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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.io.Serializable;
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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.Iterator;
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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.SecundumForSubtreeConfigurator;
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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.common.monitor.DefaultProgressMonitor;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.common.monitor.IRemotingProgressMonitor;
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import eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitor;
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import eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread;
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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.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.TreeIndex;
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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.TaxonName;
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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.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.dao.taxon.ITaxonNodeFilterDao;
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import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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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 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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@Autowired
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private INameService nameService;
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@Autowired
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private IReferenceService refService;
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@Autowired
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private ITaxonNodeFilterDao nodeFilterDao;
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@Autowired
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IProgressMonitorService progressMonitorService;
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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.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 UuidAndTitleCache<TaxonNode> getParentUuidAndTitleCache(ITaxonTreeNode child) {
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UUID uuid = child.getUuid();
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int id = child.getId();
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UuidAndTitleCache<TaxonNode> uuidAndTitleCache = new UuidAndTitleCache<>(uuid, id, null);
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return getParentUuidAndTitleCache(uuidAndTitleCache);
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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 UuidAndTitleCache<TaxonNode> getParentUuidAndTitleCache(UuidAndTitleCache<TaxonNode> child) {
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return dao.getParentUuidAndTitleCache(child);
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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 List<TaxonNodeDto> listChildNodesAsTaxonNodeDto(UuidAndTitleCache<TaxonNode> parent) {
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return dao.listChildNodesAsTaxonNodeDto(parent);
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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 List<UuidAndTitleCache<TaxonNode>> listChildNodesAsUuidAndTitleCache(UuidAndTitleCache<TaxonNode> parent) {
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return dao.listChildNodesAsUuidAndTitleCache(parent);
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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 List<UuidAndTitleCache<TaxonNode>> getUuidAndTitleCache(Integer limit, String pattern, UUID classificationUuid) {
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return dao.getUuidAndTitleCache(limit, pattern, classificationUuid);
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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 List<TaxonNodeDto> listChildNodesAsTaxonNodeDto(ITaxonTreeNode parent) {
