService.saveOrUpdate(oldTaxon);
|
|
421
|
taxonService.getSession().flush();
|
|
422
|
|
|
423
|
TaxonDeletionConfigurator conf = new TaxonDeletionConfigurator();
|
|
424
|
conf.setDeleteSynonymsIfPossible(false);
|
|
425
|
conf.setDeleteNameIfPossible(false);
|
|
426
|
DeleteResult result = taxonService.isDeletable(oldTaxon.getUuid(), conf);
|
|
427
|
|
|
428
|
|
|
429
|
if (result.isOk()){
|
|
430
|
result = taxonService.deleteTaxon(oldTaxon.getUuid(), conf, classification.getUuid());
|
|
431
|
|
|
432
|
}else{
|
|
433
|
result.setStatus(Status.OK);
|
|
434
|
TaxonNodeDeletionConfigurator config = new TaxonNodeDeletionConfigurator();
|
|
435
|
config.setDeleteElement(false);
|
|
436
|
conf.setTaxonNodeConfig(config);
|
|
437
|
result.includeResult(deleteTaxonNode(oldTaxonNode, conf));
|
|
438
|
}
|
|
439
|
|
|
440
|
result.addUpdatedObject(newAcceptedTaxon);
|
|
441
|
|
|
442
|
|
|
443
|
//oldTaxonNode.delete();
|
|
444
|
return result;
|
|
445
|
}
|
|
446
|
@Override
|
|
447
|
@Transactional(readOnly = false)
|
|
448
|
public UpdateResult makeTaxonNodeSynonymsOfAnotherTaxonNode( Set<UUID> oldTaxonNodeUuids,
|
|
449
|
UUID newAcceptedTaxonNodeUUIDs,
|
|
450
|
SynonymType synonymType,
|
|
451
|
Reference citation,
|
|
452
|
String citationMicroReference,
|
|
453
|
boolean setNameInSource) {
|
|
454
|
UpdateResult result = new UpdateResult();
|
|
455
|
for (UUID nodeUuid: oldTaxonNodeUuids) {
|
|
456
|
result.includeResult(makeTaxonNodeASynonymOfAnotherTaxonNode(nodeUuid, newAcceptedTaxonNodeUUIDs, synonymType, citation, citationMicroReference, setNameInSource));
|
|
457
|
}
|
|
458
|
return result;
|
|
459
|
}
|
|
460
|
|
|
461
|
@Override
|
|
462
|
@Transactional(readOnly = false)
|
|
463
|
public UpdateResult makeTaxonNodeASynonymOfAnotherTaxonNode(UUID oldTaxonNodeUuid,
|
|
464
|
UUID newAcceptedTaxonNodeUUID,
|
|
465
|
SynonymType synonymType,
|
|
466
|
Reference citation,
|
|
467
|
String citationMicroReference,
|
|
468
|
boolean setNameInSource) {
|
|
469
|
|
|
470
|
TaxonNode oldTaxonNode = dao.load(oldTaxonNodeUuid);
|
|
471
|
TaxonNode oldTaxonParentNode = oldTaxonNode.getParent();
|
|
472
|
TaxonNode newTaxonNode = dao.load(newAcceptedTaxonNodeUUID);
|
|
473
|
|
|
474
|
UpdateResult result = makeTaxonNodeASynonymOfAnotherTaxonNode(oldTaxonNode,
|
|
475
|
newTaxonNode,
|
|
476
|
synonymType,
|
|
477
|
citation,
|
|
478
|
citationMicroReference, setNameInSource);
|
|
479
|
result.addUpdatedCdmId(new CdmEntityIdentifier(oldTaxonParentNode.getId(), TaxonNode.class));
|
|
480
|
result.addUpdatedCdmId(new CdmEntityIdentifier(newTaxonNode.getId(), TaxonNode.class));
|
|
481
|
result.setCdmEntity(oldTaxonParentNode);
|
|
482
|
return result;
|
|
483
|
}
|
|
484
|
|
|
485
|
@Override
|
|
486
|
@Transactional(readOnly = false)
|
|
487
|
public DeleteResult deleteTaxonNodes(List<TaxonNode> list, TaxonDeletionConfigurator config) {
|
|
488
|
|
|
489
|
if (config == null){
|
|
490
|
config = new TaxonDeletionConfigurator();
|
|
491
|
}
|
|
492
|
DeleteResult result = new DeleteResult();
|
|
493
|
Classification classification = null;
|
|
494
|
List<TaxonNode> taxonNodes = new ArrayList<>(list);
|
|
495
|
|
|
496
|
for (TaxonNode treeNode:taxonNodes){
|
|
497
|
if (treeNode != null){
|
|
498
|
|
|
499
|
TaxonNode taxonNode;
|
|
500
|
taxonNode = CdmBase.deproxy(treeNode);
|
|
501
|
TaxonNode parent = taxonNode.getParent();
|
|
502
|
//check whether the node has children or the children are already deleted
|
|
503
|
if(taxonNode.hasChildNodes()) {
|
|
504
|
List<TaxonNode> children = new ArrayList<> ();
|
|
505
|
List<TaxonNode> childNodesList = taxonNode.getChildNodes();
|
|
506
|
children.addAll(childNodesList);
|
|
507
|
//To avoid NPE when child is also in list of taxonNodes, remove it from the list
|
|
508
|
Iterator<TaxonNode> it = taxonNodes.iterator();
|
|
509
|
for (TaxonNode child: children) {
|
|
510
|
while (it.hasNext()) {
|
|
511
|
if (it.next().equals(child)) {
|
|
512
|
it.remove();
|
|
513
|
}
|
|
514
|
}
|
|
515
|
}
|
|
516
|
int compare = config.getTaxonNodeConfig().getChildHandling().compareTo(ChildHandling.DELETE);
|
|
517
|
boolean childHandling = (compare == 0)? true: false;
|
|
518
|
if (childHandling){
|
|
519
|
boolean changeDeleteTaxon = false;
|
|
520
|
if (!config.getTaxonNodeConfig().isDeleteTaxon()){
|
|
521
|
config.getTaxonNodeConfig().setDeleteTaxon(true);
|
|
522
|
changeDeleteTaxon = true;
|
|
523
|
}
|
|
524
|
DeleteResult resultNodes = deleteTaxonNodes(children, config);
|
|
525
|
if (!resultNodes.isOk()){
|
|
526
|
result.addExceptions(resultNodes.getExceptions());
|
|
527
|
result.setStatus(resultNodes.getStatus());
|
|
528
|
}
|
|
529
|
if (changeDeleteTaxon){
|
|
530
|
config.getTaxonNodeConfig().setDeleteTaxon(false);
|
|
531
|
}
|
|
532
|
|
|
533
|
} else {
|
|
534
|
//move the children to the parent
|
|
535
|
|
|
536
|
for (TaxonNode child: childNodesList){
|
|
537
|
parent.addChildNode(child, child.getReference(), child.getMicroReference());
|
|
538
|
}
|
|
539
|
|
|
540
|
}
|
|
541
|
}
|
|
542
|
|
|
543
|
classification = taxonNode.getClassification();
|
|
544
|
|
|
545
|
if (classification.getRootNode().equals(taxonNode)){
|
|
546
|