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UUID uuid = parent.getUuid();
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int id = parent.getId();
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UuidAndTitleCache<TaxonNode> uuidAndTitleCache = new UuidAndTitleCache<>(uuid, id, null);
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return listChildNodesAsTaxonNodeDto(uuidAndTitleCache);
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}
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@Override
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public List<UuidAndTitleCache<TaxonNode>> listChildNodesAsUuidAndTitleCache(ITaxonTreeNode parent) {
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UUID uuid = parent.getUuid();
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int id = parent.getId();
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UuidAndTitleCache<TaxonNode> uuidAndTitleCache = new UuidAndTitleCache<>(uuid, id, null);
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return listChildNodesAsUuidAndTitleCache(uuidAndTitleCache);
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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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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 record : PagerUtils.pageList(allRecords, pageIndex, pageSize)) {
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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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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,
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SynonymType synonymType, 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.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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Set<Synonym> syns = new HashSet<>(oldTaxon.getSynonyms());
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for(Synonym synonym : syns){
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SynonymType srt;
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if(synonym.getHomotypicGroup()!= null
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&& synonym.getHomotypicGroup().equals(newAcceptedTaxonName.getHomotypicalGroup())) {
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srt = SynonymType.HOMOTYPIC_SYNONYM_OF();
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} else if(synonym.getType() != null && synonym.getType().equals(SynonymType.HOMOTYPIC_SYNONYM_OF())) {
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if (synonymType.equals(SynonymType.HOMOTYPIC_SYNONYM_OF())){
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srt = SynonymType.HOMOTYPIC_SYNONYM_OF();
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} else{
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srt = SynonymType.HETEROTYPIC_SYNONYM_OF();
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}
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} else {
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if (synonymsInHomotypicalGroup != null && synonymsInHomotypicalGroup.contains(synonym)){
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srt = SynonymType.HOMOTYPIC_SYNONYM_OF();
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}else{
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srt = synonym.getType();
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}
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}
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newAcceptedTaxon.addSynonym(synonym, srt);
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/*if (synonymsInHomotypicalGroup.contains(synRelation.getSynonym()) && srt.equals(SynonymType.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<>();
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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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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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|
335
|
if (fromTaxon == oldTaxon){
|
|
336
|
newAcceptedTaxon.addTaxonRelation(taxonRelationship.getToTaxon(), taxonRelationship.getType(),
|
|
337
|
taxonRelationship.getCitation(), taxonRelationship.getCitationMicroReference());
|
|
338
|
|
|
339
|
}else if(toTaxon == oldTaxon){
|
|
340
|
fromTaxon.addTaxonRelation(newAcceptedTaxon, taxonRelationship.getType(),
|
|
341
|
taxonRelationship.getCitation(), taxonRelationship.getCitationMicroReference());
|
|
342
|
taxonService.saveOrUpdate(fromTaxon);
|
|
343
|
|
|
344
|
}else{
|
|
345
|
logger.warn("Taxon is not part of its own Taxonrelationship");
|
|
346
|
}
|
|
347
|
// Remove old relationships
|
|
348
|
|
|
349
|
fromTaxon.removeTaxonRelation(taxonRelationship);
|
|
350
|
toTaxon.removeTaxonRelation(taxonRelationship);
|
|
351
|
taxonRelationship.setToTaxon(null);
|
|
352
|
taxonRelationship.setFromTaxon(null);
|
|
353
|
}
|
|
354
|
|
|
355
|
|
|
356
|
//Move descriptions to new taxon
|
|
357
|
List<TaxonDescription> descriptions = new ArrayList<TaxonDescription>( oldTaxon.getDescriptions()); //to avoid concurrent modification errors (newAcceptedTaxon.addDescription() modifies also oldtaxon.descritpions())
|
|
358
|
for(TaxonDescription description : descriptions){
|
|
359
|
String message = "Description copied from former accepted taxon: %s (Old title: %s)";
|
|
360
|
message = String.format(message, oldTaxon.getTitleCache(), description.getTitleCache());
|
|
361
|
description.setTitleCache(message, true);
|
|
362
|
//oldTaxon.removeDescription(description, false);
|
|
363
|
newAcceptedTaxon.addDescription(description);
|
|
364
|
}
|
|
365
|
oldTaxon.clearDescriptions();
|
|
366
|
|
|
367
|
taxonService.saveOrUpdate(newAcceptedTaxon);
|
|
368
|
|
|
369
|
taxonService.saveOrUpdate(oldTaxon);
|
|
370
|
taxonService.getSession().flush();
|
|
371
|
|
|
372
|
TaxonDeletionConfigurator conf = new TaxonDeletionConfigurator();
|
|
373
|
conf.setDeleteSynonymsIfPossible(false);
|
|
374
|
conf.setDeleteNameIfPossible(false);
|
|
375
|
DeleteResult result = taxonService.isDeletable(oldTaxon.getUuid(), conf);
|
|
376
|
|
|
377
|
|
|
378
|
if (result.isOk()){
|
|
379
|
result = taxonService.deleteTaxon(oldTaxon.getUuid(), conf, classification.getUuid());
|
|
380
|
|
|
381
|
}else{
|
|
382
|
result.setStatus(Status.OK);
|
|
383
|
TaxonNodeDeletionConfigurator config = new TaxonNodeDeletionConfigurator();
|
|
384
|
config.setDeleteElement(false);
|
|
385
|
conf.setTaxonNodeConfig(config);
|
|
386
|
result.includeResult(deleteTaxonNode(oldTaxonNode, conf));
|
|
387
|
}
|
|
388
|
|
|
389
|
result.addUpdatedObject(newAcceptedTaxon);
|
|
390
|
|
|
391
|
|
|
392
|
//oldTaxonNode.delete();
|
|
393
|
return result;
|
|
394
|
}
|
|
395
|
@Override
|
|
396
|
@Transactional(readOnly = false)
|
|
397
|
public UpdateResult makeTaxonNodeSynonymsOfAnotherTaxonNode( Set<UUID> oldTaxonNodeUuids,
|
|
398
|
UUID newAcceptedTaxonNodeUUIDs,
|
|
399
|
SynonymType synonymType,
|
|
400
|
Reference citation,
|
|
401
|
String citationMicroReference) {
|
|
402
|
UpdateResult result = new UpdateResult();
|
|
403
|
for (UUID nodeUuid: oldTaxonNodeUuids) {
|
|
404
|
result.includeResult(makeTaxonNodeASynonymOfAnotherTaxonNode(nodeUuid, newAcceptedTaxonNodeUUIDs, synonymType, citation, citationMicroReference));
|
|
405
|
}
|
|
406
|
return result;
|
|
407
|
}
|
|
408
|
|
|
409
|
@Override
|
|
410
|
@Transactional(readOnly = false)
|
|
411
|
public UpdateResult makeTaxonNodeASynonymOfAnotherTaxonNode(UUID oldTaxonNodeUuid,
|
|
412
|
UUID newAcceptedTaxonNodeUUID,
|
|
413
|
SynonymType synonymType,
|
|
414
|
Reference citation,
|
|
415
|
String citationMicroReference) {
|
|
416
|
|
|
417
|
TaxonNode oldTaxonNode = dao.load(oldTaxonNodeUuid);
|
|
418
|
TaxonNode oldTaxonParentNode = oldTaxonNode.getParent();
|
|
419
|
TaxonNode newTaxonNode = dao.load(newAcceptedTaxonNodeUUID);
|
|
420
|
|
|
421
|
UpdateResult result = makeTaxonNodeASynonymOfAnotherTaxonNode(oldTaxonNode,
|
|
422
|
newTaxonNode,
|
|
423
|
synonymType,
|
|
424
|
citation,
|
|
425
|
citationMicroReference);
|
|
426
|
result.addUpdatedCdmId(new CdmEntityIdentifier(oldTaxonParentNode.getId(), TaxonNode.class));
|
|
427
|
result.addUpdatedCdmId(new CdmEntityIdentifier(newTaxonNode.getId(), TaxonNode.class));
|
|
428
|
result.setCdmEntity(oldTaxonParentNode);
|
|
429
|
return result;
|
|
430
|
}
|
|
431
|
|
|