classification.removeRootNode();
|
|
547
|
classification = null;
|
|
548
|
}else if (classification.getChildNodes().contains(taxonNode)){
|
|
549
|
Taxon taxon = taxonNode.getTaxon();
|
|
550
|
classification.deleteChildNode(taxonNode);
|
|
551
|
|
|
552
|
//node is rootNode
|
|
553
|
if (taxon != null){
|
|
554
|
|
|
555
|
if (config.getTaxonNodeConfig().isDeleteTaxon()){
|
|
556
|
taxonService.saveOrUpdate(taxon);
|
|
557
|
saveOrUpdate(taxonNode);
|
|
558
|
|
|
559
|
TaxonDeletionConfigurator configNew = new TaxonDeletionConfigurator();
|
|
560
|
configNew.setClassificationUuid(classification.getUuid());
|
|
561
|
DeleteResult resultTaxon = taxonService.deleteTaxon(taxon.getUuid(), configNew, classification.getUuid());
|
|
562
|
if (!resultTaxon.isOk()){
|
|
563
|
result.addExceptions(resultTaxon.getExceptions());
|
|
564
|
result.setStatus(resultTaxon.getStatus());
|
|
565
|
}
|
|
566
|
|
|
567
|
}
|
|
568
|
}
|
|
569
|
classification = null;
|
|
570
|
|
|
571
|
} else {
|
|
572
|
//classification = null;
|
|
573
|
Taxon taxon = taxonNode.getTaxon();
|
|
574
|
taxon = CdmBase.deproxy(taxon);
|
|
575
|
if (taxon != null){
|
|
576
|
taxon.removeTaxonNode(taxonNode);
|
|
577
|
if (config.getTaxonNodeConfig().isDeleteTaxon()){
|
|
578
|
TaxonDeletionConfigurator configNew = new TaxonDeletionConfigurator();
|
|
579
|
saveOrUpdate(taxonNode);
|
|
580
|
taxonService.saveOrUpdate(taxon);
|
|
581
|
DeleteResult resultTaxon = taxonService.deleteTaxon(taxon.getUuid(), configNew, classification.getUuid());
|
|
582
|
|
|
583
|
if (!resultTaxon.isOk()){
|
|
584
|
result.addExceptions(resultTaxon.getExceptions());
|
|
585
|
result.setStatus(resultTaxon.getStatus());
|
|
586
|
}
|
|
587
|
}
|
|
588
|
}
|
|
589
|
|
|
590
|
}
|
|
591
|
|
|
592
|
result.addUpdatedObject(parent);
|
|
593
|
if(result.getCdmEntity() == null){
|
|
594
|
result.setCdmEntity(taxonNode);
|
|
595
|
}
|
|
596
|
UUID uuid = dao.delete(taxonNode);
|
|
597
|
logger.debug("Deleted node " +uuid.toString());
|
|
598
|
|
|
599
|
}
|
|
600
|
}
|
|
601
|
/*if (classification != null){
|
|
602
|
result.addUpdatedObject(classification);
|
|
603
|
DeleteResult resultClassification = classService.delete(classification);
|
|
604
|
if (!resultClassification.isOk()){
|
|
605
|
result.addExceptions(resultClassification.getExceptions());
|
|
606
|
result.setStatus(resultClassification.getStatus());
|
|
607
|
}
|
|
608
|
}*/
|
|
609
|
return result;
|
|
610
|
}
|
|
611
|
|
|
612
|
|
|
613
|
@Override
|
|
614
|
@Transactional(readOnly = false)
|
|
615
|
public DeleteResult deleteTaxonNodes(Collection<UUID> nodeUuids, TaxonDeletionConfigurator config) {
|
|
616
|
List<TaxonNode> nodes = new ArrayList<>();
|
|
617
|
for(UUID nodeUuid : nodeUuids) {
|
|
618
|
nodes.add(dao.load(nodeUuid));
|
|
619
|
}
|
|
620
|
return deleteTaxonNodes(nodes, config);
|
|
621
|
}
|
|
622
|
|
|
623
|
|
|
624
|
@Override
|
|
625
|
@Transactional(readOnly = false)
|
|
626
|
public DeleteResult deleteTaxonNode(UUID nodeUUID, TaxonDeletionConfigurator config) {
|
|
627
|
|
|
628
|
TaxonNode node = CdmBase.deproxy(dao.load(nodeUUID));
|
|
629
|
return deleteTaxonNode(node, config);
|
|
630
|
}
|
|
631
|
|
|
632
|
@Override
|
|
633
|
@Transactional(readOnly = false)
|
|
634
|
public DeleteResult deleteTaxonNode(TaxonNode node, TaxonDeletionConfigurator config) {
|
|
635
|
DeleteResult result = new DeleteResult();
|
|
636
|
if (node == null){
|
|
637
|
result.setAbort();
|
|
638
|
result.addException(new Exception("The TaxonNode was already deleted."));
|
|
639
|
return result;
|
|
640
|
}
|
|
641
|
Taxon taxon = null;
|
|
642
|
try{
|
|
643
|
taxon = HibernateProxyHelper.deproxy(node.getTaxon());
|
|
644
|
}catch(NullPointerException e){
|
|
645
|
result.setAbort();
|
|
646
|
result.addException(new Exception("The Taxon was already deleted."));
|
|
647
|
|
|
648
|
}
|
|
649
|
|
|
650
|
|
|
651
|
TaxonNode parent = HibernateProxyHelper.deproxy(node.getParent(), TaxonNode.class);
|
|
652
|
if (config == null){
|
|
653
|
config = new TaxonDeletionConfigurator();
|
|
654
|
}
|
|
655
|
|
|
656
|
|
|
657
|
if (config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.MOVE_TO_PARENT)){
|
|
658
|
Object[] children = node.getChildNodes().toArray();
|
|
659
|
TaxonNode childNode;
|
|
660
|
for (Object child: children){
|
|
661
|
childNode = (TaxonNode) child;
|
|
662
|
parent.addChildNode(childNode, childNode.getReference(), childNode.getMicroReference());
|
|
663
|
|
|
664
|
}
|
|
665
|
}else{
|
|
666
|
result.includeResult(deleteTaxonNodes(node.getChildNodes(), config));
|
|
667
|
}
|
|
668
|
|
|
669
|
//remove node from DescriptiveDataSet
|
|
670
|
commonService.getReferencingObjects(node).stream()
|
|
671
|
.filter(obj->obj instanceof DescriptiveDataSet)
|
|
672
|
.forEach(dataSet->{
|
|
673
|
((DescriptiveDataSet)dataSet).removeTaxonSubtree(node);
|
|
674
|
dataSetService.saveOrUpdate((DescriptiveDataSet) dataSet);
|
|
675
|
});
|
|
676
|
|
|
677
|
if (taxon != null){
|
|
678
|
if (config.getTaxonNodeConfig().isDeleteTaxon() && (config.isDeleteInAllClassifications() || taxon.getTaxonNodes().size() == 1)){
|
|
679
|
result = taxonService.deleteTaxon(taxon.getUuid(), config, node.getClassification().getUuid());
|
|
680
|
result.addUpdatedObject(parent);
|
|
681
|
if (result.isOk()){
|
|
682
|
return result;
|
|
683
|
}
|
|
684
|
} else {
|
|
685
|
result.addUpdatedObject(taxon);
|
|
686
|
}
|
|
687
|
}
|
|
688
|
result.setCdmEntity(node);
|
|
689
|
boolean success = true;
|
|
690
|
if (taxon != null){
|
|
691
|
success = taxon.removeTaxonNode(node);
|
|
692
|
taxonService.saveOrUpdate(taxon);
|
|
693
|
}
|
|
694
|
dao.saveOrUpdate(parent);
|
|
695
|
|
|
696
|
result.addUpdatedObject(parent);
|
|
697
|
|
|
698
|
if (success){
|
|
699
|
result.setStatus(Status.OK);
|
|
700
|
if (parent != null){
|
|
701
|
parent = HibernateProxyHelper.deproxy(parent, TaxonNode.class);
|
|
702
|
int index = parent.getChildNodes().indexOf(node);
|
|
703
|
if (index > -1){
|
|
704
|
parent.removeChild(index);
|
|
705
|
}
|
|
706
|
}
|
|
707
|
if (!dao.delete(node, config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.DELETE)).equals(null)){
|
|
708
|
result.getUpdatedObjects().remove(node);
|
|
709
|
result.addDeletedObject(node);
|
|
710
|
return result;
|
|
711
|
} else {
|
|
712
|
result.setError();
|
|
713
|
return result;
|
|
714
|
}
|
|
715
|
}else{
|
|
716
|
if (dao.findByUuid(node.getUuid()) != null){
|
|
717
|
result.setError();
|
|
718
|
result.addException(new Exception("The node can not be removed from the taxon."));
|
|
719
|
}
|
|
720
|
return result;
|
|
721
|
}
|
|
722
|
}
|
|
723
|
|
|
724
|
|
|
725
|
@Override
|
|
726
|
public List<TaxonNode> listAllNodesForClassification(Classification classification, Integer start, Integer end) {
|
|
727
|
return dao.getTaxonOfAcceptedTaxaByClassification(classification, start, end);
|
|
728
|
}
|
|
729
|
|
|
730
|
@Override
|
|
731
|
public int countAllNodesForClassification(Classification classification) {
|
|
732
|
return dao.countTaxonOfAcceptedTaxaByClassification(classification);
|
|
733
|
}
|
|
734
|
|
|
735
|
@Override
|
|
736
|
@Transactional
|
|
737
|
public UpdateResult moveTaxonNode(UUID taxonNodeUuid, UUID targetNodeUuid, int movingType){
|
|
738
|
TaxonNode taxonNode = HibernateProxyHelper.deproxy(dao.load(taxonNodeUuid));
|
|
739
|
TaxonNode targetNode = HibernateProxyHelper.deproxy(dao.load(targetNodeUuid));
|
|
740
|
UpdateResult result = moveTaxonNode(taxonNode, targetNode, movingType);
|
|
741
|
return result;
|
|
742
|
}
|
|
743
|
|
|
744
|
@Override
|
|
745
|
@Transactional
|
|
746
|
public UpdateResult moveTaxonNode(TaxonNode taxonNode, TaxonNode newParent, int movingType){
|
|
747
|
UpdateResult result = new UpdateResult();
|
|
748
|
|
|
749
|
TaxonNode parentParent = HibernateProxyHelper.deproxy(newParent.getParent());
|
|
750
|
Integer sortIndex = -1;
|
|
751
|
if (movingType == 0){
|
|
752
|
sortIndex = 0;
|
|
753
|
}else if (movingType == 1){
|
|
754
|
sortIndex = newParent.getSortIndex();
|
|
755
|
newParent = parentParent;
|
|
756
|
} else if (movingType == 2){
|
|
757
|
sortIndex = newParent.getSortIndex() +1;
|
|
758
|
newParent = parentParent;
|
|
759
|
} else{
|
|
760
|
result.setAbort();
|
|
761
|
result.addException(new Exception("The moving type "+ movingType +" is not supported."));
|
|
762
|
}
|
|
763
|
|
|
764
|
taxonNode = newParent.addChildNode(taxonNode, sortIndex, taxonNode.getReference(), taxonNode.getMicroReference());
|
|
765
|
result.addUpdatedObject(taxonNode);
|
|
766
|
|
|
767
|
return result;
|
|
768
|
}
|
|
769
|
|
|
770
|
@Override
|
|
771
|
@Transactional
|
|
772
|
public UpdateResult moveTaxonNodes(Set<UUID> taxonNodeUuids, UUID newParentNodeUuid, int movingType, IProgressMonitor monitor){
|
|
773
|
|
|
774
|
if (monitor == null){
|
|
775
|
monitor = DefaultProgressMonitor.NewInstance();
|
|
776
|
}
|
|
777
|
UpdateResult result = new UpdateResult();
|
|
778
|
|
|
779
|
TaxonNode targetNode = dao.load(newParentNodeUuid);
|
|
780
|
List<TaxonNode> nodes = dao.list(taxonNodeUuids, null, null, null, null);
|
|
781
|
|
|
782
|
monitor.beginTask("Move Taxonnodes", nodes.size()*2);
|
|
783
|
monitor.subTask("move taxon nodes");
|
|
784
|
for (TaxonNode node: nodes){
|
|
785
|
if (!monitor.isCanceled()){
|
|
786
|
if (!nodes.contains(node.getParent())){
|
|
787
|
result.includeResult(moveTaxonNode(node,targetNode, movingType));
|
|
788
|
}
|
|
789
|
monitor.worked(1);
|
|
790
|
}else{
|
|
791
|
monitor.done();
|
|
792
|
result.setAbort();
|
|
793
|
break;
|
|
794
|
}
|
|
795
|
}
|
|
796
|
if (!monitor.isCanceled()){
|
|
797
|
monitor.subTask("saving and reindex");
|
|
798
|
dao.saveOrUpdateAll(nodes);
|
|
799
|
}else{
|
|
800
|
TransactionAspectSupport.currentTransactionStatus().setRollbackOnly();
|
|
801
|
}
|
|
802
|
|
|
803
|
monitor.done();
|
|
804
|
return result;
|
|
805
|
}
|
|
806
|
|
|
807
|
@Override
|
|
808
|
public Pager<TaxonNodeAgentRelation> pageTaxonNodeAgentRelations(UUID taxonUuid, UUID classificationUuid,
|
|
809
|
UUID agentUuid, UUID rankUuid, UUID relTypeUuid, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
|
|
810
|
|
|
811
|
|
|
812
|
List<TaxonNodeAgentRelation> records = null;
|
|
813
|
|
|
814
|
long count = dao.countTaxonNodeAgentRelations(taxonUuid, classificationUuid, agentUuid, rankUuid, relTypeUuid);
|
|
815
|