432
|
@Override
|
|
433
|
@Transactional(readOnly = false)
|
|
434
|
public DeleteResult deleteTaxonNodes(List<TaxonNode> list, TaxonDeletionConfigurator config) {
|
|
435
|
|
|
436
|
if (config == null){
|
|
437
|
config = new TaxonDeletionConfigurator();
|
|
438
|
}
|
|
439
|
DeleteResult result = new DeleteResult();
|
|
440
|
Classification classification = null;
|
|
441
|
List<TaxonNode> taxonNodes = new ArrayList<>(list);
|
|
442
|
|
|
443
|
for (TaxonNode treeNode:taxonNodes){
|
|
444
|
if (treeNode != null){
|
|
445
|
|
|
446
|
TaxonNode taxonNode;
|
|
447
|
taxonNode = HibernateProxyHelper.deproxy(treeNode, TaxonNode.class);
|
|
448
|
TaxonNode parent = taxonNode.getParent();
|
|
449
|
//check whether the node has children or the children are already deleted
|
|
450
|
if(taxonNode.hasChildNodes()) {
|
|
451
|
List<TaxonNode> children = new ArrayList<TaxonNode> ();
|
|
452
|
List<TaxonNode> childNodesList = taxonNode.getChildNodes();
|
|
453
|
children.addAll(childNodesList);
|
|
454
|
//To avoid NPE when child is also in list of taxonNodes, remove it from the list
|
|
455
|
Iterator<TaxonNode> it = taxonNodes.iterator();
|
|
456
|
for (TaxonNode child: children) {
|
|
457
|
while (it.hasNext()) {
|
|
458
|
if (it.next().equals(child)) {
|
|
459
|
it.remove();
|
|
460
|
}
|
|
461
|
}
|
|
462
|
}
|
|
463
|
int compare = config.getTaxonNodeConfig().getChildHandling().compareTo(ChildHandling.DELETE);
|
|
464
|
boolean childHandling = (compare == 0)? true: false;
|
|
465
|
if (childHandling){
|
|
466
|
boolean changeDeleteTaxon = false;
|
|
467
|
if (!config.getTaxonNodeConfig().isDeleteTaxon()){
|
|
468
|
config.getTaxonNodeConfig().setDeleteTaxon(true);
|
|
469
|
changeDeleteTaxon = true;
|
|
470
|
}
|
|
471
|
DeleteResult resultNodes = deleteTaxonNodes(children, config);
|
|
472
|
if (!resultNodes.isOk()){
|
|
473
|
result.addExceptions(resultNodes.getExceptions());
|
|
474
|
result.setStatus(resultNodes.getStatus());
|
|
475
|
}
|
|
476
|
if (changeDeleteTaxon){
|
|
477
|
config.getTaxonNodeConfig().setDeleteTaxon(false);
|
|
478
|
}
|
|
479
|
|
|
480
|
} else {
|
|
481
|
//move the children to the parent
|
|
482
|
|
|
483
|
for (TaxonNode child: childNodesList){
|
|
484
|
parent.addChildNode(child, child.getReference(), child.getMicroReference());
|
|
485
|
}
|
|
486
|
|
|
487
|
}
|
|
488
|
}
|
|
489
|
|
|
490
|
classification = taxonNode.getClassification();
|
|
491
|
|
|
492
|
if (classification.getRootNode().equals(taxonNode)){
|
|
493
|
classification.removeRootNode();
|
|
494
|
classification = null;
|
|
495
|
}else if (classification.getChildNodes().contains(taxonNode)){
|
|
496
|
Taxon taxon = taxonNode.getTaxon();
|
|
497
|
classification.deleteChildNode(taxonNode);
|
|
498
|
|
|
499
|
//node is rootNode
|
|
500
|
if (taxon != null){
|
|
501
|
|
|
502
|
if (config.getTaxonNodeConfig().isDeleteTaxon()){
|
|
503
|
taxonService.saveOrUpdate(taxon);
|
|
504
|
saveOrUpdate(taxonNode);
|
|
505
|
|
|
506
|
TaxonDeletionConfigurator configNew = new TaxonDeletionConfigurator();
|
|
507
|
DeleteResult resultTaxon = taxonService.deleteTaxon(taxon.getUuid(), configNew, classification.getUuid());
|
|
508
|
if (!resultTaxon.isOk()){
|
|
509
|
result.addExceptions(resultTaxon.getExceptions());
|
|
510
|
result.setStatus(resultTaxon.getStatus());
|
|
511
|
}
|
|
512
|
|
|
513
|
}
|
|
514
|
}
|
|
515
|
classification = null;
|
|
516
|
|
|
517
|
} else {
|
|
518
|
classification = null;
|
|
519
|
Taxon taxon = taxonNode.getTaxon();
|
|
520
|
taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);
|
|
521
|
if (taxon != null){
|
|
522
|
taxon.removeTaxonNode(taxonNode);
|
|
523
|
if (config.getTaxonNodeConfig().isDeleteTaxon()){
|
|
524
|
TaxonDeletionConfigurator configNew = new TaxonDeletionConfigurator();
|
|
525
|
saveOrUpdate(taxonNode);
|
|
526
|
taxonService.saveOrUpdate(taxon);
|
|
527
|
DeleteResult resultTaxon = taxonService.deleteTaxon(taxon.getUuid(), configNew, null);
|
|
528
|
|
|
529
|
if (!resultTaxon.isOk()){
|
|
530
|
result.addExceptions(resultTaxon.getExceptions());
|
|
531
|
result.setStatus(resultTaxon.getStatus());
|
|
532
|
}
|
|
533
|
}
|
|
534
|
}
|
|
535
|
|
|
536
|
}
|
|
537
|
|
|
538
|
result.addUpdatedObject(parent);
|
|
539
|