if(PagerUtils.hasResultsInRange(count, pageIndex, pageSize)) {
|
|
816
|
records = dao.listTaxonNodeAgentRelations(taxonUuid, classificationUuid,
|
|
817
|
agentUuid, rankUuid, relTypeUuid, PagerUtils.startFor(pageSize, pageIndex), PagerUtils.limitFor(pageSize), propertyPaths);
|
|
818
|
}
|
|
819
|
|
|
820
|
Pager<TaxonNodeAgentRelation> pager = new DefaultPagerImpl<>(pageIndex, count, pageSize, records);
|
|
821
|
return pager;
|
|
822
|
}
|
|
823
|
|
|
824
|
@Override
|
|
825
|
@Transactional
|
|
826
|
public UpdateResult createNewTaxonNode(UUID parentNodeUuid, CreateTaxonDTO taxonDto,
|
|
827
|
DescriptionElementSource source, String microref,
|
|
828
|
TaxonNodeStatus status, Map<Language,LanguageString> statusNote){
|
|
829
|
|
|
830
|
UpdateResult result = new UpdateResult();
|
|
831
|
TaxonName name = null;
|
|
832
|
if (taxonDto.getNameUuid() != null){
|
|
833
|
name = nameService.load(taxonDto.getNameUuid());
|
|
834
|
|
|
835
|
}else{
|
|
836
|
UpdateResult tmpResult = nameService.parseName(taxonDto.getTaxonNameString(),
|
|
837
|
taxonDto.getCode(), taxonDto.getPreferredRank(), true);
|
|
838
|
result.addUpdatedObjects(tmpResult.getUpdatedObjects());
|
|
839
|
name = (TaxonName)tmpResult.getCdmEntity();
|
|
840
|
}
|
|
841
|
Reference sec = null;
|
|
842
|
if (taxonDto.getSecUuid() != null ){
|
|
843
|
sec = referenceService.load(taxonDto.getSecUuid());
|
|
844
|
}
|
|
845
|
if (!name.isPersited()){
|
|
846
|
for (HybridRelationship rel : name.getHybridChildRelations()){
|
|
847
|
if (!rel.getHybridName().isPersited()) {
|
|
848
|
nameService.save(rel.getHybridName());
|
|
849
|
}
|
|
850
|
if (!rel.getParentName().isPersited()) {
|
|
851
|
nameService.save(rel.getParentName());
|
|
852
|
}
|
|
853
|
}
|
|
854
|
}
|
|
855
|
|
|
856
|
Taxon newTaxon = Taxon.NewInstance(name, sec);
|
|
857
|
newTaxon.setPublish(taxonDto.isPublish());
|
|
858
|
// UUID taxonUuid = taxonService.saveOrUpdate(newTaxon);
|
|
859
|
// newTaxon = (Taxon) taxonService.load(taxonUuid);
|
|
860
|
|
|
861
|
TaxonNode parent = dao.load(parentNodeUuid);
|
|
862
|
TaxonNode child = null;
|
|
863
|
Reference ref = null;
|
|
864
|
if (source != null){
|
|
865
|
if (source.isPersited()){
|
|
866
|
source = (DescriptionElementSource) sourceDao.load(source.getUuid());
|
|
867
|
}
|
|
868
|
if (source.getCitation() != null){
|
|
869
|
source.setCitation(referenceService.load(source.getCitation().getUuid()));
|
|
870
|
}
|
|
871
|
if (source.getNameUsedInSource() !=null){
|
|
872
|
source.setNameUsedInSource(nameService.load(source.getNameUsedInSource().getUuid()));
|
|
873
|
}
|
|
874
|
}
|
|
875
|
|
|
876
|
try{
|
|
877
|
child = parent.addChildTaxon(newTaxon, source);
|
|
878
|
child.setStatus(status);
|
|
879
|
|
|
880
|
if (statusNote != null){
|
|
881
|
child.getStatusNote().putAll(statusNote);
|
|
882
|
}
|
|
883
|
|
|
884
|
}catch(Exception e){
|
|
885
|
result.addException(e);
|
|
886
|
result.setError();
|
|
887
|
return result;
|
|
888
|
}
|
|
889
|
child = dao.save(child);
|
|
890
|
|
|
891
|
result.addUpdatedObject(parent);
|
|
892
|
if (child != null){
|
|
893
|
result.setCdmEntity(child);
|
|
894
|
}
|
|
895
|
return result;
|
|
896
|
}
|
|
897
|
|
|
898
|
@Override
|
|
899
|
@Transactional
|
|
900
|
public UpdateResult saveNewTaxonNode(TaxonNode newTaxonNode){
|
|
901
|
UpdateResult result = new UpdateResult();
|
|
902
|
UUID parentUuid = newTaxonNode.getParent().getUuid();
|
|
903
|
Taxon taxon = null;
|
|
904
|
|
|
905
|
if (newTaxonNode.getTaxon().isPersited()){
|
|
906
|
taxon = (Taxon)taxonService.load(newTaxonNode.getTaxon().getUuid());
|
|
907
|
}else if (newTaxonNode.getTaxon().getName().isPersited()){
|
|
908
|
TaxonName name = nameService.load(newTaxonNode.getTaxon().getName().getUuid());
|
|
909
|
taxon = newTaxonNode.getTaxon();
|
|
910
|
taxon.setName(name);
|
|
911
|
}else{
|
|
912
|
//taxon and name is not persisted, persist possible related names
|
|
913
|
for (HybridRelationship rel : newTaxonNode.getTaxon().getName().getHybridChildRelations()){
|
|
914
|
if (!rel.getHybridName().isPersited()) {
|
|
915
|
nameService.save(rel.getHybridName());
|
|
916
|
}
|
|
917
|
if (!rel.getParentName().isPersited()) {
|
|
918
|
nameService.save(rel.getParentName());
|
|
919
|
}
|
|
920
|
}
|
|
921
|
}
|
|
922
|
if (taxon == null){
|
|
923
|
taxon = newTaxonNode.getTaxon();
|
|
924
|
}
|
|
925
|
taxon.removeTaxonNode(newTaxonNode);
|
|
926
|
|
|
927
|
if (taxon.getSec() != null && taxon.getSec().isPersited()){
|
|
928
|
Reference sec = referenceService.load(taxon.getSec().getUuid());
|
|
929
|
taxon.setSec(sec);
|
|
930
|
}
|
|
931
|
if (!taxon.isPersited()){
|
|
932
|
MergeResult<TaxonBase> mergeResult = taxonService.merge(taxon, true);
|
|
933
|
taxon = (Taxon) mergeResult.getMergedEntity();
|
|
934
|
|
|
935
|
}
|
|
936
|
|
|
937
|
TaxonNode parent = dao.load(parentUuid);
|
|
938
|
TaxonNode child = null;
|
|
939
|
try{
|
|
940
|
child = parent.addChildTaxon(taxon, newTaxonNode.getReference(), newTaxonNode.getMicroReference());
|
|
941
|
}catch(Exception e){
|
|
942
|
result.addException(e);
|
|
943
|
result.setError();
|
|
944
|
return result;
|
|
945
|
}
|
|
946
|
|
|
947
|
//TODO can't we work with clone method here?
|
|
948
|
child.setStatus(newTaxonNode.getStatus());
|
|
949
|
for (TaxonNodeAgentRelation agentRel :newTaxonNode.getAgentRelations()){
|
|
950
|
child.addAgentRelation(agentRel.getType(), agentRel.getAgent());
|
|
951
|
}
|
|
952
|
for (Entry<Language, LanguageString> entry: newTaxonNode.getStatusNote().entrySet()){
|
|
953
|
child.putStatusNote(entry.getKey(), entry.getValue().getText());
|
|
954
|
}
|
|
955
|
|
|
956
|
newTaxonNode = null;
|
|
957
|
MergeResult<TaxonNode> mergeNode = dao.merge(child,true);
|
|
958
|
child = mergeNode.getMergedEntity();
|
|
959
|
result.addUpdatedObject(child.getParent());
|
|
960
|
result.setCdmEntity(child);
|
|
961
|
return result;
|
|
962
|
}
|
|
963
|
|
|
964
|
@Override
|
|
965
|
@Transactional
|
|
966
|
public UpdateResult createNewTaxonNode(UUID parentNodeUuid, UUID taxonUuid, UUID refUuid, String microref){
|
|
967
|
UpdateResult result = new UpdateResult();
|
|
968
|
TaxonNode parent = dao.load(parentNodeUuid);
|
|
969
|
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
|
|
970
|
TaxonNode child = null;
|
|
971
|
try{
|
|
972
|
child = parent.addChildTaxon(taxon, parent.getReference(), parent.getMicroReference());
|
|
973
|
}catch(Exception e){
|
|
974
|
result.addException(e);
|
|
975
|
result.setError();
|
|
976
|
return result;
|
|
977
|
}
|
|
978
|
|
|
979
|
result.addUpdatedObject(parent);
|
|
980
|
if (child != null){
|
|
981
|
result.setCdmEntity(child);
|
|
982
|
}
|
|
983
|
return result;
|
|
984
|
}
|
|
985
|
|
|
986
|
@Override
|
|
987
|
@Transactional
|
|
988
|
public UpdateResult addTaxonNodeAgentRelation(UUID taxonNodeUUID, UUID agentUUID, DefinedTerm relationshipType){
|
|
989
|
UpdateResult result = new UpdateResult();
|
|
990
|
TaxonNode node = dao.load(taxonNodeUUID);
|
|
991
|
TeamOrPersonBase<?> agent = (TeamOrPersonBase<?>) agentService.load(agentUUID);
|
|
992
|
node.addAgentRelation(relationshipType, agent);
|
|
993
|
try{
|
|
994
|
dao.merge(node, true);
|
|
995
|
}catch (Exception e){
|
|
996
|
result.setError();
|
|
997
|
result.addException(e);
|
|
998
|
}
|
|
999
|
result.setCdmEntity(node);
|
|
1000
|
return result;
|
|
1001
|
}
|
|
1002
|
|
|
1003
|
@Override
|
|
1004
|
@Transactional(readOnly=false)
|
|
1005
|
public UpdateResult setSecundumForSubtree(SecundumForSubtreeConfigurator config) {
|
|
1006
|
UpdateResult result = new UpdateResult();
|
|
1007
|
IProgressMonitor monitor = config.getMonitor();
|
|
1008
|
|
|
1009
|
if (monitor == null){
|
|
1010
|
monitor = DefaultProgressMonitor.NewInstance();
|
|
1011
|
}
|
|
1012
|
TaxonNode subTree = load(config.getSubtreeUuid());
|
|
1013
|
TreeIndex subTreeIndex = null;
|
|
1014
|
Reference newSec = null;
|
|
1015
|
if (config.getNewSecundum() != null){
|
|
1016
|
newSec = referenceService.load(config.getNewSecundum().getUuid());
|
|
1017
|
}
|
|
1018
|
|
|
1019
|
if (config.getSubtreeUuid() == null){
|
|
1020
|
result.setError();
|
|
1021
|
result.addException(new NullPointerException("No subtree given"));
|
|
1022
|
monitor.done();
|
|
1023
|
return result;
|
|
1024
|
}
|
|
1025
|
|
|
1026
|
if (subTree == null){
|
|
1027
|
result.setError();
|
|
1028
|
result.addException(new NullPointerException("Subtree does not exist"));
|
|
1029
|
monitor.done();
|
|
1030
|
return result;
|
|
1031
|
}else{
|
|
1032
|
subTreeIndex = TreeIndex.NewInstance(subTree.treeIndex());
|
|
1033
|
int count = config.isIncludeAcceptedTaxa() ? dao.countSecundumForSubtreeAcceptedTaxa(subTreeIndex, newSec, config.isOverwriteExistingAccepted(), config.isIncludeSharedTaxa(), config.isEmptySecundumDetail()):0;
|
|
1034
|
count += config.isIncludeSynonyms() ? dao.countSecundumForSubtreeSynonyms(subTreeIndex, newSec, config.isOverwriteExistingSynonyms(), config.isIncludeSharedTaxa() , config.isEmptySecundumDetail()) :0;
|
|
1035
|
monitor.beginTask("Update Secundum Reference", count);
|
|
1036
|
}
|
|
1037
|
|
|
1038
|
//Reference ref = config.getNewSecundum();
|
|
1039
|
if (config.isIncludeAcceptedTaxa()){
|
|
1040
|
monitor.subTask("Update Accepted Taxa");
|
|
1041
|
|
|
1042
|
Set<TaxonBase> updatedTaxa = dao.setSecundumForSubtreeAcceptedTaxa(subTreeIndex, newSec, config.isOverwriteExistingAccepted(), config.isIncludeSharedTaxa(), config.isEmptySecundumDetail(), monitor);
|
|
1043
|
result.addUpdatedObjects(updatedTaxa);
|
|
1044
|
}
|
|
1045
|
if (config.isIncludeSynonyms()){
|
|
1046
|
monitor.subTask("Update Synonyms");
|
|
1047
|
Set<TaxonBase> updatedSynonyms = dao.setSecundumForSubtreeSynonyms(subTreeIndex, newSec, config.isOverwriteExistingSynonyms(), config.isIncludeSharedTaxa() , config.isEmptySecundumDetail(), monitor);
|
|
1048
|