if(result.getCdmEntity() == null){
|
|
540
|
result.setCdmEntity(taxonNode);
|
|
541
|
}
|
|
542
|
UUID uuid = dao.delete(taxonNode);
|
|
543
|
logger.debug("Deleted node " +uuid.toString());
|
|
544
|
|
|
545
|
}
|
|
546
|
}
|
|
547
|
/*if (classification != null){
|
|
548
|
result.addUpdatedObject(classification);
|
|
549
|
DeleteResult resultClassification = classService.delete(classification);
|
|
550
|
if (!resultClassification.isOk()){
|
|
551
|
result.addExceptions(resultClassification.getExceptions());
|
|
552
|
result.setStatus(resultClassification.getStatus());
|
|
553
|
}
|
|
554
|
}*/
|
|
555
|
return result;
|
|
556
|
}
|
|
557
|
|
|
558
|
|
|
559
|
@Override
|
|
560
|
@Transactional(readOnly = false)
|
|
561
|
public DeleteResult deleteTaxonNodes(Collection<UUID> nodeUuids, TaxonDeletionConfigurator config) {
|
|
562
|
List<TaxonNode> nodes = new ArrayList<>();
|
|
563
|
for(UUID nodeUuid : nodeUuids) {
|
|
564
|
nodes.add(dao.load(nodeUuid));
|
|
565
|
}
|
|
566
|
return deleteTaxonNodes(nodes, config);
|
|
567
|
}
|
|
568
|
|
|
569
|
|
|
570
|
@Override
|
|
571
|
@Transactional(readOnly = false)
|
|
572
|
public DeleteResult deleteTaxonNode(UUID nodeUUID, TaxonDeletionConfigurator config) {
|
|
573
|
|
|
574
|
TaxonNode node = HibernateProxyHelper.deproxy(dao.load(nodeUUID), TaxonNode.class);
|
|
575
|
return deleteTaxonNode(node, config);
|
|
576
|
}
|
|
577
|
|
|
578
|
@Override
|
|
579
|
@Transactional(readOnly = false)
|
|
580
|
public DeleteResult deleteTaxonNode(TaxonNode node, TaxonDeletionConfigurator config) {
|
|
581
|
DeleteResult result = new DeleteResult();
|
|
582
|
if (node == null){
|
|
583
|
result.setAbort();
|
|
584
|
result.addException(new Exception("The TaxonNode was already deleted."));
|
|
585
|
return result;
|
|
586
|
}
|
|
587
|
Taxon taxon = null;
|
|
588
|
try{
|
|
589
|
taxon = HibernateProxyHelper.deproxy(node.getTaxon());
|
|
590
|
}catch(NullPointerException e){
|
|
591
|
result.setAbort();
|
|
592
|
result.addException(new Exception("The Taxon was already deleted."));
|
|
593
|
|
|
594
|
}
|
|
595
|
|
|
596
|
|
|
597
|
TaxonNode parent = HibernateProxyHelper.deproxy(node.getParent(), TaxonNode.class);
|
|
598
|
if (config == null){
|
|
599
|
config = new TaxonDeletionConfigurator();
|
|
600
|
}
|
|
601
|
|
|
602
|
|
|
603
|
if (config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.MOVE_TO_PARENT)){
|
|
604
|
Object[] children = node.getChildNodes().toArray();
|
|
605
|
TaxonNode childNode;
|
|
606
|
for (Object child: children){
|
|
607
|
childNode = (TaxonNode) child;
|
|
608
|
parent.addChildNode(childNode, childNode.getReference(), childNode.getMicroReference());
|
|
609
|
|
|
610
|
}
|
|
611
|
}else{
|
|
612
|
result.includeResult(deleteTaxonNodes(node.getChildNodes(), config));
|
|
613
|
}
|
|
614
|
|
|
615
|
if (taxon != null){
|
|
616
|
if (config.getTaxonNodeConfig().isDeleteTaxon() && (config.isDeleteInAllClassifications() || taxon.getTaxonNodes().size() == 1)){
|
|
617
|
result = taxonService.deleteTaxon(taxon.getUuid(), config, node.getClassification().getUuid());
|
|
618
|
result.addUpdatedObject(parent);
|
|
619
|
if (result.isOk()){
|
|
620
|
return result;
|
|
621
|
}
|
|
622
|
} else {
|
|
623
|
result.addUpdatedObject(taxon);
|
|
624
|
}
|
|
625
|
}
|
|
626
|
result.setCdmEntity(node);
|
|
627
|
boolean success = true;
|
|
628
|
if (taxon != null){
|
|
629
|
success = taxon.removeTaxonNode(node);
|
|
630
|
taxonService.saveOrUpdate(taxon);
|
|
631
|
}
|
|
632
|
dao.saveOrUpdate(parent);
|
|
633
|
|
|
634
|
result.addUpdatedObject(parent);
|
|
635
|
|
|
636
|
if (success){
|
|
637
|
result.setStatus(Status.OK);
|
|
638
|
if (parent != null){
|
|
639
|
parent = HibernateProxyHelper.deproxy(parent, TaxonNode.class);
|
|
640
|
int index = parent.getChildNodes().indexOf(node);
|
|
641
|
if (index > -1){
|
|
642
|
parent.removeChild(index);
|
|
643
|
}
|
|
644
|
}
|
|
645
|
if (!dao.delete(node, config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.DELETE)).equals(null)){
|
|
646
|
result.getUpdatedObjects().remove(node);
|
|
647
|
result.addDeletedObject(node);
|
|
648
|
return result;
|
|
649
|
} else {
|
|
650
|
result.setError();
|
|
651
|
return result;
|
|
652
|
}
|
|
653
|
}else{
|
|
654
|