result.addUpdatedObjects(updatedSynonyms);
|
|
1049
|
}
|
|
1050
|
|
|
1051
|
monitor.done();
|
|
1052
|
return result;
|
|
1053
|
}
|
|
1054
|
|
|
1055
|
@Override
|
|
1056
|
@Transactional(readOnly=false)
|
|
1057
|
public UpdateResult setPublishForSubtree(PublishForSubtreeConfigurator config){
|
|
1058
|
UpdateResult result = new UpdateResult();
|
|
1059
|
IProgressMonitor monitor = config.getMonitor();
|
|
1060
|
if (monitor == null){
|
|
1061
|
monitor = DefaultProgressMonitor.NewInstance();
|
|
1062
|
}
|
|
1063
|
TreeIndex subTreeIndex = null;
|
|
1064
|
|
|
1065
|
if (config.getSubtreeUuid() == null){
|
|
1066
|
result.setError();
|
|
1067
|
result.addException(new NullPointerException("No subtree given"));
|
|
1068
|
monitor.done();
|
|
1069
|
return result;
|
|
1070
|
}
|
|
1071
|
TaxonNode subTree = find(config.getSubtreeUuid());
|
|
1072
|
boolean includeAcceptedTaxa = config.isIncludeAcceptedTaxa();
|
|
1073
|
boolean publish = config.isPublish();
|
|
1074
|
boolean includeSynonyms = config.isIncludeSynonyms();
|
|
1075
|
boolean includeSharedTaxa = config.isIncludeSharedTaxa();
|
|
1076
|
boolean includeHybrids = config.isIncludeHybrids();
|
|
1077
|
boolean includeRelatedTaxa = config.isIncludeProParteSynonyms() || config.isIncludeMisapplications();
|
|
1078
|
if (subTree == null){
|
|
1079
|
result.setError();
|
|
1080
|
result.addException(new NullPointerException("Subtree does not exist"));
|
|
1081
|
monitor.done();
|
|
1082
|
return result;
|
|
1083
|
}else{
|
|
1084
|
subTreeIndex = TreeIndex.NewInstance(subTree.treeIndex());
|
|
1085
|
int count = includeAcceptedTaxa ? dao.countPublishForSubtreeAcceptedTaxa(subTreeIndex, publish, includeSharedTaxa, includeHybrids):0;
|
|
1086
|
count += includeSynonyms ? dao.countPublishForSubtreeSynonyms(subTreeIndex, publish, includeSharedTaxa, includeHybrids):0;
|
|
1087
|
count += includeRelatedTaxa ? dao.countPublishForSubtreeRelatedTaxa(subTreeIndex, publish, includeSharedTaxa, includeHybrids):0;
|
|
1088
|
monitor.beginTask("Update publish flag", count);
|
|
1089
|
}
|
|
1090
|
|
|
1091
|
|
|
1092
|
if (includeAcceptedTaxa){
|
|
1093
|
monitor.subTask("Update Accepted Taxa");
|
|
1094
|
@SuppressWarnings("rawtypes")
|
|
1095
|
Set<TaxonBase> updatedTaxa = dao.setPublishForSubtreeAcceptedTaxa(subTreeIndex, publish, includeSharedTaxa, includeHybrids, monitor);
|
|
1096
|
result.addUpdatedObjects(updatedTaxa);
|
|
1097
|
}
|
|
1098
|
if (includeSynonyms){
|
|
1099
|
monitor.subTask("Update Synonyms");
|
|
1100
|
@SuppressWarnings("rawtypes")
|
|
1101
|
Set<TaxonBase> updatedSynonyms = dao.setPublishForSubtreeSynonyms(subTreeIndex, publish, includeSharedTaxa, includeHybrids, monitor);
|
|
1102
|
result.addUpdatedObjects(updatedSynonyms);
|
|
1103
|
}
|
|
1104
|
if (includeRelatedTaxa){
|
|
1105
|
monitor.subTask("Update Related Taxa");
|
|
1106
|
Set<UUID> relationTypes = new HashSet<>();
|
|
1107
|
if (config.isIncludeMisapplications()){
|
|
1108
|
relationTypes.addAll(TaxonRelationshipType.misappliedNameUuids());
|
|
1109
|
}
|
|
1110
|
if (config.isIncludeProParteSynonyms()){
|
|
1111
|
relationTypes.addAll(TaxonRelationshipType.proParteOrPartialSynonymUuids());
|
|
1112
|
}
|
|
1113
|
@SuppressWarnings("rawtypes")
|
|
1114
|
Set<TaxonBase> updatedTaxa = dao.setPublishForSubtreeRelatedTaxa(subTreeIndex, publish,
|
|
1115
|
relationTypes, includeSharedTaxa, includeHybrids, monitor);
|
|
1116
|
result.addUpdatedObjects(updatedTaxa);
|
|
1117
|
}
|
|
1118
|
|
|
1119
|
monitor.done();
|
|
1120
|
return result;
|
|
1121
|
}
|
|
1122
|
|
|
1123
|
@Override
|
|
1124
|
public long count(TaxonNodeFilter filter){
|
|
1125
|
return nodeFilterDao.count(filter);
|
|
1126
|
}
|
|
1127
|
|
|
1128
|
@Override
|
|
1129
|
public List<UUID> uuidList(TaxonNodeFilter filter){
|
|
1130
|
return nodeFilterDao.listUuids(filter);
|
|
1131
|
}
|
|
1132
|
|
|
1133
|
@Override
|
|
1134
|
public List<Integer> idList(TaxonNodeFilter filter){
|
|
1135
|
return nodeFilterDao.idList(filter);
|
|
1136
|
}
|
|
1137
|
|
|
1138
|
@Override
|
|
1139
|
public TaxonNodeDto findCommonParentDto(Collection<TaxonNodeDto> nodes) {
|
|
1140
|
TaxonNodeDto commonParent = null;
|
|
1141
|
List<String> treePath = null;
|
|
1142
|
for (TaxonNodeDto nodeDto : nodes) {
|
|
1143
|
String nodeTreeIndex = nodeDto.getTreeIndex();
|
|
1144
|
nodeTreeIndex = nodeTreeIndex.replaceFirst("#", "");
|
|
1145
|
String[] split = nodeTreeIndex.split("#");
|
|
1146
|
if(treePath == null){
|
|
1147
|
treePath = Arrays.asList(split);
|
|
1148
|
}
|
|
1149
|
else{
|
|
1150
|
List<String> match = new ArrayList<>();
|
|
1151
|
for(int i=0;i<treePath.size();i++){
|
|
1152
|
if(i>=split.length){
|
|
1153
|
//current tree index is shorter so break
|
|
1154
|
break;
|
|
1155
|
}
|
|
1156
|
else if(split[i].equals(treePath.get(i))){
|
|
1157
|
//match found
|
|
1158
|
match.add(treePath.get(i));
|
|
1159
|
}
|
|
1160
|
else{
|
|
1161
|
//first mismatch found
|
|
1162
|
break;
|
|
1163
|
}
|
|
1164
|
}
|
|
1165
|
treePath = match;
|
|
1166
|
if(treePath.isEmpty()){
|
|
1167
|
//no common parent found for at least two nodes
|
|
1168
|
//-> they belong to a different classification
|
|
1169
|
break;
|
|
1170
|
}
|
|
1171
|
}
|
|
1172
|
}
|
|
1173
|
if(treePath!=null && !treePath.isEmpty()) {
|
|
1174
|
//get last index
|
|
1175
|
int nodeId = Integer.parseInt(treePath.get(treePath.size()-1));
|
|
1176
|
TaxonNode taxonNode = dao.load(nodeId, null);
|
|
1177
|
commonParent = new TaxonNodeDto(taxonNode);
|
|
1178
|
}
|
|
1179
|
return commonParent;
|
|
1180
|
}
|
|
1181
|
|
|
1182
|
@Override
|
|
1183
|
public List<TaxonDistributionDTO> getTaxonDistributionDTO(List<UUID> nodeUuids, List<String> propertyPaths, Authentication authentication, boolean openChildren){
|
|
1184
|
Set<TaxonNode> nodes = new HashSet<>();
|
|
1185
|
if (openChildren){
|
|
1186
|
List<TaxonNode> parentNodes = load(nodeUuids, propertyPaths);
|
|
1187
|
for (TaxonNode node: parentNodes){
|
|
1188
|
nodes.addAll(listChildrenOf(node, null, null, true, true, propertyPaths));
|
|
1189
|
}
|
|
1190
|
nodes.addAll(parentNodes);
|
|
1191
|
|
|
1192
|
}
|
|
1193
|
List<TaxonDistributionDTO> result = new ArrayList<>();
|
|
1194
|
boolean hasPermission = false;
|
|
1195
|
//TaxonDescription instance = TaxonDescription.NewInstance();
|
|
1196
|
//hasPermission = permissionEvaluator.hasPermission(authentication, instance, Operation.UPDATE);
|
|
1197
|
for(TaxonNode node:nodes){
|
|
1198
|
if (authentication != null ) {
|
|
1199
|
hasPermission = permissionEvaluator.hasPermission(authentication, node, Operation.UPDATE);
|
|
1200
|
}else {
|
|
1201
|
hasPermission = true;
|
|
1202
|
}
|
|
1203
|
if (node.getTaxon() != null && hasPermission){
|
|
1204
|
try{
|
|
1205
|
TaxonDistributionDTO dto = new TaxonDistributionDTO(node);
|
|
1206
|
result.add(dto);
|
|
1207
|
}catch(Exception e){
|
|
1208
|
logger.error(e.getMessage(), e);
|
|
1209
|
}
|
|
1210
|
}
|
|
1211
|
}
|
|
1212
|
// result.sort(new TaxonDistributionDTOComparator());
|
|
1213
|
return result;
|
|
1214
|
}
|
|
1215
|
|
|
1216
|
@Override
|
|
1217
|
public <S extends TaxonNode> Pager<S> page(Class<S> clazz, List<Restriction<?>> restrictions, Integer pageSize,
|
|
1218
|
Integer pageIndex, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1219
|
return page(clazz, restrictions, pageSize, pageIndex, orderHints, propertyPaths, INCLUDE_UNPUBLISHED);
|
|
1220
|
}
|
|
1221
|
|
|
1222
|
@Override
|
|
1223
|
public <S extends TaxonNode> Pager<S> page(Class<S> clazz, List<Restriction<?>> restrictions, Integer pageSize,
|
|
1224
|
Integer pageIndex, List<OrderHint> orderHints, List<String> propertyPaths, boolean includeUnpublished) {
|
|
1225
|
|
|
1226
|
List<S> records;
|
|
1227
|
long resultSize = dao.count(clazz, restrictions);
|
|
1228
|
if(AbstractPagerImpl.hasResultsInRange(resultSize, pageIndex, pageSize)){
|
|
1229
|
records = dao.list(clazz, restrictions, pageSize, pageIndex, orderHints, propertyPaths, includeUnpublished);
|
|
1230
|
} else {
|
|
1231
|
records = new ArrayList<>();
|
|
1232
|
}
|
|
1233
|
Pager<S> pager = new DefaultPagerImpl<>(pageIndex, resultSize, pageSize, records);
|
|
1234
|
return pager;
|
|
1235
|
}
|
|
1236
|
|
|
1237
|
// @Override
|
|
1238
|
// public List<TaxonDistributionDTO> getTaxonDistributionDTOForSubtree(UUID parentNodeUuid,
|
|
1239
|
// List<String> propertyPaths, boolean openChildren) {
|
|
1240
|
// return getTaxonDistributionDTOForSubtree(parentNodeUuid, propertyPaths, null, openChildren);
|
|
1241
|
// }
|
|
1242
|
|
|
1243
|
@Override
|
|
1244
|
public List<TaxonDistributionDTO> getTaxonDistributionDTO(List<UUID> nodeUuids,
|
|
1245
|
List<String> propertyPaths, boolean openChildren) {
|
|
1246
|
return getTaxonDistributionDTO(nodeUuids, propertyPaths, null, openChildren);
|
|
1247
|
}
|
|
1248
|
|
|
1249
|
|
|
1250
|
@Override
|
|
1251
|
@Transactional(readOnly = false)
|
|
1252
|
public UpdateResult cloneSubtree(SubtreeCloneConfigurator config) {
|
|
1253
|
UpdateResult result = new UpdateResult();
|
|
1254
|
|
|
1255
|
if (config.getSubTreeUuids().isEmpty()){
|
|
1256
|
return result;
|
|
1257
|
}
|
|
1258
|
|
|
1259
|
//TODO error handling
|
|
1260
|
Reference taxonSecundum = config.isReuseTaxa() || config.isReuseTaxonSecundum() || config.getTaxonSecundumUuid() == null ?