if (dao.findByUuid(node.getUuid()) != null){
|
|
655
|
result.setError();
|
|
656
|
result.addException(new Exception("The node can not be removed from the taxon."));
|
|
657
|
}
|
|
658
|
return result;
|
|
659
|
}
|
|
660
|
}
|
|
661
|
|
|
662
|
|
|
663
|
@Override
|
|
664
|
public List<TaxonNode> listAllNodesForClassification(Classification classification, Integer start, Integer end) {
|
|
665
|
return dao.getTaxonOfAcceptedTaxaByClassification(classification, start, end);
|
|
666
|
}
|
|
667
|
|
|
668
|
@Override
|
|
669
|
public int countAllNodesForClassification(Classification classification) {
|
|
670
|
return dao.countTaxonOfAcceptedTaxaByClassification(classification);
|
|
671
|
}
|
|
672
|
|
|
673
|
@Override
|
|
674
|
@Transactional
|
|
675
|
public UpdateResult moveTaxonNode(UUID taxonNodeUuid, UUID targetNodeUuid, int movingType){
|
|
676
|
TaxonNode taxonNode = HibernateProxyHelper.deproxy(dao.load(taxonNodeUuid), TaxonNode.class);
|
|
677
|
TaxonNode targetNode = HibernateProxyHelper.deproxy(dao.load(targetNodeUuid), TaxonNode.class);
|
|
678
|
return moveTaxonNode(taxonNode, targetNode, movingType);
|
|
679
|
}
|
|
680
|
|
|
681
|
@Override
|
|
682
|
@Transactional
|
|
683
|
public UpdateResult moveTaxonNode(TaxonNode taxonNode, TaxonNode newParent, int movingType){
|
|
684
|
UpdateResult result = new UpdateResult();
|
|
685
|
|
|
686
|
TaxonNode parentParent = HibernateProxyHelper.deproxy(newParent.getParent());
|
|
687
|
TaxonNode oldParent = HibernateProxyHelper.deproxy(taxonNode.getParent());
|
|
688
|
Integer sortIndex = -1;
|
|
689
|
if (movingType == 0){
|
|
690
|
sortIndex = 0;
|
|
691
|
}else if (movingType == 1){
|
|
692
|
sortIndex = newParent.getSortIndex();
|
|
693
|
newParent = parentParent;
|
|
694
|
} else if (movingType == 2){
|
|
695
|
sortIndex = newParent.getSortIndex() +1;
|
|
696
|
newParent = parentParent;
|
|
697
|
} else{
|
|
698
|
result.setAbort();
|
|
699
|
result.addException(new Exception("The moving type "+ movingType +" is not supported."));
|
|
700
|
}
|
|
701
|
|
|
702
|
|
|
703
|
taxonNode = newParent.addChildNode(taxonNode, sortIndex, taxonNode.getReference(), taxonNode.getMicroReference());
|
|
704
|
result.addUpdatedObject(newParent);
|
|
705
|
result.addUpdatedObject(oldParent);
|
|
706
|
result.setCdmEntity(taxonNode);
|
|
707
|
|
|
708
|
dao.saveOrUpdate(taxonNode);
|
|
709
|
dao.saveOrUpdate(oldParent);
|
|
710
|
|
|
711
|
return result;
|
|
712
|
}
|
|
713
|
|
|
714
|
|
|
715
|
|
|
716
|
@Override
|
|
717
|
@Transactional
|
|
718
|
public UpdateResult moveTaxonNodes(Set<UUID> taxonNodeUuids, UUID newParentNodeUuid, int movingType){
|
|
719
|
UpdateResult result = new UpdateResult();
|
|
720
|
TaxonNode targetNode = dao.load(newParentNodeUuid);
|
|
721
|
for (UUID taxonNodeUuid: taxonNodeUuids){
|
|
722
|
TaxonNode taxonNode = dao.load(taxonNodeUuid);
|
|
723
|
result.includeResult(moveTaxonNode(taxonNode,targetNode, movingType));
|
|
724
|
}
|
|
725
|
return result;
|
|
726
|
}
|
|
727
|
|
|
728
|
@Override
|
|
729
|
public Pager<TaxonNodeAgentRelation> pageTaxonNodeAgentRelations(UUID taxonUuid, UUID classificationUuid,
|
|
730
|
UUID agentUuid, UUID rankUuid, UUID relTypeUuid, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
|
|
731
|
|
|
732
|
|
|
733
|
List<TaxonNodeAgentRelation> records = null;
|
|
734
|
|
|
735
|
long count = dao.countTaxonNodeAgentRelations(taxonUuid, classificationUuid, agentUuid, rankUuid, relTypeUuid);
|
|
736
|
if(PagerUtils.hasResultsInRange(count, pageIndex, pageSize)) {
|
|
737
|
records = dao.listTaxonNodeAgentRelations(taxonUuid, classificationUuid,
|
|
738
|
agentUuid, rankUuid, relTypeUuid, PagerUtils.startFor(pageSize, pageIndex), PagerUtils.limitFor(pageSize), propertyPaths);
|
|
739
|
}
|
|
740
|
|
|
741
|
Pager<TaxonNodeAgentRelation> pager = new DefaultPagerImpl<>(pageIndex, count, pageSize, records);
|
|
742
|
return pager;
|
|
743
|
}
|
|
744
|
|
|
745
|
@Override
|
|
746
|
@Transactional
|
|
747
|
public UpdateResult createNewTaxonNode(UUID parentNodeUuid, Taxon newTaxon, Reference ref, String microref){
|
|
748
|
UpdateResult result = new UpdateResult();
|
|
749
|
if (newTaxon.getName().getId() != 0){
|
|
750
|
TaxonName name = nameService.load(newTaxon.getName().getUuid());
|
|
751
|