|
|
1261
|
null : referenceDao.findByUuid(config.getTaxonSecundumUuid());
|
|
1262
|
config.setTaxonSecundum(taxonSecundum);
|
|
1263
|
|
|
1264
|
Reference parentChildReference = config.isReuseParentChildReference() || config.getParentChildReferenceUuid() == null ?
|
|
1265
|
null : referenceDao.findByUuid(config.getParentChildReferenceUuid());
|
|
1266
|
config.setParentChildReference(parentChildReference);
|
|
1267
|
|
|
1268
|
Reference taxonRelationshipReference = config.getRelationTypeToOldTaxon() == null ?
|
|
1269
|
null : referenceDao.findByUuid(config.getRelationshipReferenceUuid());
|
|
1270
|
config.setRelationshipReference(taxonRelationshipReference);
|
|
1271
|
|
|
1272
|
Classification classificationClone = Classification.NewInstance(config.getNewClassificationName());
|
|
1273
|
|
|
1274
|
if (config.isReuseClassificationReference()){
|
|
1275
|
TaxonNode anyNode = dao.findByUuid(config.getSubTreeUuids().iterator().next());
|
|
1276
|
if (anyNode != null){
|
|
1277
|
Reference oldClassificationRef = anyNode.getClassification().getReference();
|
|
1278
|
classificationClone.setReference(oldClassificationRef);
|
|
1279
|
}
|
|
1280
|
}else if (config.getClassificationReferenceUuid() != null) {
|
|
1281
|
Reference classificationReference = referenceDao.findByUuid(config.getClassificationReferenceUuid());
|
|
1282
|
classificationClone.setReference(classificationReference);
|
|
1283
|
}
|
|
1284
|
|
|
1285
|
//clone taxa and taxon nodes
|
|
1286
|
// List<Integer> childNodeIds = taxonNodeService.idList(taxonNodeFilter);
|
|
1287
|
// List<TaxonNode> childNodes = taxonNodeService.loadByIds(childNodeIds, null);
|
|
1288
|
List<TaxonNode> rootNodes = this.find(config.getSubTreeUuids());
|
|
1289
|
for (TaxonNode taxonNode : rootNodes) {
|
|
1290
|
cloneTaxonRecursive(taxonNode, classificationClone.getRootNode(), config);
|
|
1291
|
}
|
|
1292
|
classificationDao.saveOrUpdate(classificationClone);
|
|
1293
|
result.setCdmEntity(classificationClone);
|
|
1294
|
return result;
|
|
1295
|
}
|
|
1296
|
|
|
1297
|
private void cloneTaxonRecursive(TaxonNode originalParentNode, TaxonNode parentNodeClone,
|
|
1298
|
SubtreeCloneConfigurator config){
|
|
1299
|
|
|
1300
|
Taxon originalTaxon = CdmBase.deproxy(originalParentNode.getTaxon());
|
|
1301
|
TaxonNode childNodeClone;
|
|
1302
|
if (originalTaxon != null){
|
|
1303
|
String microReference = null;
|
|
1304
|
if (config.isReuseTaxa()){
|
|
1305
|
childNodeClone = parentNodeClone.addChildTaxon(originalTaxon, config.getParentChildReference(), microReference);
|
|
1306
|
}else{
|
|
1307
|
Taxon cloneTaxon = originalTaxon.clone(config.isIncludeSynonymsIncludingManAndProParte(),
|
|
1308
|
config.isIncludeTaxonRelationshipsExcludingManAndProParte(),
|
|
1309
|
config.isIncludeDescriptiveData(), config.isIncludeMedia());
|
|
1310
|
|
|
1311
|
//name
|
|
1312
|
if (!config.isReuseNames()){
|
|
1313
|
cloneTaxon.setName(cloneTaxon.getName().clone());
|
|
1314
|
//TODO needs further handling for name relationships etc., see #9349
|
|
1315
|
cloneTaxon.getSynonyms().forEach(syn ->
|
|
1316
|
syn.setName(syn.getName() == null ? null : syn.getName().clone()));
|
|
1317
|
}
|
|
1318
|
|
|
1319
|
if (!config.isReuseTaxonSecundum()){
|
|
1320
|
cloneTaxon.setSec(config.getTaxonSecundum());
|
|
1321
|
}
|
|
1322
|
|
|
1323
|
//add relation between taxa
|
|
1324
|
if (config.getRelationTypeToOldTaxon() != null){
|
|
1325
|
TaxonRelationship rel = cloneTaxon.addTaxonRelation(originalParentNode.getTaxon(), config.getRelationTypeToOldTaxon(),
|
|
1326
|
config.getRelationshipReference(), microReference);
|
|
1327
|
rel.setDoubtful(config.isRelationDoubtful());
|
|
1328
|
}
|
|
1329
|
childNodeClone = parentNodeClone.addChildTaxon(cloneTaxon, config.getParentChildReference(), microReference);
|
|
1330
|
}
|
|
1331
|
|
|
1332
|
//probably necessary as taxon nodes do not cascade
|
|
1333
|
dao.saveOrUpdate(childNodeClone);
|
|
1334
|
|
|
1335
|
}else{
|
|
1336
|
childNodeClone = parentNodeClone;
|
|
1337
|
}
|
|
1338
|
//add children
|
|
1339
|
if (config.isDoRecursive()){
|
|
1340
|
List<TaxonNode> originalChildNodes = originalParentNode.getChildNodes();
|
|
1341
|
HHH_9751_Util.removeAllNull(originalChildNodes);
|
|
1342
|
|
|
1343
|
for (TaxonNode originalChildNode : originalChildNodes) {
|
|
1344
|
cloneTaxonRecursive(originalChildNode, childNodeClone, config);
|
|
1345
|
}
|
|
1346
|
}
|
|
1347
|
}
|
|
1348
|
|
|
1349
|
}
|