newTaxon.setName(name);
|
|
752
|
}else{
|
|
753
|
for (HybridRelationship rel : newTaxon.getName().getHybridChildRelations()){
|
|
754
|
if (!rel.getHybridName().isPersited()) {
|
|
755
|
nameService.save(rel.getHybridName());
|
|
756
|
}
|
|
757
|
if (!rel.getParentName().isPersited()) {
|
|
758
|
nameService.save(rel.getParentName());
|
|
759
|
}
|
|
760
|
}
|
|
761
|
}
|
|
762
|
UUID taxonUUID = taxonService.saveOrUpdate(newTaxon);
|
|
763
|
newTaxon = (Taxon) taxonService.load(taxonUUID);
|
|
764
|
|
|
765
|
TaxonNode parent = dao.load(parentNodeUuid);
|
|
766
|
TaxonNode child = null;
|
|
767
|
try{
|
|
768
|
child = parent.addChildTaxon(newTaxon, parent.getReference(), parent.getMicroReference());
|
|
769
|
}catch(Exception e){
|
|
770
|
result.addException(e);
|
|
771
|
result.setError();
|
|
772
|
return result;
|
|
773
|
}
|
|
774
|
// child = dao.save(child);
|
|
775
|
|
|
776
|
dao.saveOrUpdate(parent);
|
|
777
|
result.addUpdatedObject(parent);
|
|
778
|
if (child != null){
|
|
779
|
result.setCdmEntity(child);
|
|
780
|
}
|
|
781
|
return result;
|
|
782
|
|
|
783
|
}
|
|
784
|
@Override
|
|
785
|
@Transactional
|
|
786
|
public UpdateResult createNewTaxonNode(UUID parentNodeUuid, UUID taxonUuid, Reference ref, String microref){
|
|
787
|
UpdateResult result = new UpdateResult();
|
|
788
|
TaxonNode parent = dao.load(parentNodeUuid);
|
|
789
|
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
|
|
790
|
TaxonNode child = null;
|
|
791
|
try{
|
|
792
|
child = parent.addChildTaxon(taxon, parent.getReference(), parent.getMicroReference());
|
|
793
|
}catch(Exception e){
|
|
794
|
result.addException(e);
|
|
795
|
result.setError();
|
|
796
|
return result;
|
|
797
|
}
|
|
798
|
// child = dao.save(child);
|
|
799
|
|
|
800
|
// dao.saveOrUpdate(child);
|
|
801
|
result.addUpdatedObject(parent);
|
|
802
|
if (child != null){
|
|
803
|
result.setCdmEntity(child);
|
|
804
|
}
|
|
805
|
return result;
|
|
806
|
|
|
807
|
}
|
|
808
|
|
|
809
|
@Override
|
|
810
|
@Transactional
|
|
811
|
public UpdateResult addTaxonNodeAgentRelation(UUID taxonNodeUUID, UUID agentUUID, DefinedTerm relationshipType){
|
|
812
|
UpdateResult result = new UpdateResult();
|
|
813
|
TaxonNode node = dao.load(taxonNodeUUID);
|
|
814
|
TeamOrPersonBase<?> agent = (TeamOrPersonBase<?>) agentService.load(agentUUID);
|
|
815
|
node.addAgentRelation(relationshipType, agent);
|
|
816
|
try{
|
|
817
|
dao.merge(node, true);
|
|
818
|
}catch (Exception e){
|
|
819
|
result.setError();
|
|
820
|
result.addException(e);
|
|
821
|
}
|
|
822
|
result.setCdmEntity(node);
|
|
823
|
return result;
|
|
824
|
}
|
|
825
|
|
|
826
|
@Override
|
|
827
|
@Transactional(readOnly=false)
|
|
828
|
public UpdateResult setSecundumForSubtree(SecundumForSubtreeConfigurator config) {
|
|
829
|
UpdateResult result = new UpdateResult();
|
|
830
|
IProgressMonitor monitor = config.getMonitor();
|
|
831
|
if (monitor == null){
|
|
832
|
monitor = DefaultProgressMonitor.NewInstance();
|
|
833
|
}
|
|
834
|
TaxonNode subTree = load(config.getSubtreeUuid());
|
|
835
|
TreeIndex subTreeIndex = null;
|
|
836
|
Reference newSec = null;
|
|
837
|
if (config.getNewSecundum() != null){
|
|
838
|
newSec = refService.load(config.getNewSecundum().getUuid());
|
|
839
|
}
|
|
840
|
|
|
841
|
if (config.getSubtreeUuid() == null){
|
|
842
|
result.setError();
|
|
843
|
result.addException(new NullPointerException("No subtree given"));
|
|
844
|
monitor.done();
|
|
845
|
return result;
|
|
846
|
}
|
|
847
|
|
|
848
|
if (subTree == null){
|
|
849
|
result.setError();
|
|
850
|
result.addException(new NullPointerException("Subtree does not exist"));
|
|
851
|
monitor.done();
|
|
852
|
return result;
|
|
853
|
}else{
|
|
854
|
subTreeIndex = TreeIndex.NewInstance(subTree.treeIndex());
|
|
855
|
int count = config.isIncludeAcceptedTaxa() ? dao.countSecundumForSubtreeAcceptedTaxa(subTreeIndex, newSec, config.isOverwriteExistingAccepted(), config.isIncludeSharedTaxa(), config.isEmptySecundumDetail()):0;
|
|
856
|
count += config.isIncludeSynonyms() ? dao.countSecundumForSubtreeSynonyms(subTreeIndex, newSec, config.isOverwriteExistingSynonyms(), config.isIncludeSharedTaxa() , config.isEmptySecundumDetail()) :0;
|
|
857
|
monitor.beginTask("Update Secundum Reference", count);
|
|
858
|
}
|
|
859
|
|
|
860
|
//Reference ref = config.getNewSecundum();
|
|
861
|
if (config.isIncludeAcceptedTaxa()){
|
|
862
|
monitor.subTask("Update Accepted Taxa");
|
|
863
|
|
|
864
|
Set<TaxonBase> updatedTaxa = dao.setSecundumForSubtreeAcceptedTaxa(subTreeIndex, newSec, config.isOverwriteExistingAccepted(), config.isIncludeSharedTaxa(), config.isEmptySecundumDetail(), monitor);
|
|
865
|
result.addUpdatedObjects(updatedTaxa);
|
|
866
|
}
|
|
867
|
if (config.isIncludeSynonyms()){
|
|
868
|
monitor.subTask("Update Synonyms");
|
|
869
|
Set<TaxonBase> updatedSynonyms = dao.setSecundumForSubtreeSynonyms(subTreeIndex, newSec, config.isOverwriteExistingSynonyms(), config.isIncludeSharedTaxa() , config.isEmptySecundumDetail(), monitor);
|
|
870
|
result.addUpdatedObjects(updatedSynonyms);
|
|
871
|
}
|
|
872
|
((RemotingProgressMonitor)monitor).setResult(result);
|
|
873
|
monitor.done();
|
|
874
|
return result;
|
|
875
|
}
|
|
876
|
|
|
877
|
|
|
878
|
/**
|
|
879
|
* {@inheritDoc}
|
|
880
|
*/
|
|
881
|
@Override
|
|
882
|
@Transactional(readOnly=false)
|
|
883
|
public UpdateResult setPublishForSubtree(UUID subtreeUuid, boolean publish, boolean includeAcceptedTaxa,
|
|
884
|
boolean includeSynonyms, boolean includeSharedTaxa, IProgressMonitor monitor) {
|
|
885
|
UpdateResult result = new UpdateResult();
|
|
886
|
if (monitor == null){
|
|
887
|
monitor = DefaultProgressMonitor.NewInstance();
|
|
888
|
}
|
|
889
|
TreeIndex subTreeIndex = null;
|
|
890
|
|
|
891
|
if (subtreeUuid == null){
|
|
892
|
result.setError();
|
|
893
|
result.addException(new NullPointerException("No subtree given"));
|
|
894
|
monitor.done();
|
|
895
|
return result;
|
|
896
|
}
|
|
897
|
TaxonNode subTree = find(subtreeUuid);
|
|
898
|
if (subTree == null){
|
|
899
|
result.setError();
|
|
900
|
result.addException(new NullPointerException("Subtree does not exist"));
|
|
901
|
monitor.done();
|
|
902
|
return result;
|
|
903
|
}else{
|
|
904
|
subTreeIndex = TreeIndex.NewInstance(subTree.treeIndex());
|
|
905
|
int count = includeAcceptedTaxa ? dao.countPublishForSubtreeAcceptedTaxa(subTreeIndex, publish, includeSharedTaxa):0;
|
|
906
|
count += includeSynonyms ? dao.countPublishForSubtreeSynonyms(subTreeIndex, publish, includeSharedTaxa):0;
|
|
907
|
monitor.beginTask("Update publish flag", count);
|
|
908
|
}
|
|
909
|
|
|
910
|
|
|
911
|
if (includeAcceptedTaxa){
|
|
912
|
monitor.subTask("Update Accepted Taxa");
|
|
913
|
Set<TaxonBase> updatedTaxa = dao.setPublishForSubtreeAcceptedTaxa(subTreeIndex, publish, includeSharedTaxa, monitor);
|
|
914
|
result.addUpdatedObjects(updatedTaxa);
|
|
915
|
}
|
|
916
|
if (includeSynonyms){
|
|
917
|
monitor.subTask("Update Synonyms");
|
|
918
|
Set<TaxonBase> updatedSynonyms = dao.setPublishForSubtreeSynonyms(subTreeIndex, publish, includeSharedTaxa, monitor);
|
|
919
|
result.addUpdatedObjects(updatedSynonyms);
|
|
920
|
}
|
|
921
|
((RemotingProgressMonitor)monitor).setResult(result);
|
|
922
|
monitor.done();
|
|
923
|
return result;
|
|
924
|
}
|
|
925
|
|
|
926
|
|
|
927
|
@Override
|
|
928
|
public long count(TaxonNodeFilter filter){
|
|
929
|
return nodeFilterDao.count(filter);
|
|
930
|
}
|
|
931
|
|
|
932
|
@Override
|
|
933
|
public List<UUID> uuidList(TaxonNodeFilter filter){
|
|
934
|
return nodeFilterDao.listUuids(filter);
|
|
935
|
}
|
|
936
|
|
|
937
|
@Override
|
|
938
|
public List<Integer> idList(TaxonNodeFilter filter){
|
|
939
|
return nodeFilterDao.idList(filter);
|
|
940
|
}
|
|
941
|
|
|
942
|
@Override
|
|
943
|
@Transactional(readOnly=false)
|
|
944
|
public UUID monitSetSecundum(final SecundumForSubtreeConfigurator configurator) {
|
|
945
|
RemotingProgressMonitorThread monitorThread = new RemotingProgressMonitorThread() {
|
|
946
|
@Override
|
|
947
|
public Serializable doRun(IRemotingProgressMonitor monitor) {
|
|
948
|
configurator.setMonitor(monitor);
|
|
949
|
UpdateResult result = setSecundumForSubtree(configurator);
|
|
950
|
return result;
|
|
951
|
}
|
|
952
|
};
|
|
953
|
UUID uuid = progressMonitorService.registerNewRemotingMonitor(monitorThread);
|
|
954
|
monitorThread.setPriority(3);
|
|
955
|
monitorThread.start();
|
|
956
|
return uuid;
|
|
957
|
}
|
|
958
|
|
|
959
|
}
|